Tue Feb 18 09:14:22 UTC 2025 I: starting to build gromacs/trixie/amd64 on jenkins on '2025-02-18 09:14' Tue Feb 18 09:14:22 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_1/30716/console.log Tue Feb 18 09:14:22 UTC 2025 I: Downloading source for trixie/gromacs=2025.0-2 --2025-02-18 09:14:22-- http://deb.debian.org/debian/pool/main/g/gromacs/gromacs_2025.0-2.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 3276 (3.2K) [text/prs.lines.tag] Saving to: ‘gromacs_2025.0-2.dsc’ 0K ... 100% 318M=0s 2025-02-18 09:14:22 (318 MB/s) - ‘gromacs_2025.0-2.dsc’ saved [3276/3276] Tue Feb 18 09:14:22 UTC 2025 I: gromacs_2025.0-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: gromacs Binary: gromacs, gromacs-data, libgromacs10, libgromacs-dev, libnblib-gmx0, libnblib-gmx-dev Architecture: any all Version: 2025.0-2 Maintainer: Debichem Team Uploaders: Nicholas Breen Homepage: https://www.gromacs.org/ Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/debichem-team/gromacs Vcs-Git: https://salsa.debian.org/debichem-team/gromacs.git Testsuite: autopkgtest Testsuite-Triggers: build-essential, mpi-default-bin, perl Build-Depends: architecture-is-64-bit, bash-completion, chrpath, cmake (>= 3.13), debhelper-compat (= 13), dh-python, libblas-dev, libboost-dev, libfftw3-dev, libhwloc-dev, liblapack-dev, libmuparser-dev (>= 2.3.4), lsb-release, mpi-default-bin, mpi-default-dev, pkgconf, python3-dev, python3-mpi4py, python3-networkx, python3-numpy, python3-pybind11, python3-pytest, zlib1g-dev Build-Depends-Indep: doxygen, furo, ghostscript, graphicsmagick, graphviz, mscgen, python3-pygments, python3-sphinx, python3-sphinx-argparse, python3-sphinx-copybutton, python3-sphinx-inline-tabs, python3-sphinxcontrib.autoprogram, rdfind, symlinks, tex-gyre, texlive-fonts-recommended, texlive-latex-base, texlive-latex-extra Package-List: gromacs deb science optional arch=any gromacs-data deb science optional arch=all libgromacs-dev deb libdevel optional arch=any libgromacs10 deb libs optional arch=any libnblib-gmx-dev deb libdevel optional arch=any libnblib-gmx0 deb libs optional arch=any Checksums-Sha1: 5c3a2bfe23c39b0dafa54bd876f4d4a69db950f9 32653708 gromacs_2025.0.orig-regressiontests.tar.gz 8a0a15947819463879a033a2f558332cfc97fb7f 44417653 gromacs_2025.0.orig.tar.gz 966b6eab155813293ec03b0e45e8568e86595ab4 37216 gromacs_2025.0-2.debian.tar.xz Checksums-Sha256: 86bb8733e337889e7591d8c3871d67cf89bc97cb34ac402f6e8f3296e978ce39 32653708 gromacs_2025.0.orig-regressiontests.tar.gz a27ad35a646295bbec129abe684d9d03d1e2e0bd76b0d625e9055746aaefae82 44417653 gromacs_2025.0.orig.tar.gz 097423b3d5f2f40c6a2bfb1178b9052b073b4f8ef1adc82d7f5a2d75dc9c64dc 37216 gromacs_2025.0-2.debian.tar.xz Files: bee79b13a6d7d66eaa6f0e2cd20dc009 32653708 gromacs_2025.0.orig-regressiontests.tar.gz 4e9f043fea964cb2b4dd72d6f39ea006 44417653 gromacs_2025.0.orig.tar.gz 56529283dafca0965075cb53d5f6ead2 37216 gromacs_2025.0-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJGBAEBCgAwFiEEhD5fph5gYziYdtLl7kr9aexlEI8FAmew3FISHG5icmVlbkBk ZWJpYW4ub3JnAAoJEO5K/WnsZRCPhWkQAJPSUmTcWghh4xsVvHTazvFOLV6wxErE tjVWCiFAJNC24sQ24eaXNLGx6vHud0TqTpF7BxZcTc9D6k7XSDKDNXmPjeNl8sjs sN8eZQp5M2Nr2yB6lhkUkdT+T1b/888Shmw+NxoS3ek4/2Ywj+gZwPJ2oymN9uLD d9jzZJZYBF1ORWLPK3TO0vku9HY0JSe0Gy877op+f98/kAmKJfX9Zt5qCEq37QwV PEEp4hbiusMa2CiI1uKhDVjMx7K+aZP7qby7nB0VKWIeSo8bu1CfOT/r0FQx03oo 3wPlwXCiD17KiSkudxc/GmdvQk2LYelM6m2pLYPh/q4vVQdGjA37NclDneLkGWju 1RQK1J7B0BzxB7ZqYViLnICXPi9x8BNWKnB54LWkOGYcb2WZ5+4Qfey9rXyKx55O c4yuZwIW0r1mxFTekiXTv9TZTUznFr5fYtbDYKq1dGEDTMi/KyQ2/qTwDsYc55/J IpfhsPOKxDbvXXUqYcjjl8R9q1vWV1Xa1kNd6iIg3IrctBJ5rpS6yVsnZF0N1oom B7nDHGx3gP+lqjbSHBJRsgAFHakNK78OG6FIn6QzlDSRKLLQbWcOP7d2TttHbOc0 RZ8vPxEvRrfmz8pYFS4sup0gFInITqICebxf5BxDmi6/TYamAaSjxBFQwNUkx05u jJLV/m4UJAt6 =ilzs -----END PGP SIGNATURE----- Tue Feb 18 09:14:22 UTC 2025 I: Checking whether the package is not for us Tue Feb 18 09:14:22 UTC 2025 I: Starting 1st build on remote node ionos1-amd64.debian.net. Tue Feb 18 09:14:22 UTC 2025 I: Preparing to do remote build '1' on ionos1-amd64.debian.net. Tue Feb 18 11:56:27 UTC 2025 I: Deleting $TMPDIR on ionos1-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Feb 17 21:14:26 -12 2025 I: pbuilder-time-stamp: 1739870066 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [gromacs_2025.0-2.dsc] I: copying [./gromacs_2025.0.orig-regressiontests.tar.gz] I: copying [./gromacs_2025.0.orig.tar.gz] I: copying [./gromacs_2025.0-2.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./gromacs_2025.0-2.dsc: unsupported subcommand dpkg-source: info: extracting gromacs in gromacs-2025.0 dpkg-source: info: unpacking gromacs_2025.0.orig.tar.gz dpkg-source: info: unpacking gromacs_2025.0.orig-regressiontests.tar.gz dpkg-source: info: unpacking gromacs_2025.0-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying readme.patch dpkg-source: info: applying copyright-file.patch dpkg-source: info: applying disable-cpuinfotest.patch dpkg-source: info: applying mdrun-test-timeout.patch dpkg-source: info: applying manual-local-mathjax.patch dpkg-source: info: applying mpi-tests-localhost.patch dpkg-source: info: applying manual-image-conversion.patch dpkg-source: info: applying disable-gmxtimingtests.patch dpkg-source: info: applying script-shebang-line.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3465466/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='c34212bf93d94f3eb6113f975eaf4a3c' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='3465466' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.9nJ0JTN3/pbuilderrc_jPfn --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.9nJ0JTN3/b1 --logfile b1/build.log gromacs_2025.0-2.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos1-amd64 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3465466/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: architecture-is-64-bit, bash-completion, chrpath, cmake (>= 3.13), debhelper-compat (= 13), dh-python, libblas-dev, libboost-dev, libfftw3-dev, libhwloc-dev, liblapack-dev, libmuparser-dev (>= 2.3.4), lsb-release, mpi-default-bin, mpi-default-dev, pkgconf, python3-dev, python3-mpi4py, python3-networkx, python3-numpy, python3-pybind11, python3-pytest, zlib1g-dev, doxygen, furo, ghostscript, graphicsmagick, graphviz, mscgen, python3-pygments, python3-sphinx, python3-sphinx-argparse, python3-sphinx-copybutton, python3-sphinx-inline-tabs, python3-sphinxcontrib.autoprogram, rdfind, symlinks, tex-gyre, texlive-fonts-recommended, texlive-latex-base, texlive-latex-extra dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19809 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on architecture-is-64-bit; however: Package architecture-is-64-bit is not installed. pbuilder-satisfydepends-dummy depends on bash-completion; however: Package bash-completion is not installed. pbuilder-satisfydepends-dummy depends on chrpath; however: Package chrpath is not installed. pbuilder-satisfydepends-dummy depends on cmake (>= 3.13); however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on libblas-dev; however: Package libblas-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-dev; however: Package libboost-dev is not installed. pbuilder-satisfydepends-dummy depends on libfftw3-dev; however: Package libfftw3-dev is not installed. pbuilder-satisfydepends-dummy depends on libhwloc-dev; however: Package libhwloc-dev is not installed. pbuilder-satisfydepends-dummy depends on liblapack-dev; however: Package liblapack-dev is not installed. pbuilder-satisfydepends-dummy depends on libmuparser-dev (>= 2.3.4); however: Package libmuparser-dev is not installed. pbuilder-satisfydepends-dummy depends on lsb-release; however: Package lsb-release is not installed. pbuilder-satisfydepends-dummy depends on mpi-default-bin; however: Package mpi-default-bin is not installed. pbuilder-satisfydepends-dummy depends on mpi-default-dev; however: Package mpi-default-dev is not installed. pbuilder-satisfydepends-dummy depends on pkgconf; however: Package pkgconf is not installed. pbuilder-satisfydepends-dummy depends on python3-dev; however: Package python3-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-mpi4py; however: Package python3-mpi4py is not installed. pbuilder-satisfydepends-dummy depends on python3-networkx; however: Package python3-networkx is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on python3-pybind11; however: Package python3-pybind11 is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on doxygen; however: Package doxygen is not installed. pbuilder-satisfydepends-dummy depends on furo; however: Package furo is not installed. pbuilder-satisfydepends-dummy depends on ghostscript; however: Package ghostscript is not installed. pbuilder-satisfydepends-dummy depends on graphicsmagick; however: Package graphicsmagick is not installed. pbuilder-satisfydepends-dummy depends on graphviz; however: Package graphviz is not installed. pbuilder-satisfydepends-dummy depends on mscgen; however: Package mscgen is not installed. pbuilder-satisfydepends-dummy depends on python3-pygments; however: Package python3-pygments is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx; however: Package python3-sphinx is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx-argparse; however: Package python3-sphinx-argparse is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx-copybutton; however: Package python3-sphinx-copybutton is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx-inline-tabs; however: Package python3-sphinx-inline-tabs is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinxcontrib.autoprogram; however: Package python3-sphinxcontrib.autoprogram is not installed. pbuilder-satisfydepends-dummy depends on rdfind; however: Package rdfind is not installed. pbuilder-satisfydepends-dummy depends on symlinks; however: Package symlinks is not installed. pbuilder-satisfydepends-dummy depends on tex-gyre; however: Package tex-gyre is not installed. pbuilder-satisfydepends-dummy depends on texlive-fonts-recommended; however: Package texlive-fonts-recommended is not installed. pbuilder-satisfydepends-dummy depends on texlive-latex-base; however: Package texlive-latex-base is not installed. pbuilder-satisfydepends-dummy depends on texlive-latex-extra; however: Package texlive-latex-extra is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: architecture-properties{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bash-completion{a} bsdextrautils{a} ca-certificates{a} chrpath{a} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} docutils-common{a} doxygen{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-lmodern{a} fonts-urw-base35{a} furo{a} gettext{a} gettext-base{a} gfortran-14{a} gfortran-14-x86-64-linux-gnu{a} ghostscript{a} graphicsmagick{a} graphviz{a} groff-base{a} ibverbs-providers{a} intltool-debian{a} libabsl20230802{a} libamd-comgr2{a} libamdhip64-5{a} libann0{a} libaom3{a} libapache-pom-java{a} libarchive-zip-perl{a} libarchive13t64{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libavif16{a} libblas-dev{a} libblas3{a} libboost-dev{a} libboost1.83-dev{a} libbrotli1{a} libcairo2{a} libcbor0.10{a} libcdt5{a} libcgraph6{a} libclang-cpp19{a} libclang1-19{a} libcom-err2{a} libcommons-logging-java{a} libcommons-parent-java{a} libcups2t64{a} libcurl4t64{a} libdatrie1{a} libdav1d7{a} libdbus-1-3{a} libde265-0{a} libdebhelper-perl{a} libdeflate0{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm2{a} libedit2{a} libelf1t64{a} libevent-2.1-7t64{a} libevent-core-2.1-7t64{a} libevent-dev{a} libevent-extra-2.1-7t64{a} libevent-openssl-2.1-7t64{a} libevent-pthreads-2.1-7t64{a} libexpat1{a} libexpat1-dev{a} libfabric1{a} libffi8{a} libfftw3-bin{a} libfftw3-dev{a} libfftw3-double3{a} libfftw3-long3{a} libfftw3-quad3{a} libfftw3-single3{a} libfido2-1{a} libfile-stripnondeterminism-perl{a} libfmt10{a} libfontbox-java{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgav1-1{a} libgd3{a} libgfortran-14-dev{a} libgfortran5{a} libgif7{a} libglib2.0-0t64{a} libgnutls30t64{a} libgraphicsmagick-q16-3t64{a} libgraphite2-3{a} libgs-common{a} libgs10{a} libgs10-common{a} libgssapi-krb5-2{a} libgts-0.7-5t64{a} libgvc6{a} libgvpr2{a} libharfbuzz0b{a} libheif-plugin-dav1d{a} libheif-plugin-libde265{a} libheif1{a} libhsa-runtime64-1{a} libhsakmt1{a} libhwloc-dev{a} libhwloc-plugins{a} libhwloc15{a} libhwy1t64{a} libibmad5{a} libibumad3{a} libibverbs-dev{a} libibverbs1{a} libice6{a} libicu72{a} libidn12{a} libidn2-0{a} libijs-0.35{a} libimagequant0{a} libimath-3-1-29t64{a} libjbig0{a} libjbig2dec0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-sphinxdoc{a} libjs-underscore{a} libjson-perl{a} libjsoncpp26{a} libjxl0.10{a} libk5crypto3{a} libkeyutils1{a} libkpathsea6{a} libkrb5-3{a} libkrb5support0{a} liblab-gamut1{a} liblapack-dev{a} liblapack3{a} liblcms2-2{a} libldap2{a} liblerc4{a} libllvm17t64{a} libllvm19{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1t64{a} libmpfi0{a} libmunge2{a} libmuparser-dev{a} libmuparser2v5{a} libnghttp2-14{a} libnl-3-200{a} libnl-3-dev{a} libnl-route-3-200{a} libnl-route-3-dev{a} libnuma-dev{a} libnuma1{a} libopenexr-3-1-30{a} libopenjp2-7{a} libopenmpi-dev{a} libopenmpi40{a} libp11-kit0{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper2{a} libpathplan4{a} libpciaccess0{a} libpdfbox-java{a} libpipeline1{a} libpixman-1-0{a} libpkgconf3{a} libpmix-dev{a} libpmix2t64{a} libpng16-16t64{a} libpotrace0{a} libproc2-0{a} libpsl5t64{a} libpsm-infinipath1{a} libpsm2-2{a} libptexenc1{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.13{a} libpython3.13-dev{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libraqm0{a} librav1e0.7{a} librdmacm1t64{a} libreadline8t64{a} librhash1{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libsm6{a} libssh2-1t64{a} libsvtav1enc2{a} libsynctex2{a} libtasn1-6{a} libteckit0{a} libtexlua53-5{a} libtext-charwidth-perl{a} libtext-wrapi18n-perl{a} libthai-data{a} libthai0{a} libtiff6{a} libtool{a} libuchardet0{a} libucx0{a} libunistring5{a} libuv1t64{a} libwebp7{a} libwebpmux3{a} libwmflite-0.2-7{a} libx11-6{a} libx11-data{a} libxau6{a} libxaw7{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxi6{a} libxml2{a} libxmu6{a} libxnvctrl0{a} libxpm4{a} libxrender1{a} libxt6t64{a} libyuv0{a} libz3-4{a} libzzip-0-13t64{a} lsb-release{a} m4{a} man-db{a} media-types{a} mpi-default-bin{a} mpi-default-dev{a} mscgen{a} netbase{a} ocl-icd-libopencl1{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} openssl{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} poppler-data{a} preview-latex-style{a} procps{a} pybind11-dev{a} python-babel-localedata{a} python3{a} python3-alabaster{a} python3-autocommand{a} python3-babel{a} python3-bs4{a} python3-certifi{a} python3-chardet{a} python3-charset-normalizer{a} python3-defusedxml{a} python3-dev{a} python3-docutils{a} python3-idna{a} python3-imagesize{a} python3-inflect{a} python3-iniconfig{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-jinja2{a} python3-markupsafe{a} python3-minimal{a} python3-more-itertools{a} python3-mpi4py{a} python3-networkx{a} python3-numpy{a} python3-packaging{a} python3-pkg-resources{a} python3-pluggy{a} python3-pybind11{a} python3-pygments{a} python3-pytest{a} python3-requests{a} python3-roman{a} python3-setuptools{a} python3-snowballstemmer{a} python3-soupsieve{a} python3-sphinx{a} python3-sphinx-argparse{a} python3-sphinx-copybutton{a} python3-sphinx-inline-tabs{a} python3-sphinxcontrib.autoprogram{a} python3-typeguard{a} python3-typing-extensions{a} python3-urllib3{a} python3-zipp{a} python3.13{a} python3.13-dev{a} python3.13-minimal{a} rdfind{a} readline-common{a} sensible-utils{a} sgml-base{a} sphinx-basic-ng{a} sphinx-common{a} symlinks{a} t1utils{a} tex-common{a} tex-gyre{a} texlive-base{a} texlive-binaries{a} texlive-fonts-recommended{a} texlive-latex-base{a} texlive-latex-extra{a} texlive-latex-recommended{a} texlive-pictures{a} tzdata{a} ucf{a} x11-common{a} xdg-utils{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl dbus default-jre dvisvgm fonts-droid-fallback fonts-liberation fonts-texgyre fonts-texgyre-math javascript-common krb5-locales libarchive-cpio-perl libcoarrays-openmpi-dev libeigen3-dev libfile-mimeinfo-perl libglib2.0-data libgts-bin libheif-plugin-aomenc libheif-plugin-x265 libjson-xs-perl libldap-common libmail-sendmail-perl libnet-dbus-perl libsasl2-modules libspreadsheet-parseexcel-perl libx11-protocol-perl linux-sysctl-defaults lmodern lynx psmisc publicsuffix python3-gdal python3-lxml python3-matplotlib python3-pil python3-pydot python3-pygraphviz python3-scipy python3-yaml ruby shared-mime-info texlive-plain-generic tipa tk wget x11-utils x11-xserver-utils xauth xdg-user-dirs 0 packages upgraded, 345 newly installed, 0 to remove and 0 not upgraded. Need to get 396 MB of archives. After unpacking 1736 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 poppler-data all 0.4.12-1 [1601 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libpython3.13-minimal amd64 3.13.2-1 [859 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 python3.13-minimal amd64 3.13.2-1 [2205 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.13.1-2 [27.0 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 tzdata all 2024b-6 [257 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libffi8 amd64 3.4.7-1 [23.9 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-6 [69.4 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 libpython3.13-stdlib amd64 3.13.2-1 [1979 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 python3.13 amd64 3.13.2-1 [745 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.13.1-2 [9952 B] Get: 15 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.13.1-2 [28.0 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 sgml-base all 1.31 [15.4 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libproc2-0 amd64 2:4.0.4-7 [64.9 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 procps amd64 2:4.0.4-7 [878 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 bash-completion all 1:2.16.0-7 [319 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.4.0-2 [1422 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20241223 [164 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.23.1-1 [243 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.4-3 [92.1 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 libedit2 amd64 3.1-20250104-1 [93.8 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 libcbor0.10 amd64 0.10.2-2 [28.3 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 libfido2-1 amd64 1.15.0-1+b1 [78.7 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-4 [32.8 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.2-1 [24.0 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-4 [80.9 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 39 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-4 [326 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-4 [138 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 openssh-client amd64 1:9.9p1-3 [991 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 libtext-charwidth-perl amd64 0.04-11+b4 [9476 B] Get: 43 http://deb.debian.org/debian trixie/main amd64 libtext-wrapi18n-perl all 0.06-10 [8808 B] Get: 44 http://deb.debian.org/debian trixie/main amd64 ucf all 3.0049 [42.5 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 architecture-properties amd64 0.2.5 [2272 B] Get: 46 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-5 [294 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-3 [862 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.23.1-1 [770 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 chrpath amd64 0.18-1 [13.5 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 cmake-data all 3.31.5-2 [2267 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-6 [9421 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 libarchive13t64 amd64 3.7.4-1.1 [349 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-1 [476 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 libidn2-0 amd64 2.3.7-2+b1 [129 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8+b1 [19.9 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8+b1 [57.6 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 libldap2 amd64 2.6.9+dfsg-1 [192 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 libgnutls30t64 amd64 3.8.9-2 [1464 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.12.0+git20250209.89ed161+ds-1 [355 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 libjsoncpp26 amd64 1.9.6-3 [81.7 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 librhash1 amd64 1.4.5-1 [132 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 libuv1t64 amd64 1.50.0-2 [154 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 cmake amd64 3.31.5-2 [12.0 MB] Get: 74 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-3 [539 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 80 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-1 [1680 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.1 [920 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 python3-more-itertools all 10.6.0-1 [65.3 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 92 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 75.6.0-1 [222 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 96 http://deb.debian.org/debian trixie/main amd64 python3-setuptools all 75.6.0-1 [720 kB] Get: 97 http://deb.debian.org/debian trixie/main amd64 dh-python all 6.20250108 [113 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 xml-core all 0.19 [20.1 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 docutils-common all 0.21.2+dfsg-2 [128 kB] Get: 100 http://deb.debian.org/debian trixie/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB] Get: 101 http://deb.debian.org/debian trixie/main amd64 libllvm19 amd64 1:19.1.7-1+b1 [26.0 MB] Get: 102 http://deb.debian.org/debian trixie/main amd64 libclang-cpp19 amd64 1:19.1.7-1+b1 [13.2 MB] Get: 103 http://deb.debian.org/debian trixie/main amd64 libclang1-19 amd64 1:19.1.7-1+b1 [7614 kB] Get: 104 http://deb.debian.org/debian trixie/main amd64 libfmt10 amd64 10.1.1+ds1-4 [127 kB] Get: 105 http://deb.debian.org/debian trixie/main amd64 doxygen amd64 1.9.8+ds-2.1 [5017 kB] Get: 106 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.46-4 [284 kB] Get: 107 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get: 108 http://deb.debian.org/debian trixie/main amd64 libfontenc1 amd64 1:1.1.8-1+b2 [23.3 kB] Get: 109 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+24 [217 kB] Get: 110 http://deb.debian.org/debian trixie/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 111 http://deb.debian.org/debian trixie/main amd64 xfonts-utils amd64 1:7.7+7 [93.3 kB] Get: 112 http://deb.debian.org/debian trixie/main amd64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 113 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-2 [317 kB] Get: 114 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-2 [391 kB] Get: 115 http://deb.debian.org/debian trixie/main amd64 fontconfig amd64 2.15.0-2 [463 kB] Get: 116 http://deb.debian.org/debian trixie/main amd64 fonts-lmodern all 2.005-1 [4540 kB] Get: 117 http://deb.debian.org/debian trixie/main amd64 python3-soupsieve all 2.6-1 [38.3 kB] Get: 118 http://deb.debian.org/debian trixie/main amd64 python3-bs4 all 4.13.3-1 [166 kB] Get: 119 http://deb.debian.org/debian trixie/main amd64 python3-pygments all 2.18.0+dfsg-2 [836 kB] Get: 120 http://deb.debian.org/debian trixie/main amd64 python3-defusedxml all 0.7.1-3 [43.4 kB] Get: 121 http://deb.debian.org/debian trixie/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 122 http://deb.debian.org/debian trixie/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 123 http://deb.debian.org/debian trixie/main amd64 libjs-sphinxdoc all 8.1.3-4 [30.4 kB] Get: 124 http://deb.debian.org/debian trixie/main amd64 libjson-perl all 4.10000-1 [87.5 kB] Get: 125 http://deb.debian.org/debian trixie/main amd64 sphinx-common all 8.1.3-4 [616 kB] Get: 126 http://deb.debian.org/debian trixie/main amd64 python3-alabaster all 0.7.16-0.1 [27.9 kB] Get: 127 http://deb.debian.org/debian trixie/main amd64 python-babel-localedata all 2.17.0-1 [6050 kB] Get: 128 http://deb.debian.org/debian trixie/main amd64 python3-babel all 2.17.0-1 [117 kB] Get: 129 http://deb.debian.org/debian trixie/main amd64 python3-roman all 5.0-1 [10.6 kB] Get: 130 http://deb.debian.org/debian trixie/main amd64 python3-docutils all 0.21.2+dfsg-2 [403 kB] Get: 131 http://deb.debian.org/debian trixie/main amd64 python3-imagesize all 1.4.1-1 [6688 B] Get: 132 http://deb.debian.org/debian trixie/main amd64 python3-markupsafe amd64 2.1.5-1+b2 [13.9 kB] Get: 133 http://deb.debian.org/debian trixie/main amd64 python3-jinja2 all 3.1.5-2 [107 kB] Get: 134 http://deb.debian.org/debian trixie/main amd64 python3-packaging all 24.2-1 [55.3 kB] Get: 135 http://deb.debian.org/debian trixie/main amd64 python3-certifi all 2025.1.31+ds-1 [9652 B] Get: 136 http://deb.debian.org/debian trixie/main amd64 python3-charset-normalizer amd64 3.4.0-1+b1 [140 kB] Get: 137 http://deb.debian.org/debian trixie/main amd64 python3-idna all 3.10-1 [42.0 kB] Get: 138 http://deb.debian.org/debian trixie/main amd64 python3-urllib3 all 2.3.0-1 [114 kB] Get: 139 http://deb.debian.org/debian trixie/main amd64 python3-chardet all 5.2.0+dfsg-2 [108 kB] Get: 140 http://deb.debian.org/debian trixie/main amd64 python3-requests all 2.32.3+dfsg-1 [71.9 kB] Get: 141 http://deb.debian.org/debian trixie/main amd64 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 142 http://deb.debian.org/debian trixie/main amd64 python3-sphinx all 8.1.3-4 [468 kB] Get: 143 http://deb.debian.org/debian trixie/main amd64 sphinx-basic-ng all 1.0.0~beta2-1 [13.0 kB] Get: 144 http://deb.debian.org/debian trixie/main amd64 furo all 2024.08.06+dfsg-1 [62.8 kB] Get: 145 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-16 [836 kB] Get: 146 http://deb.debian.org/debian trixie/main amd64 libgfortran-14-dev amd64 14.2.0-16 [879 kB] Get: 147 http://deb.debian.org/debian trixie/main amd64 gfortran-14-x86-64-linux-gnu amd64 14.2.0-16 [11.7 MB] Get: 148 http://deb.debian.org/debian trixie/main amd64 gfortran-14 amd64 14.2.0-16 [13.6 kB] Get: 149 http://deb.debian.org/debian trixie/main amd64 libgs-common all 10.04.0~dfsg-2 [148 kB] Get: 150 http://deb.debian.org/debian trixie/main amd64 libgs10-common all 10.04.0~dfsg-2 [475 kB] Get: 151 http://deb.debian.org/debian trixie/main amd64 libavahi-common-data amd64 0.8-16 [112 kB] Get: 152 http://deb.debian.org/debian trixie/main amd64 libavahi-common3 amd64 0.8-16 [44.2 kB] Get: 153 http://deb.debian.org/debian trixie/main amd64 libdbus-1-3 amd64 1.16.0-1 [177 kB] Get: 154 http://deb.debian.org/debian trixie/main amd64 libavahi-client3 amd64 0.8-16 [48.4 kB] Get: 155 http://deb.debian.org/debian trixie/main amd64 libcups2t64 amd64 2.4.10-2+b1 [251 kB] Get: 156 http://deb.debian.org/debian trixie/main amd64 libidn12 amd64 1.42-3 [81.0 kB] Get: 157 http://deb.debian.org/debian trixie/main amd64 libijs-0.35 amd64 0.35-15.1+b2 [15.2 kB] Get: 158 http://deb.debian.org/debian trixie/main amd64 libjbig2dec0 amd64 0.20-1+b3 [65.1 kB] Get: 159 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB] Get: 160 http://deb.debian.org/debian trixie/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get: 161 http://deb.debian.org/debian trixie/main amd64 libopenjp2-7 amd64 2.5.3-1 [204 kB] Get: 162 http://deb.debian.org/debian trixie/main amd64 libpaper2 amd64 2.2.5-0.3+b1 [16.6 kB] Get: 163 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.23-1+b1 [47.5 kB] Get: 164 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get: 165 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get: 166 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [116 kB] Get: 167 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB] Get: 168 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB] Get: 169 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 170 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 171 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 172 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get: 173 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get: 174 http://deb.debian.org/debian trixie/main amd64 libice6 amd64 2:1.1.1-1 [65.4 kB] Get: 175 http://deb.debian.org/debian trixie/main amd64 libsm6 amd64 2:1.2.4-1 [35.2 kB] Get: 176 http://deb.debian.org/debian trixie/main amd64 libxt6t64 amd64 1:1.2.1-1.2+b2 [188 kB] Get: 177 http://deb.debian.org/debian trixie/main amd64 libgs10 amd64 10.04.0~dfsg-2+b1 [2561 kB] Get: 178 http://deb.debian.org/debian trixie/main amd64 ghostscript amd64 10.04.0~dfsg-2+b1 [50.9 kB] Get: 179 http://deb.debian.org/debian trixie/main amd64 libdav1d7 amd64 1.5.1-1 [559 kB] Get: 180 http://deb.debian.org/debian trixie/main amd64 libheif-plugin-dav1d amd64 1.19.5-1+b1 [11.5 kB] Get: 181 http://deb.debian.org/debian trixie/main amd64 libde265-0 amd64 1.0.15-1+b2 [189 kB] Get: 182 http://deb.debian.org/debian trixie/main amd64 libheif-plugin-libde265 amd64 1.19.5-1+b1 [15.5 kB] Get: 183 http://deb.debian.org/debian trixie/main amd64 libheif1 amd64 1.19.5-1+b1 [514 kB] Get: 184 http://deb.debian.org/debian trixie/main amd64 libgif7 amd64 5.2.2-1+b1 [44.2 kB] Get: 185 http://deb.debian.org/debian trixie/main amd64 libhwy1t64 amd64 1.2.0-2+b2 [676 kB] Get: 186 http://deb.debian.org/debian trixie/main amd64 libimath-3-1-29t64 amd64 3.1.12-1+b3 [45.5 kB] Get: 187 http://deb.debian.org/debian trixie/main amd64 libopenexr-3-1-30 amd64 3.1.5-5.1+b4 [935 kB] Get: 188 http://deb.debian.org/debian trixie/main amd64 libjxl0.10 amd64 0.10.4-2 [1096 kB] Get: 189 http://deb.debian.org/debian trixie/main amd64 libwebpmux3 amd64 1.5.0-0.1 [126 kB] Get: 190 http://deb.debian.org/debian trixie/main amd64 libwmflite-0.2-7 amd64 0.2.13-1.1+b3 [75.6 kB] Get: 191 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get: 192 http://deb.debian.org/debian trixie/main amd64 libgraphicsmagick-q16-3t64 amd64 1.4+really1.3.45-1+b2 [1228 kB] Get: 193 http://deb.debian.org/debian trixie/main amd64 graphicsmagick amd64 1.4+really1.3.45-1+b2 [1080 kB] Get: 194 http://deb.debian.org/debian trixie/main amd64 libann0 amd64 1.1.2+doc-9+b1 [25.1 kB] Get: 195 http://deb.debian.org/debian trixie/main amd64 libcdt5 amd64 2.42.4-2+b4 [40.5 kB] Get: 196 http://deb.debian.org/debian trixie/main amd64 libcgraph6 amd64 2.42.4-2+b4 [64.2 kB] Get: 197 http://deb.debian.org/debian trixie/main amd64 libaom3 amd64 3.12.0-1 [1870 kB] Get: 198 http://deb.debian.org/debian trixie/main amd64 libabsl20230802 amd64 20230802.1-4 [464 kB] Get: 199 http://deb.debian.org/debian trixie/main amd64 libgav1-1 amd64 0.19.0-3 [350 kB] Get: 200 http://deb.debian.org/debian trixie/main amd64 librav1e0.7 amd64 0.7.1-9+b1 [946 kB] Get: 201 http://deb.debian.org/debian trixie/main amd64 libsvtav1enc2 amd64 2.3.0+dfsg-1 [2489 kB] Get: 202 http://deb.debian.org/debian trixie/main amd64 libyuv0 amd64 0.0.1904.20250204-1 [174 kB] Get: 203 http://deb.debian.org/debian trixie/main amd64 libavif16 amd64 1.1.1-1 [117 kB] Get: 204 http://deb.debian.org/debian trixie/main amd64 libimagequant0 amd64 2.18.0-1+b2 [35.2 kB] Get: 205 http://deb.debian.org/debian trixie/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB] Get: 206 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.83.3-2 [1511 kB] Get: 207 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get: 208 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 10.2.0-1 [479 kB] Get: 209 http://deb.debian.org/debian trixie/main amd64 libraqm0 amd64 0.10.2-1 [13.9 kB] Get: 210 http://deb.debian.org/debian trixie/main amd64 libxpm4 amd64 1:3.5.17-1+b3 [56.2 kB] Get: 211 http://deb.debian.org/debian trixie/main amd64 libgd3 amd64 2.3.3-12+b1 [126 kB] Get: 212 http://deb.debian.org/debian trixie/main amd64 libgts-0.7-5t64 amd64 0.7.6+darcs121130-5.2+b1 [160 kB] Get: 213 http://deb.debian.org/debian trixie/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get: 214 http://deb.debian.org/debian trixie/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get: 215 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get: 216 http://deb.debian.org/debian trixie/main amd64 libxrender1 amd64 1:0.9.10-1.1+b4 [27.8 kB] Get: 217 http://deb.debian.org/debian trixie/main amd64 libcairo2 amd64 1.18.2-2 [535 kB] Get: 218 http://deb.debian.org/debian trixie/main amd64 libltdl7 amd64 2.5.4-3 [415 kB] Get: 219 http://deb.debian.org/debian trixie/main amd64 libthai-data all 0.1.29-2 [168 kB] Get: 220 http://deb.debian.org/debian trixie/main amd64 libdatrie1 amd64 0.2.13-3+b1 [38.1 kB] Get: 221 http://deb.debian.org/debian trixie/main amd64 libthai0 amd64 0.1.29-2+b1 [49.4 kB] Get: 222 http://deb.debian.org/debian trixie/main amd64 libpango-1.0-0 amd64 1.56.1-1 [226 kB] Get: 223 http://deb.debian.org/debian trixie/main amd64 libpangoft2-1.0-0 amd64 1.56.1-1 [55.3 kB] Get: 224 http://deb.debian.org/debian trixie/main amd64 libpangocairo-1.0-0 amd64 1.56.1-1 [35.8 kB] Get: 225 http://deb.debian.org/debian trixie/main amd64 libpathplan4 amd64 2.42.4-2+b4 [42.8 kB] Get: 226 http://deb.debian.org/debian trixie/main amd64 libgvc6 amd64 2.42.4-2+b4 [685 kB] Get: 227 http://deb.debian.org/debian trixie/main amd64 libgvpr2 amd64 2.42.4-2+b4 [193 kB] Get: 228 http://deb.debian.org/debian trixie/main amd64 liblab-gamut1 amd64 2.42.4-2+b4 [198 kB] Get: 229 http://deb.debian.org/debian trixie/main amd64 libxmu6 amd64 2:1.1.3-3+b4 [59.0 kB] Get: 230 http://deb.debian.org/debian trixie/main amd64 libxaw7 amd64 2:1.0.16-1 [212 kB] Get: 231 http://deb.debian.org/debian trixie/main amd64 graphviz amd64 2.42.4-2+b4 [619 kB] Get: 232 http://deb.debian.org/debian trixie/main amd64 libnl-3-200 amd64 3.7.0-0.3+b1 [59.4 kB] Get: 233 http://deb.debian.org/debian trixie/main amd64 libnl-route-3-200 amd64 3.7.0-0.3+b1 [182 kB] Get: 234 http://deb.debian.org/debian trixie/main amd64 libibverbs1 amd64 55.0-1 [62.2 kB] Get: 235 http://deb.debian.org/debian trixie/main amd64 ibverbs-providers amd64 55.0-1 [351 kB] Get: 236 http://deb.debian.org/debian trixie/main amd64 libllvm17t64 amd64 1:17.0.6-21 [23.6 MB] Get: 237 http://deb.debian.org/debian trixie/main amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3+b2 [13.0 MB] Get: 238 http://deb.debian.org/debian trixie/main amd64 libdrm-common all 2.4.123-1 [8084 B] Get: 239 http://deb.debian.org/debian trixie/main amd64 libdrm2 amd64 2.4.123-1 [38.7 kB] Get: 240 http://deb.debian.org/debian trixie/main amd64 libdrm-amdgpu1 amd64 2.4.123-1 [22.3 kB] Get: 241 http://deb.debian.org/debian trixie/main amd64 libnuma1 amd64 2.0.18-1+b1 [22.3 kB] Get: 242 http://deb.debian.org/debian trixie/main amd64 libhsakmt1 amd64 6.2.4+ds-1 [61.1 kB] Get: 243 http://deb.debian.org/debian trixie/main amd64 libhsa-runtime64-1 amd64 6.1.2-3 [535 kB] Get: 244 http://deb.debian.org/debian trixie/main amd64 libamdhip64-5 amd64 5.7.1-5 [8877 kB] Get: 245 http://deb.debian.org/debian trixie/main amd64 libapache-pom-java all 33-2 [5852 B] Get: 246 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.1-2 [160 kB] Get: 247 http://deb.debian.org/debian trixie/main amd64 libblas-dev amd64 3.12.1-2 [170 kB] Get: 248 http://deb.debian.org/debian trixie/main amd64 libboost1.83-dev amd64 1.83.0-4.1 [10.6 MB] Get: 249 http://deb.debian.org/debian trixie/main amd64 libboost-dev amd64 1.83.0.2+b2 [3836 B] Get: 250 http://deb.debian.org/debian trixie/main amd64 libcommons-parent-java all 56-1 [10.8 kB] Get: 251 http://deb.debian.org/debian trixie/main amd64 libcommons-logging-java all 1.3.0-1 [68.6 kB] Get: 252 http://deb.debian.org/debian trixie/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get: 253 http://deb.debian.org/debian trixie/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-10+b1 [132 kB] Get: 254 http://deb.debian.org/debian trixie/main amd64 libevent-extra-2.1-7t64 amd64 2.1.12-stable-10+b1 [108 kB] Get: 255 http://deb.debian.org/debian trixie/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-10+b1 [54.3 kB] Get: 256 http://deb.debian.org/debian trixie/main amd64 libevent-openssl-2.1-7t64 amd64 2.1.12-stable-10+b1 [61.1 kB] Get: 257 http://deb.debian.org/debian trixie/main amd64 libevent-dev amd64 2.1.12-stable-10+b1 [305 kB] Get: 258 http://deb.debian.org/debian trixie/main amd64 libexpat1-dev amd64 2.6.4-1 [158 kB] Get: 259 http://deb.debian.org/debian trixie/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.3 [170 kB] Get: 260 http://deb.debian.org/debian trixie/main amd64 libpsm2-2 amd64 11.2.185-2.1 [181 kB] Get: 261 http://deb.debian.org/debian trixie/main amd64 librdmacm1t64 amd64 55.0-1 [70.2 kB] Get: 262 http://deb.debian.org/debian trixie/main amd64 libfabric1 amd64 1.17.0-3.1 [631 kB] Get: 263 http://deb.debian.org/debian trixie/main amd64 libfftw3-double3 amd64 3.3.10-2+b1 [781 kB] Get: 264 http://deb.debian.org/debian trixie/main amd64 libfftw3-long3 amd64 3.3.10-2+b1 [347 kB] Get: 265 http://deb.debian.org/debian trixie/main amd64 libfftw3-quad3 amd64 3.3.10-2+b1 [618 kB] Get: 266 http://deb.debian.org/debian trixie/main amd64 libfftw3-single3 amd64 3.3.10-2+b1 [809 kB] Get: 267 http://deb.debian.org/debian trixie/main amd64 libfftw3-bin amd64 3.3.10-2+b1 [51.3 kB] Get: 268 http://deb.debian.org/debian trixie/main amd64 libfftw3-dev amd64 3.3.10-2+b1 [2118 kB] Get: 269 http://deb.debian.org/debian trixie/main amd64 libfontbox-java all 1:1.8.16-5 [211 kB] Get: 270 http://deb.debian.org/debian trixie/main amd64 libhwloc15 amd64 2.11.2-1 [164 kB] Get: 271 http://deb.debian.org/debian trixie/main amd64 libnuma-dev amd64 2.0.18-1+b1 [36.6 kB] Get: 272 http://deb.debian.org/debian trixie/main amd64 libltdl-dev amd64 2.5.4-3 [167 kB] Get: 273 http://deb.debian.org/debian trixie/main amd64 libhwloc-dev amd64 2.11.2-1 [254 kB] Get: 274 http://deb.debian.org/debian trixie/main amd64 libpciaccess0 amd64 0.17-3+b3 [51.9 kB] Get: 275 http://deb.debian.org/debian trixie/main amd64 libxnvctrl0 amd64 535.171.04-1+b2 [14.2 kB] Get: 276 http://deb.debian.org/debian trixie/main amd64 ocl-icd-libopencl1 amd64 2.3.2-1+b2 [40.2 kB] Get: 277 http://deb.debian.org/debian trixie/main amd64 libhwloc-plugins amd64 2.11.2-1 [18.1 kB] Get: 278 http://deb.debian.org/debian trixie/main amd64 libibumad3 amd64 55.0-1 [28.5 kB] Get: 279 http://deb.debian.org/debian trixie/main amd64 libibmad5 amd64 55.0-1 [43.3 kB] Get: 280 http://deb.debian.org/debian trixie/main amd64 libnl-3-dev amd64 3.7.0-0.3+b1 [100 kB] Get: 281 http://deb.debian.org/debian trixie/main amd64 libnl-route-3-dev amd64 3.7.0-0.3+b1 [200 kB] Get: 282 http://deb.debian.org/debian trixie/main amd64 libibverbs-dev amd64 55.0-1 [648 kB] Get: 283 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 284 http://deb.debian.org/debian trixie/main amd64 libkpathsea6 amd64 2024.20240313.70630+ds-5+b1 [157 kB] Get: 285 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.1-2 [2452 kB] Get: 286 http://deb.debian.org/debian trixie/main amd64 liblapack-dev amd64 3.12.1-2 [4998 kB] Get: 287 http://deb.debian.org/debian trixie/main amd64 libmpfi0 amd64 1.5.4+ds-4 [35.5 kB] Get: 288 http://deb.debian.org/debian trixie/main amd64 libmunge2 amd64 0.5.16-1 [19.7 kB] Get: 289 http://deb.debian.org/debian trixie/main amd64 libmuparser2v5 amd64 2.3.4-1+b1 [149 kB] Get: 290 http://deb.debian.org/debian trixie/main amd64 libmuparser-dev amd64 2.3.4-1+b1 [33.6 kB] Get: 291 http://deb.debian.org/debian trixie/main amd64 libpmix2t64 amd64 5.0.6-3 [651 kB] Get: 292 http://deb.debian.org/debian trixie/main amd64 libucx0 amd64 1.17.0+ds-3 [1130 kB] Get: 293 http://deb.debian.org/debian trixie/main amd64 libopenmpi40 amd64 5.0.6-4 [2356 kB] Get: 294 http://deb.debian.org/debian trixie/main amd64 openmpi-common all 5.0.6-4 [97.1 kB] Get: 295 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 296 http://deb.debian.org/debian trixie/main amd64 libpmix-dev amd64 5.0.6-3 [3961 kB] Get: 297 http://deb.debian.org/debian trixie/main amd64 openmpi-bin amd64 5.0.6-4 [189 kB] Get: 298 http://deb.debian.org/debian trixie/main amd64 libopenmpi-dev amd64 5.0.6-4 [1088 kB] Get: 299 http://deb.debian.org/debian trixie/main amd64 libpaper-utils amd64 2.2.5-0.3+b1 [16.4 kB] Get: 300 http://deb.debian.org/debian trixie/main amd64 libpdfbox-java all 1:1.8.16-5 [5527 kB] Get: 301 http://deb.debian.org/debian trixie/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 302 http://deb.debian.org/debian trixie/main amd64 libpotrace0 amd64 1.16-2+b2 [25.6 kB] Get: 303 http://deb.debian.org/debian trixie/main amd64 libptexenc1 amd64 2024.20240313.70630+ds-5+b1 [49.4 kB] Get: 304 http://deb.debian.org/debian trixie/main amd64 libpython3.13 amd64 3.13.2-1 [2151 kB] Get: 305 http://deb.debian.org/debian trixie/main amd64 libpython3.13-dev amd64 3.13.2-1 [5005 kB] Get: 306 http://deb.debian.org/debian trixie/main amd64 libpython3-dev amd64 3.13.1-2 [10.2 kB] Get: 307 http://deb.debian.org/debian trixie/main amd64 libsynctex2 amd64 2024.20240313.70630+ds-5+b1 [63.0 kB] Get: 308 http://deb.debian.org/debian trixie/main amd64 libteckit0 amd64 2.5.12+ds1-1+b1 [341 kB] Get: 309 http://deb.debian.org/debian trixie/main amd64 libtexlua53-5 amd64 2024.20240313.70630+ds-5+b1 [115 kB] Get: 310 http://deb.debian.org/debian trixie/main amd64 libxi6 amd64 2:1.8.2-1 [78.9 kB] Get: 311 http://deb.debian.org/debian trixie/main amd64 libzzip-0-13t64 amd64 0.13.72+dfsg.1-1.2+b1 [56.2 kB] Get: 312 http://deb.debian.org/debian trixie/main amd64 lsb-release all 12.1-1 [5912 B] Get: 313 http://deb.debian.org/debian trixie/main amd64 mpi-default-bin amd64 1.18 [2576 B] Get: 314 http://deb.debian.org/debian trixie/main amd64 mpi-default-dev amd64 1.18 [3372 B] Get: 315 http://deb.debian.org/debian trixie/main amd64 mscgen amd64 0.20-16 [46.8 kB] Get: 316 http://deb.debian.org/debian trixie/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 317 http://deb.debian.org/debian trixie/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 318 http://deb.debian.org/debian trixie/main amd64 tex-common all 6.18 [32.5 kB] Get: 319 http://deb.debian.org/debian trixie/main amd64 preview-latex-style all 13.2-1 [350 kB] Get: 320 http://deb.debian.org/debian trixie/main amd64 pybind11-dev all 2.13.6-2 [205 kB] Get: 321 http://deb.debian.org/debian trixie/main amd64 python3.13-dev amd64 3.13.2-1 [507 kB] Get: 322 http://deb.debian.org/debian trixie/main amd64 python3-dev amd64 3.13.1-2 [26.1 kB] Get: 323 http://deb.debian.org/debian trixie/main amd64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 324 http://deb.debian.org/debian trixie/main amd64 python3-mpi4py amd64 4.0.1-7 [996 kB] Get: 325 http://deb.debian.org/debian trixie/main amd64 python3-networkx all 3.2.1-5 [13.0 MB] Get: 326 http://deb.debian.org/debian trixie/main amd64 python3-numpy amd64 1:1.26.4+ds-13 [4736 kB] Get: 327 http://deb.debian.org/debian trixie/main amd64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 328 http://deb.debian.org/debian trixie/main amd64 python3-pybind11 all 2.13.6-2 [215 kB] Get: 329 http://deb.debian.org/debian trixie/main amd64 python3-pytest all 8.3.4-1 [250 kB] Get: 330 http://deb.debian.org/debian trixie/main amd64 python3-sphinx-argparse all 0.5.2-1 [59.6 kB] Get: 331 http://deb.debian.org/debian trixie/main amd64 python3-sphinx-copybutton all 0.5.2-2 [17.9 kB] Get: 332 http://deb.debian.org/debian trixie/main amd64 python3-sphinx-inline-tabs all 2023.4.21-1 [35.9 kB] Get: 333 http://deb.debian.org/debian trixie/main amd64 python3-sphinxcontrib.autoprogram all 0.1.9-1 [10.6 kB] Get: 334 http://deb.debian.org/debian trixie/main amd64 rdfind amd64 1.6.0-1+b1 [44.7 kB] Get: 335 http://deb.debian.org/debian trixie/main amd64 symlinks amd64 1.4-5+b1 [9692 B] Get: 336 http://deb.debian.org/debian trixie/main amd64 t1utils amd64 1.41-4 [62.1 kB] Get: 337 http://deb.debian.org/debian trixie/main amd64 tex-gyre all 20180621-6 [6209 kB] Get: 338 http://deb.debian.org/debian trixie/main amd64 texlive-binaries amd64 2024.20240313.70630+ds-5+b1 [8504 kB] Get: 339 http://deb.debian.org/debian trixie/main amd64 xdg-utils all 1.2.1-2 [75.8 kB] Get: 340 http://deb.debian.org/debian trixie/main amd64 texlive-base all 2024.20250114-1 [22.8 MB] Get: 341 http://deb.debian.org/debian trixie/main amd64 texlive-fonts-recommended all 2024.20250114-1 [4991 kB] Get: 342 http://deb.debian.org/debian trixie/main amd64 texlive-latex-base all 2024.20250114-1 [1282 kB] Get: 343 http://deb.debian.org/debian trixie/main amd64 texlive-latex-recommended all 2024.20250114-1 [8760 kB] Get: 344 http://deb.debian.org/debian trixie/main amd64 texlive-pictures all 2024.20250114-1 [17.1 MB] Get: 345 http://deb.debian.org/debian trixie/main amd64 texlive-latex-extra all 2024.20250114-1 [24.7 MB] Fetched 396 MB in 23s (17.1 MB/s) Preconfiguring packages ... Selecting previously unselected package poppler-data. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19809 files and directories currently installed.) Preparing to unpack .../poppler-data_0.4.12-1_all.deb ... Unpacking poppler-data (0.4.12-1) ... Selecting previously unselected package libpython3.13-minimal:amd64. Preparing to unpack .../libpython3.13-minimal_3.13.2-1_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.2-1) ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.2-1_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.2-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.2-1_amd64.deb ... Unpacking python3.13 (3.13.2-1) ... Selecting previously unselected package libpython3-stdlib:amd64. 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Unpacking libidn2-0:amd64 (2.3.7-2+b1) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../044-libsasl2-modules-db_2.1.28+dfsg1-8+b1_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg1-8+b1) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../045-libsasl2-2_2.1.28+dfsg1-8+b1_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg1-8+b1) ... Selecting previously unselected package libldap2:amd64. Preparing to unpack .../046-libldap2_2.6.9+dfsg-1_amd64.deb ... Unpacking libldap2:amd64 (2.6.9+dfsg-1) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../047-libnghttp2-14_1.64.0-1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.64.0-1) ... Selecting previously unselected package libpsl5t64:amd64. Preparing to unpack .../048-libpsl5t64_0.21.2-1.1+b1_amd64.deb ... Unpacking libpsl5t64:amd64 (0.21.2-1.1+b1) ... Selecting previously unselected package libp11-kit0:amd64. 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Unpacking libcurl4t64:amd64 (8.12.0+git20250209.89ed161+ds-1) ... Selecting previously unselected package libjsoncpp26:amd64. Preparing to unpack .../055-libjsoncpp26_1.9.6-3_amd64.deb ... Unpacking libjsoncpp26:amd64 (1.9.6-3) ... Selecting previously unselected package librhash1:amd64. Preparing to unpack .../056-librhash1_1.4.5-1_amd64.deb ... Unpacking librhash1:amd64 (1.4.5-1) ... Selecting previously unselected package libuv1t64:amd64. Preparing to unpack .../057-libuv1t64_1.50.0-2_amd64.deb ... Unpacking libuv1t64:amd64 (1.50.0-2) ... Selecting previously unselected package cmake. Preparing to unpack .../058-cmake_3.31.5-2_amd64.deb ... Unpacking cmake (3.31.5-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../059-libdebhelper-perl_13.24.1_all.deb ... Unpacking libdebhelper-perl (13.24.1) ... Selecting previously unselected package libtool. Preparing to unpack .../060-libtool_2.5.4-3_all.deb ... Unpacking libtool (2.5.4-3) ... 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Setting up liblapack-dev:amd64 (3.12.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode Setting up libgssapi-krb5-2:amd64 (1.21.3-4) ... Setting up libgav1-1:amd64 (0.19.0-3) ... Setting up ucf (3.0049) ... Setting up libjs-sphinxdoc (8.1.3-4) ... Setting up libevent-extra-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up libreadline8t64:amd64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up libgvpr2:amd64 (2.42.4-2+b4) ... Setting up libdrm2:amd64 (2.4.123-1) ... Setting up libnl-3-dev:amd64 (3.7.0-0.3+b1) ... Setting up groff-base (1.23.0-7) ... Setting up xml-core (0.19) ... Setting up libharfbuzz0b:amd64 (10.2.0-1) ... Setting up libgts-0.7-5t64:amd64 (0.7.6+darcs121130-5.2+b1) ... Setting up libhwloc-dev:amd64 (2.11.2-1) ... Setting up libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3+b2) ... 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Setting up xfonts-utils (1:7.7+7) ... Setting up python3-autocommand (2.2.2-3) ... Setting up libhwloc-plugins:amd64 (2.11.2-1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up python3-markupsafe (2.1.5-1+b2) ... Setting up tex-common (6.18) ... update-language: texlive-base not installed and configured, doing nothing! Setting up libnl-route-3-dev:amd64 (3.7.0-0.3+b1) ... Setting up python3-roman (5.0-1) ... Setting up python3-jinja2 (3.1.5-2) ... Setting up python3-pygments (2.18.0+dfsg-2) ... Setting up doxygen (1.9.8+ds-2.1) ... Setting up python3-packaging (24.2-1) ... Setting up python3-chardet (5.2.0+dfsg-2) ... Setting up python3-certifi (2025.1.31+ds-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up python3-snowballstemmer (2.2.0-4) ... Setting up libraqm0:amd64 (0.10.2-1) ... Setting up libpython3.13-dev:amd64 (3.13.2-1) ... Setting up sphinx-common (8.1.3-4) ... Setting up libxt6t64:amd64 (1:1.2.1-1.2+b2) ... Setting up libevent-dev (2.1.12-stable-10+b1) ... Setting up python3-idna (3.10-1) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up libpmix2t64:amd64 (5.0.6-3) ... Setting up python3-numpy (1:1.26.4+ds-13) ... Setting up python3-urllib3 (2.3.0-1) ... Setting up python3-pluggy (1.5.0-1) ... Setting up librdmacm1t64:amd64 (55.0-1) ... Setting up libcups2t64:amd64 (2.4.10-2+b1) ... Setting up python3-soupsieve (2.6-1) ... Setting up tex-gyre (20180621-6) ... Setting up libpmix-dev:amd64 (5.0.6-3) ... Setting up libhsakmt1:amd64 (6.2.4+ds-1) ... Setting up python3-imagesize (1.4.1-1) ... Setting up python3-more-itertools (10.6.0-1) ... Setting up libfabric1:amd64 (1.17.0-3.1) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up libxmu6:amd64 (2:1.1.3-3+b4) ... Setting up libpython3-dev:amd64 (3.13.1-2) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up libcurl4t64:amd64 (8.12.0+git20250209.89ed161+ds-1) ... Setting up python3-babel (2.17.0-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3-defusedxml (0.7.1-3) ... Setting up python3-charset-normalizer (3.4.0-1+b1) ... Setting up python3.13-dev (3.13.2-1) ... Setting up python3-pytest (8.3.4-1) ... Setting up python3-alabaster (0.7.16-0.1) ... Setting up preview-latex-style (13.2-1) ... Setting up python3-typeguard (4.4.1-1) ... Setting up debhelper (13.24.1) ... Setting up libxaw7:amd64 (2:1.0.16-1) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up libibverbs-dev:amd64 (55.0-1) ... Setting up pybind11-dev (2.13.6-2) ... Setting up python3-bs4 (4.13.3-1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-dev (3.13.1-2) ... Setting up python3-requests (2.32.3+dfsg-1) ... Setting up libhsa-runtime64-1:amd64 (6.1.2-3) ... Setting up cmake (3.31.5-2) ... Setting up python3-pybind11 (2.13.6-2) ... Setting up python3-pkg-resources (75.6.0-1) ... Setting up libgs10-common (10.04.0~dfsg-2) ... Setting up python3-setuptools (75.6.0-1) ... Setting up fontconfig-config (2.15.0-2) ... Setting up python3-networkx (3.2.1-5) ... Setting up libamdhip64-5 (5.7.1-5) ... Setting up libfontconfig1:amd64 (2.15.0-2) ... Setting up libgs10:amd64 (10.04.0~dfsg-2+b1) ... Setting up dh-python (6.20250108) ... Setting up fontconfig (2.15.0-2) ... Regenerating fonts cache... done. Setting up libucx0:amd64 (1.17.0+ds-3) ... Setting up libpango-1.0-0:amd64 (1.56.1-1) ... Setting up ghostscript (10.04.0~dfsg-2+b1) ... Setting up libcairo2:amd64 (1.18.2-2) ... Setting up texlive-binaries (2024.20240313.70630+ds-5+b1) ... update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode Setting up libpangoft2-1.0-0:amd64 (1.56.1-1) ... Setting up texlive-base (2024.20250114-1) ... tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex Setting up libpangocairo-1.0-0:amd64 (1.56.1-1) ... Setting up libopenmpi40:amd64 (5.0.6-4) ... Setting up texlive-latex-base (2024.20250114-1) ... Setting up texlive-latex-recommended (2024.20250114-1) ... Setting up texlive-pictures (2024.20250114-1) ... Setting up texlive-fonts-recommended (2024.20250114-1) ... Setting up openmpi-bin (5.0.6-4) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: warning: skip creation of /usr/share/man/man1/mpiexec.1.gz because associated file /usr/share/man/man1/mpiexec.openmpi.1.gz (of link group mpirun) doesn't exist update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up mpi-default-bin (1.18) ... Setting up texlive-latex-extra (2024.20250114-1) ... Setting up python3-mpi4py (4.0.1-7) ... Setting up libopenmpi-dev:amd64 (5.0.6-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openmpi/include to provide /usr/include/x86_64-linux-gnu/mpi (mpi-x86_64-linux-gnu) in auto mode Setting up mpi-default-dev (1.18) ... Setting up libheif-plugin-libde265:amd64 (1.19.5-1+b1) ... Setting up libheif1:amd64 (1.19.5-1+b1) ... Setting up libgd3:amd64 (2.3.3-12+b1) ... Setting up libgvc6 (2.42.4-2+b4) ... Setting up libheif-plugin-dav1d:amd64 (1.19.5-1+b1) ... Setting up graphviz (2.42.4-2+b4) ... Setting up libgraphicsmagick-q16-3t64 (1.4+really1.3.45-1+b2) ... Setting up mscgen (0.20-16) ... Setting up graphicsmagick (1.4+really1.3.45-1+b2) ... Processing triggers for libc-bin (2.40-6) ... Processing triggers for sgml-base (1.31) ... Setting up docutils-common (0.21.2+dfsg-2) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.21.2+dfsg-2) ... Setting up python3-sphinx (8.1.3-4) ... Setting up python3-sphinx-copybutton (0.5.2-2) ... Setting up python3-sphinx-argparse (0.5.2-1) ... Setting up sphinx-basic-ng (1.0.0~beta2-1) ... Setting up python3-sphinx-inline-tabs (2023.4.21-1) ... Setting up python3-sphinxcontrib.autoprogram (0.1.9-1) ... Setting up furo (2024.08.06+dfsg-1) ... Processing triggers for ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Processing triggers for tex-common (6.18) ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building format(s) --all. This may take some time... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/gromacs-2025.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../gromacs_2025.0-2_source.changes dpkg-buildpackage: info: source package gromacs dpkg-buildpackage: info: source version 2025.0-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nicholas Breen dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh_testdir dh_testroot dh_clean build-basic build-mpi build-manual build/ py3clean admin docs debian/rules binary dh_testdir (mkdir -p build/basic; cd build/basic; cmake \ /build/reproducible-path/gromacs-2025.0 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_USE_MUPARSER=EXTERNAL -DGMX_VERSION_STRING_OF_FORK="Debian-2025.0-2" -DGMX_GIT_VERSION_INFO=OFF -DGMX_HWLOC=ON -DGMX_SIMD=SSE4.1 -DGMX_MPI=OFF -DGMX_INSTALL_LEGACY_API=ON) -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Python3: /usr/bin/python3 (found suitable version "3.13.2", minimum required is "3.9") found components: Interpreter Development Development.Module Development.Embed -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- Torch not found. Neural network potential support will be disabled. -- Using default binary suffix: "" -- Using default library suffix: "" -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /usr/lib/x86_64-linux-gnu/libhwloc.so (found suitable version "2.11.0", minimum required is "1.5") -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Performing Test TEST_ATOMICS -- Performing Test TEST_ATOMICS - Success -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.3.1") -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so - found -- Performing Test C_msse4_1_FLAG_ACCEPTED -- Performing Test C_msse4_1_FLAG_ACCEPTED - Success -- Performing Test C_msse4_1_COMPILE_WORKS -- Performing Test C_msse4_1_COMPILE_WORKS - Success -- Performing Test CXX_msse4_1_FLAG_ACCEPTED -- Performing Test CXX_msse4_1_FLAG_ACCEPTED - Success -- Performing Test CXX_msse4_1_COMPILE_WORKS -- Performing Test CXX_msse4_1_COMPILE_WORKS - Success -- Enabling SSE4.1 SIMD instructions using CXX flags: -msse4.1 -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - supported -- Detected build CPU vendor - AMD -- Detected build CPU brand - AMD Opteron 62xx class CPU -- Detected build CPU family - 21 -- Detected build CPU model - 1 -- Detected build CPU stepping - 2 -- Detected build CPU features - aes amd apic avx clfsh cmov cx8 cx16 lahf misalignsse mmx msr pclmuldq pdpe1gb popcnt pse rdtscp sse2 sse3 sse4a sse4.1 sse4.2 ssse3 x2apic -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - not present -- Checking for module 'fftw3f' -- Found fftw3f, version 3.3.10 -- Looking for fftwf_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/x86_64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- Found LAPACK: /usr/lib/x86_64-linux-gnu/liblapack.so;/usr/lib/x86_64-linux-gnu/libblas.so -- Performing Test HAS_WARNING_EVERYTHING -- Performing Test HAS_WARNING_EVERYTHING - Failed -- Found Python: /usr/bin/python3 (found version "3.13.2") found components: Interpreter -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Looking for inttypes.h -- Looking for inttypes.h - found -- Looking for dlopen -- Looking for dlopen - found -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success -- Performing Test COMPILER_HAS_DEPRECATED_ATTR -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success -- Found Sphinx: /usr/bin/sphinx-build (found suitable version "8.1.3", minimum required is "4.0.0") found components: pygments -- Found LATEX: /usr/bin/latex -- Configuring done (63.4s) -- Generating done (1.9s) -- Build files have been written to: /build/reproducible-path/gromacs-2025.0/build/basic (mkdir -p build/basic-dp; cd build/basic-dp; cmake \ /build/reproducible-path/gromacs-2025.0 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_USE_MUPARSER=EXTERNAL -DGMX_VERSION_STRING_OF_FORK="Debian-2025.0-2" -DGMX_GIT_VERSION_INFO=OFF -DGMX_HWLOC=ON -DGMX_SIMD=SSE4.1 -DGMX_MPI=OFF -DGMX_DOUBLE=ON) -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Python3: /usr/bin/python3 (found suitable version "3.13.2", minimum required is "3.9") found components: Interpreter Development Development.Module Development.Embed -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- Torch not found. Neural network potential support will be disabled. -- Using default binary suffix: "_d" -- Using default library suffix: "_d" -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /usr/lib/x86_64-linux-gnu/libhwloc.so (found suitable version "2.11.0", minimum required is "1.5") -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Performing Test TEST_ATOMICS -- Performing Test TEST_ATOMICS - Success -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.3.1") -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so - found -- Performing Test C_msse4_1_FLAG_ACCEPTED -- Performing Test C_msse4_1_FLAG_ACCEPTED - Success -- Performing Test C_msse4_1_COMPILE_WORKS -- Performing Test C_msse4_1_COMPILE_WORKS - Success -- Performing Test CXX_msse4_1_FLAG_ACCEPTED -- Performing Test CXX_msse4_1_FLAG_ACCEPTED - Success -- Performing Test CXX_msse4_1_COMPILE_WORKS -- Performing Test CXX_msse4_1_COMPILE_WORKS - Success -- Enabling SSE4.1 SIMD instructions using CXX flags: -msse4.1 -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - supported -- Detected build CPU vendor - AMD -- Detected build CPU brand - AMD Opteron 62xx class CPU -- Detected build CPU family - 21 -- Detected build CPU model - 1 -- Detected build CPU stepping - 2 -- Detected build CPU features - aes amd apic avx clfsh cmov cx8 cx16 lahf misalignsse mmx msr pclmuldq pdpe1gb popcnt pse rdtscp sse2 sse3 sse4a sse4.1 sse4.2 ssse3 x2apic -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - not present -- Checking for module 'fftw3' -- Found fftw3, version 3.3.10 -- Looking for fftw_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3.so - found -- Looking for fftw_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3.so - found -- Looking for fftw_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3.so - found -- Looking for fftw_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3.so - found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/x86_64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- Found LAPACK: /usr/lib/x86_64-linux-gnu/liblapack.so;/usr/lib/x86_64-linux-gnu/libblas.so -- Performing Test HAS_WARNING_EVERYTHING -- Performing Test HAS_WARNING_EVERYTHING - Failed -- Found Python: /usr/bin/python3 (found version "3.13.2") found components: Interpreter -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Looking for inttypes.h -- Looking for inttypes.h - found -- Looking for dlopen -- Looking for dlopen - found -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success -- Performing Test COMPILER_HAS_DEPRECATED_ATTR -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success -- Found Sphinx: /usr/bin/sphinx-build (found suitable version "8.1.3", minimum required is "4.0.0") found components: pygments -- Found LATEX: /usr/bin/latex -- Configuring done (29.9s) -- Generating done (1.4s) -- Build files have been written to: /build/reproducible-path/gromacs-2025.0/build/basic-dp (mkdir -p build/mpi; cd build/mpi; CC=/usr/bin/mpicc CXX=/usr/bin/mpicxx cmake \ /build/reproducible-path/gromacs-2025.0 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_USE_MUPARSER=EXTERNAL -DGMX_VERSION_STRING_OF_FORK="Debian-2025.0-2" -DGMX_GIT_VERSION_INFO=OFF -DGMX_HWLOC=ON -DGMX_SIMD=SSE4.1 -DGMX_MPI=ON -DMPIEXEC="/usr/bin/mpiexec" -DGMXAPI=ON -DGMX_PYTHON_PACKAGE=ON) -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/mpicc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/mpicxx - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Python3: /usr/bin/python3 (found suitable version "3.13.2", minimum required is "3.9") found components: Interpreter Development Development.Module Development.Embed -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- MPI is not compatible with thread-MPI. Disabling thread-MPI. -- Found MPI_CXX: /usr/bin/mpicxx (found version "3.1") -- Found MPI: TRUE (found version "3.1") found components: CXX -- GROMACS library will use OpenMPI 5.0.6 -- Performing Test HAS_WARNING_NO_OLD_STYLE_CAST -- Performing Test HAS_WARNING_NO_OLD_STYLE_CAST - Success -- Performing Test HAS_WARNING_NO_CAST_QUAL -- Performing Test HAS_WARNING_NO_CAST_QUAL - Success -- Performing Test HAS_WARNING_NO_SUGGEST_OVERRIDE -- Performing Test HAS_WARNING_NO_SUGGEST_OVERRIDE - Success -- Performing Test HAS_WARNING_NO_SUGGEST_DESTRUCTOR_OVERRIDE -- Performing Test HAS_WARNING_NO_SUGGEST_DESTRUCTOR_OVERRIDE - Success -- Performing Test HAS_WARNING_NO_ZERO_AS_NULL_POINTER_CONSTANT -- Performing Test HAS_WARNING_NO_ZERO_AS_NULL_POINTER_CONSTANT - Success -- Torch not found. Neural network potential support will be disabled. -- Using default binary suffix: "_mpi" -- Using default library suffix: "_mpi" -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /usr/lib/x86_64-linux-gnu/libhwloc.so (found suitable version "2.11.0", minimum required is "1.5") -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Performing Test TEST_ATOMICS -- Performing Test TEST_ATOMICS - Success -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.3.1") -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so - found -- Performing Test C_msse4_1_FLAG_ACCEPTED -- Performing Test C_msse4_1_FLAG_ACCEPTED - Success -- Performing Test C_msse4_1_COMPILE_WORKS -- Performing Test C_msse4_1_COMPILE_WORKS - Success -- Performing Test CXX_msse4_1_FLAG_ACCEPTED -- Performing Test CXX_msse4_1_FLAG_ACCEPTED - Success -- Performing Test CXX_msse4_1_COMPILE_WORKS -- Performing Test CXX_msse4_1_COMPILE_WORKS - Success -- Enabling SSE4.1 SIMD instructions using CXX flags: -msse4.1 -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - supported -- Detected build CPU vendor - AMD -- Detected build CPU brand - AMD Opteron 62xx class CPU -- Detected build CPU family - 21 -- Detected build CPU model - 1 -- Detected build CPU stepping - 2 -- Detected build CPU features - aes amd apic avx clfsh cmov cx8 cx16 lahf misalignsse mmx msr pclmuldq pdpe1gb popcnt pse rdtscp sse2 sse3 sse4a sse4.1 sse4.2 ssse3 x2apic -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - not present -- Checking for module 'fftw3f' -- Found fftw3f, version 3.3.10 -- Looking for fftwf_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/x86_64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- Found LAPACK: /usr/lib/x86_64-linux-gnu/liblapack.so;/usr/lib/x86_64-linux-gnu/libblas.so -- Performing Test HAS_WARNING_EVERYTHING -- Performing Test HAS_WARNING_EVERYTHING - Failed -- Found Python: /usr/bin/python3 (found version "3.13.2") found components: Interpreter -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Looking for inttypes.h -- Looking for inttypes.h - found -- Looking for dlopen -- Looking for dlopen - found -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success -- Performing Test COMPILER_HAS_DEPRECATED_ATTR -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success -- Performing Test HAS_FLTO -- Performing Test HAS_FLTO - Success -- Configuring Python package for gmxapi version 0.4.0 -- Using /build/reproducible-path/gromacs-2025.0/build/mpi/bin/gmx_mpi from build tree. -- Found pybind11: /usr/include (found version "2.13.6") -- Found Python interpreter: /usr/bin/python3 -- Python site-packages directory is /usr/lib/python./site-packages -- Found Doxygen: /usr/bin/doxygen (found version "1.9.8") found components: doxygen dot -- Performing Test HAVE_NO_IMPLICIT_INT_FLOAT_CONVERSION -- Performing Test HAVE_NO_IMPLICIT_INT_FLOAT_CONVERSION - Success -- Found Sphinx: /usr/bin/sphinx-build (found suitable version "8.1.3", minimum required is "4.0.0") found components: pygments -- Found LATEX: /usr/bin/latex -- Configuring done (68.3s) -- Generating done (2.3s) -- Build files have been written to: /build/reproducible-path/gromacs-2025.0/build/mpi (mkdir -p build/mpi-dp; cd build/mpi-dp; CC=/usr/bin/mpicc CXX=/usr/bin/mpicxx cmake \ /build/reproducible-path/gromacs-2025.0 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_USE_MUPARSER=EXTERNAL -DGMX_VERSION_STRING_OF_FORK="Debian-2025.0-2" -DGMX_GIT_VERSION_INFO=OFF -DGMX_HWLOC=ON -DGMX_SIMD=SSE4.1 -DGMX_MPI=ON -DMPIEXEC="/usr/bin/mpiexec" -DGMX_DOUBLE=ON) -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/mpicc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/mpicxx - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Python3: /usr/bin/python3 (found suitable version "3.13.2", minimum required is "3.9") found components: Interpreter Development Development.Module Development.Embed -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- MPI is not compatible with thread-MPI. Disabling thread-MPI. -- Found MPI_CXX: /usr/bin/mpicxx (found version "3.1") -- Found MPI: TRUE (found version "3.1") found components: CXX -- GROMACS library will use OpenMPI 5.0.6 -- Performing Test HAS_WARNING_NO_OLD_STYLE_CAST -- Performing Test HAS_WARNING_NO_OLD_STYLE_CAST - Success -- Performing Test HAS_WARNING_NO_CAST_QUAL -- Performing Test HAS_WARNING_NO_CAST_QUAL - Success -- Performing Test HAS_WARNING_NO_SUGGEST_OVERRIDE -- Performing Test HAS_WARNING_NO_SUGGEST_OVERRIDE - Success -- Performing Test HAS_WARNING_NO_SUGGEST_DESTRUCTOR_OVERRIDE -- Performing Test HAS_WARNING_NO_SUGGEST_DESTRUCTOR_OVERRIDE - Success -- Performing Test HAS_WARNING_NO_ZERO_AS_NULL_POINTER_CONSTANT -- Performing Test HAS_WARNING_NO_ZERO_AS_NULL_POINTER_CONSTANT - Success -- Torch not found. Neural network potential support will be disabled. -- Using default binary suffix: "_mpi_d" -- Using default library suffix: "_mpi_d" -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /usr/lib/x86_64-linux-gnu/libhwloc.so (found suitable version "2.11.0", minimum required is "1.5") -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Performing Test TEST_ATOMICS -- Performing Test TEST_ATOMICS - Success -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.3.1") -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so - found -- Performing Test C_msse4_1_FLAG_ACCEPTED -- Performing Test C_msse4_1_FLAG_ACCEPTED - Success -- Performing Test C_msse4_1_COMPILE_WORKS -- Performing Test C_msse4_1_COMPILE_WORKS - Success -- Performing Test CXX_msse4_1_FLAG_ACCEPTED -- Performing Test CXX_msse4_1_FLAG_ACCEPTED - Success -- Performing Test CXX_msse4_1_COMPILE_WORKS -- Performing Test CXX_msse4_1_COMPILE_WORKS - Success -- Enabling SSE4.1 SIMD instructions using CXX flags: -msse4.1 -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - supported -- Detected build CPU vendor - AMD -- Detected build CPU brand - AMD Opteron 62xx class CPU -- Detected build CPU family - 21 -- Detected build CPU model - 1 -- Detected build CPU stepping - 2 -- Detected build CPU features - aes amd apic avx clfsh cmov cx8 cx16 lahf misalignsse mmx msr pclmuldq pdpe1gb popcnt pse rdtscp sse2 sse3 sse4a sse4.1 sse4.2 ssse3 x2apic -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - not present -- Checking for module 'fftw3' -- Found fftw3, version 3.3.10 -- Looking for fftw_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3.so - found -- Looking for fftw_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3.so - found -- Looking for fftw_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3.so - found -- Looking for fftw_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3.so - found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/x86_64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- Found LAPACK: /usr/lib/x86_64-linux-gnu/liblapack.so;/usr/lib/x86_64-linux-gnu/libblas.so -- Performing Test HAS_WARNING_EVERYTHING -- Performing Test HAS_WARNING_EVERYTHING - Failed -- Found Python: /usr/bin/python3 (found version "3.13.2") found components: Interpreter -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Looking for inttypes.h -- Looking for inttypes.h - found -- Looking for dlopen -- Looking for dlopen - found -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success -- Performing Test COMPILER_HAS_DEPRECATED_ATTR -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success -- Found Sphinx: /usr/bin/sphinx-build (found suitable version "8.1.3", minimum required is "4.0.0") found components: pygments -- Found LATEX: /usr/bin/latex -- Configuring done (65.7s) -- Generating done (2.5s) -- Build files have been written to: /build/reproducible-path/gromacs-2025.0/build/mpi-dp touch configure-stamp dh_testdir /usr/bin/make -j20 -C build/basic make[1]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.0 -B/build/reproducible-path/gromacs-2025.0/build/basic --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.0/build/basic/CMakeFiles /build/reproducible-path/gromacs-2025.0/build/basic//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/selection /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/selection /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/CMakeFiles/release-version-info.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.0/build/basic/src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/CMakeFiles/colvars_objlib.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/options /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/options /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/programs /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/programs /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/CMakeFiles/gmx_objlib.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/external/rpc_xdr && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/rpc_xdr/xdr.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/energyanalysis && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/energyterm.cpp.o -MF CMakeFiles/energyanalysis.dir/energyterm.cpp.o.d -o CMakeFiles/energyanalysis.dir/energyterm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/energyterm.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/external/rpc_xdr && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/rpc_xdr/xdr_array.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/parser.cpp.o -MF CMakeFiles/scanner.dir/parser.cpp.o.d -o CMakeFiles/scanner.dir/parser.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/parser.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2025.0-Debian_2025.0_2 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2025.0 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.0/build/basic/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2025.0/build/basic/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2025.0-2 -P /build/reproducible-path/gromacs-2025.0/cmake/gmxGenerateVersionInfoWithoutGit.cmake make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -MF CMakeFiles/linearalgebra.dir/eigensolver.cpp.o.d -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/eigensolver.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/scanner.cpp.o -MF CMakeFiles/scanner.dir/scanner.cpp.o.d -o CMakeFiles/scanner.dir/scanner.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/scanner.cpp /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build cd /build/reproducible-path/gromacs-2025.0/build/basic/src/external/rpc_xdr && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_float.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_float.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_float.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/rpc_xdr/xdr_float.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -MF CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o.d -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/lmfit/lmmin.cpp /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include 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/usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/rpc_xdr/xdr_stdio.cpp /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2025.0/api/legacy/include 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/build/reproducible-path/gromacs-2025.0/src/gromacs/options/basicoptions.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvar.cpp /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/bwlzh.c make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/mdrun.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/errhandler.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 0%] Built target release-version-info cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -MF CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o.d -o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/legacymodules.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include 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/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast 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/build/reproducible-path/gromacs-2025.0/src/external/colvars/colvar_neuralnetworkcompute.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/tmpi_malloc.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 0%] Built target internal_rpc_xdr cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvaratoms.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsassigner.cpp.o -MF CMakeFiles/options.dir/optionsassigner.cpp.o.d -o CMakeFiles/options.dir/optionsassigner.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/optionsassigner.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection 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-I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsection.cpp.o -MF CMakeFiles/options.dir/optionsection.cpp.o.d -o CMakeFiles/options.dir/optionsection.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/optionsection.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/dict.c cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/fixpoint.c cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/barrier.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/huffman.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 0%] Built target gmx_objlib cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/p2p_send_recv.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsvisitor.cpp.o -MF CMakeFiles/options.dir/optionsvisitor.cpp.o.d -o CMakeFiles/options.dir/optionsvisitor.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/optionsvisitor.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/huffmem.c cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/bcast.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/p2p_wait.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/timeunitmanager.cpp.o -MF CMakeFiles/options.dir/timeunitmanager.cpp.o.d -o CMakeFiles/options.dir/timeunitmanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/timeunitmanager.cpp [ 2%] Built target lmfit_objlib cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/collective.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/profile.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/lz77.c cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/nonbonded_bench.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 2%] Built target energyanalysis cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -g 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/lib/md5.c cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/tmpi_init.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/topology.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/list.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o.d -o 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CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/type.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 2%] Built target mdrun_objlib cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias_histogram.cpp cd 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-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o.d -o 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-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/output.cpp.o -MF CMakeFiles/pulling.dir/output.cpp.o.d -o CMakeFiles/pulling.dir/output.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/output.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 2%] Built target scanner cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include 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/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/pull.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_apath.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection 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make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 6%] Built target thread_mpi cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o -MF CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o.d -o CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/pullcoordexpressionparser.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG 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/build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_distances.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_gpath.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include 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-fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_tcl.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_tcl.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_tcl.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarproxy_tcl.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_volmaps.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_volmaps.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_volmaps.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarproxy_volmaps.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvars_memstream.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvars_memstream.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvars_memstream.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvars_memstream.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvartypes.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvartypes.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvartypes.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvartypes.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarvalue.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarvalue.cpp.o.d -o 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CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/topologyholder.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include 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target taskassignment make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 16%] Built target colvars_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 18%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/reproducible-path/gromacs-2025.0/build/basic/VersionInfo.cmake -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /build/reproducible-path/gromacs-2025.0/cmake/gmxConfigureVersionInfo.cmake cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include 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-o CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/alignedallocator.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -MF CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/binaryinformation.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -MF CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/errorformat.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include 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-I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem 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-I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops 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-I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp cd 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp cd 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops 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-I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp cd 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops 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-I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp cd 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops 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-I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops 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-I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict 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-I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops 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/build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. 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-I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed 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-I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -MF 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-Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include 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/build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops 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-I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops 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-I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. 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-I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. 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-I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. 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-isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include 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/build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp cd 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include 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-Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp cd 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops 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-I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops 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-isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp cd 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops 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-isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp cd 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops 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-I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict 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-I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. 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-I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed 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-I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed 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-I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed 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-I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed 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-I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed 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-I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed 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-I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include 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-I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/gridset.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs 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-I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -c 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_1x1.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_1x1.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_1x1.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr 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-msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/distribute.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include 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-isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/dlb.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem 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-DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domainpaircomm.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domainpaircomm.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domainpaircomm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domainpaircomm.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include 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-I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include 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-Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include 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-I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include 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CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_simple.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include 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-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -MF CMakeFiles/libgromacs.dir/selection/symrec.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/symrec.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/cmake -E cmake_link_script CMakeFiles/libgromacs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file=CMakeFiles/libgromacs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgromacs.so.10 -o ../../lib/libgromacs.so.10.0.0 @CMakeFiles/libgromacs.dir/objects1.rsp /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so -lm /usr/lib/x86_64-linux-gnu/liblapack.so -lm -lm /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 -lmuparser -ldl cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgromacs.so.10.0.0 ../../lib/libgromacs.so.10 ../../lib/libgromacs.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 96%] Built target libgromacs /usr/bin/make -f share/template/CMakeFiles/template.dir/build.make share/template/CMakeFiles/template.dir/depend /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make 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-o CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/gmxcalculatorcpu.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmx.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include 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-Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/context.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/context.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/context.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/context.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/exceptions.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/molecules.cpp.o -MF CMakeFiles/nblib.dir/molecules.cpp.o.d -o CMakeFiles/nblib.dir/molecules.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/molecules.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include 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api/nblib/CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o -MF CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o.d -o CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/nbnxmsetuphelpers.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/particlesequencer.cpp.o -MF CMakeFiles/nblib.dir/particlesequencer.cpp.o.d -o CMakeFiles/nblib.dir/particlesequencer.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/particlesequencer.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/particletype.cpp.o -MF CMakeFiles/nblib.dir/particletype.cpp.o.d -o CMakeFiles/nblib.dir/particletype.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/particletype.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/include 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api/gmxapi/CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/gmxapi.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/simulationstate.cpp.o -MF CMakeFiles/nblib.dir/simulationstate.cpp.o.d -o CMakeFiles/nblib.dir/simulationstate.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/simulationstate.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 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-I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/topologyhelpers.cpp.o -MF CMakeFiles/nblib.dir/topologyhelpers.cpp.o.d -o CMakeFiles/nblib.dir/topologyhelpers.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/topologyhelpers.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include 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cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/virials.cpp.o -MF CMakeFiles/nblib.dir/virials.cpp.o.d -o CMakeFiles/nblib.dir/virials.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/virials.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/md.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/md.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/md.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/md.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmx.dir/link.d CMakeFiles/gmx_objlib.dir/gmx.cpp.o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../bin/gmx ../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/mdmodule.cpp [ 96%] Built target gmx cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/calculator.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/mdsignals.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/session.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/session.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/session.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/session.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/transformations.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/status.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/status.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/status.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/status.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/conversions.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/convertGmxToNblib.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/system.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/system.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/system.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/system.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/share/template && /usr/bin/cmake -E cmake_link_script CMakeFiles/template.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include 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/build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/workflow.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tpr.cpp /usr/bin/c++ -g -O2 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-Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgmxapi.so.0 -o ../../lib/libgmxapi.so.0.4.0 CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o CMakeFiles/gmxapi.dir/cpp/context.cpp.o CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o CMakeFiles/gmxapi.dir/cpp/md.cpp.o CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o CMakeFiles/gmxapi.dir/cpp/session.cpp.o CMakeFiles/gmxapi.dir/cpp/status.cpp.o CMakeFiles/gmxapi.dir/cpp/system.cpp.o CMakeFiles/gmxapi.dir/cpp/version.cpp.o CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o ../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a cd /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgmxapi.so.0.4.0 ../../lib/libgmxapi.so.0 ../../lib/libgmxapi.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 98%] Built target gmxapi cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file=CMakeFiles/nblib.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libnblib_gmx.so.0 -o ../../lib/libnblib_gmx.so.0.1.0 CMakeFiles/nblib.dir/box.cpp.o CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o CMakeFiles/nblib.dir/integrator.cpp.o CMakeFiles/nblib.dir/interactions.cpp.o CMakeFiles/nblib.dir/molecules.cpp.o CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o CMakeFiles/nblib.dir/particlesequencer.cpp.o CMakeFiles/nblib.dir/particletype.cpp.o CMakeFiles/nblib.dir/simulationstate.cpp.o CMakeFiles/nblib.dir/topologyhelpers.cpp.o CMakeFiles/nblib.dir/topology.cpp.o CMakeFiles/nblib.dir/tpr.cpp.o CMakeFiles/nblib.dir/virials.cpp.o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o CMakeFiles/nblib.dir/util/setup.cpp.o -lm ../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -lmuparser /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib && /usr/bin/cmake -E cmake_symlink_library ../../lib/libnblib_gmx.so.0.1.0 ../../lib/libnblib_gmx.so.0 ../../lib/libnblib_gmx.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [100%] Built target nblib /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make 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-I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fopenmp -MD -MT api/nblib/samples/CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o -MF CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o.d -o CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/samples/methane-water-integration.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/samples && /usr/bin/cmake -E cmake_link_script CMakeFiles/argon-forces-integration.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/argon-forces-integration.dir/link.d "CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o" -o ../../../bin/argon-forces-integration ../../../lib/libnblib_gmx.so.0.1.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -Wl,-rpath-link,/build/reproducible-path/gromacs-2025.0/build/basic/lib make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [100%] Built target argon-forces-integration cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/samples && /usr/bin/cmake -E cmake_link_script CMakeFiles/methane-water-integration.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 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'/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -j20 -C build/basic-dp make[1]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.0 -B/build/reproducible-path/gromacs-2025.0/build/basic-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.0/build/basic-dp/CMakeFiles /build/reproducible-path/gromacs-2025.0/build/basic-dp//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/selection /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/selection /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/depend cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/CMakeFiles/release-version-info.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/depend make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/CMakeFiles/colvars_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/parser.cpp.o -MF CMakeFiles/scanner.dir/parser.cpp.o.d -o CMakeFiles/scanner.dir/parser.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/parser.cpp /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/scanner.cpp.o -MF CMakeFiles/scanner.dir/scanner.cpp.o.d -o CMakeFiles/scanner.dir/scanner.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/scanner.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/options /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build cd /build/reproducible-path/gromacs-2025.0 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2025.0-Debian_2025.0_2 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2025.0 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.0/build/basic-dp/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2025.0/build/basic-dp/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2025.0-2 -P /build/reproducible-path/gromacs-2025.0/cmake/gmxGenerateVersionInfoWithoutGit.cmake make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/external/rpc_xdr && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/rpc_xdr/xdr.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/external/rpc_xdr && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/rpc_xdr/xdr_array.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/errhandler.cpp /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/external/rpc_xdr && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_float.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_float.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_float.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/rpc_xdr/xdr_float.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/tmpi_malloc.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/bwlzh.c /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/external/rpc_xdr && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/rpc_xdr/xdr_stdio.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/bwt.c cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/atomic.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -MF CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o.d -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/lmfit/lmmin.cpp /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/lock.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvar.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2025.0/api/legacy/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/abstractoption.cpp.o -MF CMakeFiles/options.dir/abstractoption.cpp.o.d -o CMakeFiles/options.dir/abstractoption.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/abstractoption.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/energyanalysis && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/energyterm.cpp.o -MF CMakeFiles/energyanalysis.dir/energyterm.cpp.o.d -o CMakeFiles/energyanalysis.dir/energyterm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/energyterm.cpp [ 0%] Built target release-version-info /usr/bin/make 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cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/huffmem.c cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/barrier.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/lz77.c cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/merge_sort.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 0%] Built target internal_rpc_xdr /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/CMakeFiles/gmx_objlib.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/gmx.cpp.o -MF CMakeFiles/gmx_objlib.dir/gmx.cpp.o.d -o CMakeFiles/gmx_objlib.dir/gmx.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/gmx.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 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-DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/bcast.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/mtf.c cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/rle.c cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/tng_compress.c cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/vals16.c cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/warnmalloc.c cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/p2p_wait.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/collective.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. 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-Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/topology.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 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-Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/type.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/scan.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvar_neuralnetworkcompute.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/numa_malloc.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/once.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/abstractsection.cpp.o -MF CMakeFiles/options.dir/abstractsection.cpp.o.d -o CMakeFiles/options.dir/abstractsection.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/abstractsection.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/basicoptions.cpp.o -MF CMakeFiles/options.dir/basicoptions.cpp.o.d -o CMakeFiles/options.dir/basicoptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/basicoptions.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/behaviorcollection.cpp.o -MF CMakeFiles/options.dir/behaviorcollection.cpp.o.d -o CMakeFiles/options.dir/behaviorcollection.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/behaviorcollection.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/filenameoption.cpp.o -MF CMakeFiles/options.dir/filenameoption.cpp.o.d -o CMakeFiles/options.dir/filenameoption.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/filenameoption.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/nonbonded_bench.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 0%] Built target energyanalysis cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvaratoms.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/filenameoptionmanager.cpp.o -MF CMakeFiles/options.dir/filenameoptionmanager.cpp.o.d -o CMakeFiles/options.dir/filenameoptionmanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/filenameoptionmanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/options.cpp.o -MF CMakeFiles/options.dir/options.cpp.o.d -o CMakeFiles/options.dir/options.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/options.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 0%] Built target gmx_objlib cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsassigner.cpp.o -MF CMakeFiles/options.dir/optionsassigner.cpp.o.d -o CMakeFiles/options.dir/optionsassigner.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/optionsassigner.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsection.cpp.o -MF CMakeFiles/options.dir/optionsection.cpp.o.d -o CMakeFiles/options.dir/optionsection.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/optionsection.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 0%] Built target lmfit_objlib cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsvisitor.cpp.o -MF CMakeFiles/options.dir/optionsvisitor.cpp.o.d -o CMakeFiles/options.dir/optionsvisitor.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/optionsvisitor.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/timeunitmanager.cpp.o -MF CMakeFiles/options.dir/timeunitmanager.cpp.o.d -o CMakeFiles/options.dir/timeunitmanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/timeunitmanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/treesupport.cpp.o -MF CMakeFiles/options.dir/treesupport.cpp.o.d -o CMakeFiles/options.dir/treesupport.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/treesupport.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias_abf.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias_abmd.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 0%] Built target mdrun_objlib cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias_alb.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias_histogram.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias_histogram_reweight_amd.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias_meta.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias_opes.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias_restraint.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 4%] Built target thread_mpi cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection 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CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_angles.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_apath.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_combination.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_coordnums.cpp.o -MF 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/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/output.cpp.o -MF CMakeFiles/pulling.dir/output.cpp.o.d -o CMakeFiles/pulling.dir/output.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/output.cpp cd 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&& /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_volmaps.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvardeps.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvardeps.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvardeps.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvardeps.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvargrid.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarmodule.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarmodule.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarmodule.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarmodule.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pull_rotation.cpp.o -MF CMakeFiles/pulling.dir/pull_rotation.cpp.o.d -o CMakeFiles/pulling.dir/pull_rotation.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/pull_rotation.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 6%] Built target tng_io_obj cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparams.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparams.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparams.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarparams.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparse.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparse.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparse.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarparse.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection 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/build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarproxy_io.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_replicas.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_replicas.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_replicas.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarproxy_replicas.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat 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/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/pullcoordexpressionparser.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_tcl.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_tcl.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_tcl.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarproxy_tcl.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarvalue.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarvalue.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarvalue.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarvalue.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/nr_jacobi.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 8%] Built target options make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 10%] Built target pulling /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o -MF CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o.d -o CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/decidegpuusage.cpp /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o -c 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o -MF CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o.d -o CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/decidesimulationworkload.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H 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/build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -MF CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/checkpointhelper.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.0/src/include 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/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/referencetemperaturemanager.cpp.o -MF CMakeFiles/modularsimulator.dir/referencetemperaturemanager.cpp.o.d -o CMakeFiles/modularsimulator.dir/referencetemperaturemanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/referencetemperaturemanager.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 10%] Built target taskassignment cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include 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/build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/simulatoralgorithm.cpp.o -MF CMakeFiles/modularsimulator.dir/simulatoralgorithm.cpp.o.d -o CMakeFiles/modularsimulator.dir/simulatoralgorithm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/simulatoralgorithm.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -MF CMakeFiles/modularsimulator.dir/topologyholder.cpp.o.d -o CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/topologyholder.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include 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-Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -MF CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/trajectoryelement.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -MF 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VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /build/reproducible-path/gromacs-2025.0/cmake/gmxConfigureVersionInfo.cmake cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include 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-DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/alignedallocator.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include 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-I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -MF CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/baseversion.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include 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/build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -MF CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/binaryinformation.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o -MF CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/errorcodes.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include 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/build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -MF CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/errorformat.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 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-I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -MF CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/fileredirector.cpp cd 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-isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/futil.cpp.o -MF CMakeFiles/libgromacs.dir/utility/futil.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/futil.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/futil.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o -MF CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o -c 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o -MF CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/gmxomp.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/hip_version_information.cpp.o -MF CMakeFiles/libgromacs.dir/utility/hip_version_information.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/hip_version_information.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/hip_version_information.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict 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-isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/init.cpp.o -MF CMakeFiles/libgromacs.dir/utility/init.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/init.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/init.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem 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-DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o -MF CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/int64_to_int.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o -MF CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/keyvaluetree.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT 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-I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o -MF 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/logger.cpp.o -MF CMakeFiles/libgromacs.dir/utility/logger.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/logger.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/logger.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include 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/build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o -MF CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/loggerbuilder.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include 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-isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/mpiinfo.cpp.o -MF CMakeFiles/libgromacs.dir/utility/mpiinfo.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/mpiinfo.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/mpiinfo.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o -MF CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o -c 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-I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT 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-I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. 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-I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp cd 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops 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-I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops 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-I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops 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-I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/benchmark/bench_setup.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars 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-I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include 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-I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kerneldispatch.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp cd 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops 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-I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_4x4.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_4x4.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_4x4.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict 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-isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -c 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 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-I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT 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-I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem 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-I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/collect.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/collect.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/collect.cpp.o -c 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/computemultibodycutoffs.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/computemultibodycutoffs.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/computemultibodycutoffs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/computemultibodycutoffs.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr 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-Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/dlbtiming.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include 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-g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/gpuhaloexchange_impl.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/haloexchange.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/haloexchange.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/haloexchange.cpp.o -c 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/densityfit.cpp.o -MF CMakeFiles/libgromacs.dir/math/densityfit.cpp.o.d -o 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/group.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include 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/build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/iforceprovider.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ 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-I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem 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-Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include 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-I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include 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-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_rama.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr 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-I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars 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-I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem 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-I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem 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-Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. 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-I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops 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-I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem 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-I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem 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-I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include 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/build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/fflibutil.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/gen_maxwell_velocities.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o.d -o 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-Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include 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-I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include 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-I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include 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-I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat 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/build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/sasa.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/sasa.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/sasa.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/sasa.cpp cd 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops 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-I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye-saxs.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye-saxs.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering-debye-saxs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/scattering-debye-saxs.cpp cd 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops 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-I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr 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-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o -MF CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/trjconv.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include 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-I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include 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-isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/groupcoord.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem 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-DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/md_support.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/mdatoms.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include 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-I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include 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-I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include 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-DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include 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-g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/update.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/update.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src 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-isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl_stubs.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl_stubs.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl_stubs.cpp.o -c 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-Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o 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-I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o -c 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_pp_comm_gpu_impl.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_force_sender_gpu_impl.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o -MF CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/calcgrid.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/fft.cpp.o -MF CMakeFiles/libgromacs.dir/fft/fft.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/fft.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/fft.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o -MF 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o -MF CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/parallel_3dfft.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include 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/build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o -MF CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/fft_fftw3.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict 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-isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/device_stream_manager.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/device_stream_manager.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/device_stream_manager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/device_stream_manager.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpu_utils.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include 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-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/gpueventsynchronizer_helpers.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/gpueventsynchronizer_helpers.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/gpueventsynchronizer_helpers.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpueventsynchronizer_helpers.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/hostallocator.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed 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-I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops 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-I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem 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-Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/md.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/md.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/md.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/md.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/mdmodules.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/membedholder.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/membedholder.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/membedholder.cpp.o -c 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/mimic.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/minimize.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/freeenergy.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/freeenergy.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/freeenergy.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/freeenergy.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/handlerestart.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/mdmodulesnotifiers.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/mdmodulesnotifiers.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/mdmodulesnotifiers.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/mdmodulesnotifiers.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -c 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/printtime.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/threadaffinity.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include 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-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/confio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/confio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/confio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/confio.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include 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-I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include 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CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_merge.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include 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-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_permute.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include 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-isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_position.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY 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CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_same.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_simple.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -MF CMakeFiles/libgromacs.dir/selection/symrec.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/symrec.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/cmake -E cmake_link_script CMakeFiles/libgromacs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file=CMakeFiles/libgromacs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgromacs_d.so.10 -o ../../lib/libgromacs_d.so.10.0.0 @CMakeFiles/libgromacs.dir/objects1.rsp /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so -lm /usr/lib/x86_64-linux-gnu/liblapack.so -lm -lm /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 -lmuparser -ldl cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgromacs_d.so.10.0.0 ../../lib/libgromacs_d.so.10 ../../lib/libgromacs_d.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 95%] Built target libgromacs /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/gmxapi /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/CMakeFiles/nblib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/box.cpp.o -MF CMakeFiles/nblib.dir/box.cpp.o.d -o CMakeFiles/nblib.dir/box.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/box.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o -MF CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o.d -o CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/gmxcalculatorcpu.cpp /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/integrator.cpp.o -MF CMakeFiles/nblib.dir/integrator.cpp.o.d -o CMakeFiles/nblib.dir/integrator.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/integrator.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/resourceassignment.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/interactions.cpp.o -MF CMakeFiles/nblib.dir/interactions.cpp.o.d -o CMakeFiles/nblib.dir/interactions.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/interactions.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/context.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/context.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/context.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/context.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/molecules.cpp.o -MF CMakeFiles/nblib.dir/molecules.cpp.o.d -o CMakeFiles/nblib.dir/molecules.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/molecules.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/exceptions.cpp /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/gmxapi.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o -MF CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o.d -o CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/nbnxmsetuphelpers.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/particlesequencer.cpp.o -MF CMakeFiles/nblib.dir/particlesequencer.cpp.o.d -o CMakeFiles/nblib.dir/particlesequencer.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/particlesequencer.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmx.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/md.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/md.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/md.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/md.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/particletype.cpp.o -MF CMakeFiles/nblib.dir/particletype.cpp.o.d -o CMakeFiles/nblib.dir/particletype.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/particletype.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/simulationstate.cpp.o -MF CMakeFiles/nblib.dir/simulationstate.cpp.o.d -o CMakeFiles/nblib.dir/simulationstate.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/simulationstate.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/mdmodule.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/topologyhelpers.cpp.o -MF CMakeFiles/nblib.dir/topologyhelpers.cpp.o.d -o CMakeFiles/nblib.dir/topologyhelpers.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/topologyhelpers.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/topology.cpp.o -MF CMakeFiles/nblib.dir/topology.cpp.o.d -o CMakeFiles/nblib.dir/topology.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/topology.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/mdsignals.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/tpr.cpp.o -MF CMakeFiles/nblib.dir/tpr.cpp.o.d -o CMakeFiles/nblib.dir/tpr.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tpr.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmx.dir/link.d CMakeFiles/gmx_objlib.dir/gmx.cpp.o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../bin/gmx_d ../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/session.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/session.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/session.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/session.cpp [ 95%] Built target gmx cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/status.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/status.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/status.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/status.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/system.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/system.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/system.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/system.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/version.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/version.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/version.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/version.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/workflow.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tpr.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/virials.cpp.o -MF CMakeFiles/nblib.dir/virials.cpp.o.d -o CMakeFiles/nblib.dir/virials.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/virials.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/calculator.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/transformations.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/conversions.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o.d -o 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CMakeFiles/gmxapi.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file=CMakeFiles/gmxapi.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgmxapi_d.so.0 -o ../../lib/libgmxapi_d.so.0.4.0 CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o CMakeFiles/gmxapi.dir/cpp/context.cpp.o CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o CMakeFiles/gmxapi.dir/cpp/md.cpp.o CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o CMakeFiles/gmxapi.dir/cpp/session.cpp.o CMakeFiles/gmxapi.dir/cpp/status.cpp.o CMakeFiles/gmxapi.dir/cpp/system.cpp.o CMakeFiles/gmxapi.dir/cpp/version.cpp.o CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o ../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgmxapi_d.so.0.4.0 ../../lib/libgmxapi_d.so.0 ../../lib/libgmxapi_d.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 97%] Built target gmxapi cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file=CMakeFiles/nblib.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libnblib_gmx.so.0 -o ../../lib/libnblib_gmx.so.0.1.0 CMakeFiles/nblib.dir/box.cpp.o CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o CMakeFiles/nblib.dir/integrator.cpp.o CMakeFiles/nblib.dir/interactions.cpp.o CMakeFiles/nblib.dir/molecules.cpp.o CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o CMakeFiles/nblib.dir/particlesequencer.cpp.o CMakeFiles/nblib.dir/particletype.cpp.o CMakeFiles/nblib.dir/simulationstate.cpp.o CMakeFiles/nblib.dir/topologyhelpers.cpp.o CMakeFiles/nblib.dir/topology.cpp.o CMakeFiles/nblib.dir/tpr.cpp.o CMakeFiles/nblib.dir/virials.cpp.o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o CMakeFiles/nblib.dir/util/setup.cpp.o -lm ../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -lmuparser /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib && /usr/bin/cmake -E cmake_symlink_library 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-Wl,-rpath-link,/build/reproducible-path/gromacs-2025.0/build/basic-dp/lib make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [100%] Built target methane-water-integration cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/samples && /usr/bin/cmake -E cmake_link_script CMakeFiles/argon-forces-integration.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/argon-forces-integration.dir/link.d "CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o" -o ../../../bin/argon-forces-integration ../../../lib/libnblib_gmx.so.0.1.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a 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--check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.0/build/basic/CMakeFiles 77 /usr/bin/make -f CMakeFiles/Makefile2 CMakeFiles/tests.dir/all make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend /usr/bin/make -f src/external/googletest/googletest/CMakeFiles/gtest.dir/build.make src/external/googletest/googletest/CMakeFiles/gtest.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/programs 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -Wall -Wshadow -Wno-error=dangling-else -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -MD -MT src/external/googletest/googletest/CMakeFiles/gtest.dir/src/gtest-all.cc.o -MF CMakeFiles/gtest.dir/src/gtest-all.cc.o.d -o CMakeFiles/gtest.dir/src/gtest-all.cc.o -c /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/src/gtest-all.cc /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs 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/usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[4]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[4]: Nothing to be done for 'src/gromacs/selection/CMakeFiles/scanner.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2025.0-Debian_2025.0_2 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2025.0 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.0/build/basic/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2025.0/build/basic/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2025.0-2 -P /build/reproducible-path/gromacs-2025.0/cmake/gmxGenerateVersionInfoWithoutGit.cmake /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[4]: Nothing to be done for 'src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[4]: Nothing to be done for 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'/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" [ 3%] Built target tng_io_obj make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build [ 5%] Built target lmfit_objlib make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/colvars_objlib.dir/build'. make[4]: Leaving directory 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'/build/reproducible-path/gromacs-2025.0/build/basic' make[4]: Nothing to be done for 'src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[4]: Nothing to be done for 'src/gromacs/options/CMakeFiles/options.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 7%] Built target colvars_objlib [ 7%] Built target linearalgebra /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling 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src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[4]: Nothing to be done for 'src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build [ 10%] Built target taskassignment make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[4]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 11%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs 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make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[4]: Nothing to be done for 'api/nblib/CMakeFiles/nblib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[4]: Nothing to be done for 'api/gmxapi/CMakeFiles/gmxapi.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 63%] Built target nblib /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/samples/CMakeFiles/argon-forces-integration.dir/DependInfo.cmake "--color=" /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/samples 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'/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem 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/build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/simulatorcomparison.cpp /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include 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-fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/alignedallocator.cpp.o -MF CMakeFiles/utility-test.dir/alignedallocator.cpp.o.d -o CMakeFiles/utility-test.dir/alignedallocator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -MF CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o.d -o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/tests/testasserts_tests.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem 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src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxlib/nonbonded/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxlib/nonbonded/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxlib/nonbonded/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxlib/nonbonded/tests/CMakeFiles/nonbonded-fep-test.dir/nb_free_energy.cpp.o -MF CMakeFiles/nonbonded-fep-test.dir/nb_free_energy.cpp.o.d -o CMakeFiles/nonbonded-fep-test.dir/nb_free_energy.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem 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/usr/bin/make -f src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include 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/build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/densityfitting/tests/densityfitting.cpp /usr/bin/make -f src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/build.make src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include 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-fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/densityfitting/tests/densityfittingamplitudelookup.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser 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/build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/tests/colvarsoptions.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem 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-Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testutils-mpi-test.dir/link.d "CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o" "CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o" -o ../../../bin/testutils-mpi-test ../../../lib/libtestutils.a ../../../lib/libtestutils.a ../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 66%] Built target testutils-mpi-test /usr/bin/make -f src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/build.make src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/tests /build/reproducible-path/gromacs-2025.0/build/basic 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-DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/utility-mpi-test.dir/link.d "CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o" "CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/utility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 66%] Built target utility-mpi-test /usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd 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src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/electricfield.cpp.o -MF CMakeFiles/applied_forces-test.dir/electricfield.cpp.o.d -o CMakeFiles/applied_forces-test.dir/electricfield.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/tests/electricfield.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 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"CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o" "CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o" -o ../../../bin/testutils-test ../../../lib/libtestutils.a ../../../lib/libtestutils.a ../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 66%] Built target testutils-test /usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/listed_forces/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem 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src/gromacs/gmxlib/nonbonded/tests/CMakeFiles/nonbonded-fep-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nonbonded-fep-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nonbonded-fep-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem 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-DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/onlinehelp-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/onlinehelp-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/applied_forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/applied_forces-test.dir/link.d "CMakeFiles/applied_forces-test.dir/electricfield.cpp.o" "CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/applied_forces-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -lmuparser /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 66%] Built target applied_forces-test /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include 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src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/hashedmap.cpp.o -MF CMakeFiles/domdec-test.dir/hashedmap.cpp.o.d -o CMakeFiles/domdec-test.dir/hashedmap.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/tests/hashedmap.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -P CMakeFiles/mdrun_test_infrastructure.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun_test_infrastructure.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/biasgrid.cpp.o -MF CMakeFiles/awh-test.dir/biasgrid.cpp.o.d -o CMakeFiles/awh-test.dir/biasgrid.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/biasgrid.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o -MF CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o.d -o CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/fixedcapacityvector.cpp /usr/bin/ar qc ../../../../lib/libmdrun_test_infrastructure.a CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o /usr/bin/ranlib ../../../../lib/libmdrun_test_infrastructure.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 67%] Built target mdrun_test_infrastructure cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/nnpot/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem 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CMakeFiles/colvars_applied_forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/biasstate.cpp.o -MF CMakeFiles/awh-test.dir/biasstate.cpp.o.d -o CMakeFiles/awh-test.dir/biasstate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/biasstate.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/nbnxm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nbnxm-gpu-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/colvars_applied_forces-test.dir/link.d "CMakeFiles/colvars_applied_forces-test.dir/colvars.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/colvarsforceprovider.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/colvars_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.10.0.0 ../../../../../lib/libgmock.so.1.13.0 -lm ../../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -lmuparser /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 67%] Built target colvars_applied_forces-test cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/kernel_test.cpp.o -MF CMakeFiles/nbnxm-test.dir/kernel_test.cpp.o.d -o CMakeFiles/nbnxm-test.dir/kernel_test.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/tests/kernel_test.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nbnxm-gpu-test.dir/link.d "CMakeFiles/nbnxm-gpu-test.dir/pairlist.cpp.o" "CMakeFiles/nbnxm-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/nbnxm-gpu-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 67%] Built target nbnxm-gpu-test /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o -MF CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o.d -o CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/tests/haloexchange_mpi.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o -MF CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o.d -o CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/nnpot/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nnpot_applied_forces-test.dir/link.txt --verbose=1 /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/ewald/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -MF CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/tests/pmebsplinetest.cpp /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/depend cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o -MF CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o.d -o CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/tests/kernelsetup.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/fft/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/fft/tests/CMakeFiles/fft-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/fft/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fft/tests/CMakeFiles/fft-test.dir/fft.cpp.o -MF CMakeFiles/fft-test.dir/fft.cpp.o.d -o CMakeFiles/fft-test.dir/fft.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/tests/fft.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nnpot_applied_forces-test.dir/link.d "CMakeFiles/nnpot_applied_forces-test.dir/nnpot.cpp.o" "CMakeFiles/nnpot_applied_forces-test.dir/nnpotoptions.cpp.o" "CMakeFiles/nnpot_applied_forces-test.dir/nnpottopologypreprocessor.cpp.o" "CMakeFiles/nnpot_applied_forces-test.dir/nnpotforceprovider.cpp.o" "CMakeFiles/nnpot_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/nnpot_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../../lib/libgmock.so.1.13.0 ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 67%] Built target nnpot_applied_forces-test cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -MF CMakeFiles/ewald-test.dir/pmegathertest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/tests/pmegathertest.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -DGMX_CP2K=0 -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/qmmm/tests/qmmmforceprovider.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxlib/nonbonded/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nonbonded-fep-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nonbonded-fep-test.dir/link.d "CMakeFiles/nonbonded-fep-test.dir/nb_free_energy.cpp.o" "CMakeFiles/nonbonded-fep-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/nonbonded-fep-test ../../../../../lib/libtestutils.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.10.0.0 -lm ../../../../../lib/libgmock.so.1.13.0 ../../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -lmuparser /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 67%] Built target nonbonded-fep-test cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/pairs.cpp.o -MF CMakeFiles/listed_forces-test.dir/pairs.cpp.o.d -o CMakeFiles/listed_forces-test.dir/pairs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/tests/pairs.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/density_fitting_applied_forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/cmake -P CMakeFiles/onlinehelp-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test-shared.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libonlinehelp-test-shared.a "CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o" "CMakeFiles/onlinehelp-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o" /usr/bin/ranlib ../../../../lib/libonlinehelp-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 67%] Built target onlinehelp-test-shared cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/simd_energy_accumulator.cpp.o -MF CMakeFiles/nbnxm-test.dir/simd_energy_accumulator.cpp.o.d -o CMakeFiles/nbnxm-test.dir/simd_energy_accumulator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/tests/simd_energy_accumulator.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -MF CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o.d -o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/keyvaluetreetransform.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/density_fitting_applied_forces-test.dir/link.d "CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/density_fitting_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.10.0.0 ../../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 67%] Built target density_fitting_applied_forces-test /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/tests /build/reproducible-path/gromacs-2025.0/build/basic 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-I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem 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/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/testsystem.cpp.o -MF CMakeFiles/nbnxm-test.dir/testsystem.cpp.o.d -o CMakeFiles/nbnxm-test.dir/testsystem.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/tests/testsystem.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/domdec-test.dir/link.d "CMakeFiles/domdec-test.dir/hashedmap.cpp.o" "CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o" "CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/domdec-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -lmuparser /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 68%] Built target domdec-test /usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/hardware/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/listoflists.cpp.o -MF CMakeFiles/utility-test.dir/listoflists.cpp.o.d -o CMakeFiles/utility-test.dir/listoflists.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/listoflists.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/cpuinfo.cpp.o -MF CMakeFiles/hardware-test.dir/cpuinfo.cpp.o.d -o CMakeFiles/hardware-test.dir/cpuinfo.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/tests/cpuinfo.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 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-I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o -MF CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/tests/device_buffer.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -MF CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o.d 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o -MF CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/tests/gpueventsynchronizer.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/qmmm_applied_forces-test.dir/link.d "CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o" 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-I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o -MF CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o.d -o CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/freeenergyparameters.cpp cd 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT 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/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include 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-fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pme.cpp.o -MF CMakeFiles/ewald-test.dir/pme.cpp.o.d -o CMakeFiles/ewald-test.dir/pme.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/tests/pme.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/fft/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fft/tests/CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/domdec-mpi-test.dir/link.d "CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o" "CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/domdec-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -lmuparser /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 68%] Built target domdec-mpi-test /usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/math/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/math/tests/CMakeFiles/math-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -MF CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o.d -o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/tests/pmetestcommon.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/nbnxm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nbnxm-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/range.cpp.o -MF CMakeFiles/utility-test.dir/range.cpp.o.d -o CMakeFiles/utility-test.dir/range.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/range.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nbnxm-test.dir/link.d "CMakeFiles/nbnxm-test.dir/exclusions.cpp.o" "CMakeFiles/nbnxm-test.dir/kernel_test.cpp.o" "CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o" "CMakeFiles/nbnxm-test.dir/simd_energy_accumulator.cpp.o" "CMakeFiles/nbnxm-test.dir/testsystem.cpp.o" "CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/nbnxm-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 70%] Built target nbnxm-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 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-Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/device_management.cpp.o -MF CMakeFiles/hardware-test.dir/device_management.cpp.o.d -o CMakeFiles/hardware-test.dir/device_management.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/tests/device_management.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 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-DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o -MF CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o.d -o CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/observablesreducer.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/listed_forces-test.dir/link.txt --verbose=1 cd 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/langevintestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/langevintestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/langevintestrunners.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/langevintestrunners.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -P CMakeFiles/mdrunutility-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test-shared.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/listed_forces-test.dir/link.d "CMakeFiles/listed_forces-test.dir/bonded.cpp.o" "CMakeFiles/listed_forces-test.dir/pairs.cpp.o" "CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o" "CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/listed_forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o -MF CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o.d -o CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/checkpointdata.cpp [ 71%] Built target listed_forces-test /usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/pbcutil/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 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/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/tests/com.cpp /usr/bin/ar qc ../../../../lib/libmdrunutility-test-shared.a "CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o" "CMakeFiles/mdrunutility-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o" /usr/bin/ranlib ../../../../lib/libmdrunutility-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 71%] Built target mdrunutility-test-shared /usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/random/tests /build/reproducible-path/gromacs-2025.0/build/basic 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-DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem 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../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -lmuparser /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 72%] Built target ewald-test /usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/restraint/tests /build/reproducible-path/gromacs-2025.0/build/basic 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/build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/hardware/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/hardware-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/filenameoption.cpp.o -MF CMakeFiles/options-test.dir/filenameoption.cpp.o.d -o CMakeFiles/options-test.dir/filenameoption.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/tests/filenameoption.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/hardware-test.dir/link.d "CMakeFiles/hardware-test.dir/cpuinfo.cpp.o" "CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o" "CMakeFiles/hardware-test.dir/mockhardwaretopology.cpp.o" "CMakeFiles/hardware-test.dir/device_management.cpp.o" "CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/hardware-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 72%] Built target hardware-test /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/tables/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tables/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tables/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tables/tests/CMakeFiles/table-test.dir/splinetable.cpp.o -MF CMakeFiles/table-test.dir/splinetable.cpp.o.d -o CMakeFiles/table-test.dir/splinetable.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tables/tests/splinetable.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include 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CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/tests/filenameoptionmanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include 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src/gromacs/random/tests/CMakeFiles/random-test.dir/normaldistribution.cpp.o -MF CMakeFiles/random-test.dir/normaldistribution.cpp.o.d -o CMakeFiles/random-test.dir/normaldistribution.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/random/tests/normaldistribution.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include 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/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/mshift.cpp.o -MF CMakeFiles/pbcutil-test.dir/mshift.cpp.o.d -o CMakeFiles/pbcutil-test.dir/mshift.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/tests/mshift.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/onlinehelp-test.dir/link.d "CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o" "CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o" "CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o" "CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/onlinehelp-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 72%] Built target onlinehelp-test /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/taskassignment/tests 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/build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 74%] Built target restraintpotential-test /usr/bin/make -f src/gromacs/timing/tests/CMakeFiles/timing-test.dir/build.make src/gromacs/timing/tests/CMakeFiles/timing-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/timing/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/timing/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/timing/tests/CMakeFiles/timing-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/timing/tests/CMakeFiles/timing-test.dir/build.make src/gromacs/timing/tests/CMakeFiles/timing-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/timing/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/timing/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/timing/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/timing/tests/CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/seed.cpp.o -MF CMakeFiles/random-test.dir/seed.cpp.o.d -o CMakeFiles/random-test.dir/seed.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/random/tests/seed.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o -MF CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o.d -o CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/forcebuffers.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/option.cpp.o -MF CMakeFiles/options-test.dir/option.cpp.o.d -o CMakeFiles/options-test.dir/option.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/tests/option.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H 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-isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/optionsassigner.cpp.o -MF CMakeFiles/options-test.dir/optionsassigner.cpp.o.d -o CMakeFiles/options-test.dir/optionsassigner.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/tests/optionsassigner.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/repeatingsection.cpp.o -MF CMakeFiles/options-test.dir/repeatingsection.cpp.o.d -o CMakeFiles/options-test.dir/repeatingsection.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/tests/repeatingsection.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/pbc.cpp.o -MF CMakeFiles/pbcutil-test.dir/pbc.cpp.o.d -o CMakeFiles/pbcutil-test.dir/pbc.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/tests/pbc.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdspan/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdspan-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/timing/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/timing-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/timing-test.dir/link.d "CMakeFiles/timing-test.dir/timing.cpp.o" "CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/timing-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 74%] Built target timing-test /usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/topology/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/topology/tests/CMakeFiles/topology-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/atoms.cpp.o -MF CMakeFiles/topology-test.dir/atoms.cpp.o.d -o CMakeFiles/topology-test.dir/atoms.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/atoms.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdspan-test.dir/link.d "CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o" "CMakeFiles/mdspan-test.dir/extents.cpp.o" "CMakeFiles/mdspan-test.dir/extensions.cpp.o" "CMakeFiles/mdspan-test.dir/layouts.cpp.o" "CMakeFiles/mdspan-test.dir/mdspan.cpp.o" "CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdspan-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 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'/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/simd/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/simd/tests/CMakeFiles/simd-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H 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/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include 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src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o -MF CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o.d -o CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/tests/pbcenums.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem 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-isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o -MF CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o.d -o CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/exponentialmovingaverage.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/taskassignment-test.dir/link.d "CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o" "CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o ../CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o ../CMakeFiles/taskassignment.dir/findallgputasks.cpp.o ../CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o ../CMakeFiles/taskassignment.dir/resourcedivision.cpp.o ../CMakeFiles/taskassignment.dir/taskassignment.cpp.o ../CMakeFiles/taskassignment.dir/usergpuids.cpp.o -o ../../../../bin/taskassignment-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -lmuparser /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 74%] Built target taskassignment-test /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/tests /build/reproducible-path/gromacs-2025.0/build/basic 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/compat/tests/CMakeFiles/compat-test.dir/mp11.cpp.o -MF CMakeFiles/compat-test.dir/mp11.cpp.o.d -o CMakeFiles/compat-test.dir/mp11.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/tests/mp11.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser 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-DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include 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CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -MF CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o.d -o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/bootstrap_loadstore.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include 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-fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/treesupport.cpp.o -MF CMakeFiles/options-test.dir/treesupport.cpp.o.d -o CMakeFiles/options-test.dir/treesupport.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/tests/treesupport.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -MF CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o.d -o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/simulationsignal.cpp cd 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/build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/functions.cpp.o -MF CMakeFiles/math-test.dir/functions.cpp.o.d -o CMakeFiles/math-test.dir/functions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/functions.cpp [ 75%] Built target gpu_utils-test /usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxana/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/entropy.cpp.o -MF CMakeFiles/gmxana-test.dir/entropy.cpp.o.d -o CMakeFiles/gmxana-test.dir/entropy.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/tests/entropy.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include 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/build/reproducible-path/gromacs-2025.0/src/gromacs/compat/tests/pointers.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem 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"CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o" "CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o" "CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o" "CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o" "CMakeFiles/utility-test.dir/listoflists.cpp.o" "CMakeFiles/utility-test.dir/logger.cpp.o" "CMakeFiles/utility-test.dir/message_string_collector.cpp.o" "CMakeFiles/utility-test.dir/path.cpp.o" "CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o" "CMakeFiles/utility-test.dir/range.cpp.o" "CMakeFiles/utility-test.dir/scope_guard.cpp.o" "CMakeFiles/utility-test.dir/strconvert.cpp.o" "CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o" "CMakeFiles/utility-test.dir/stringutil.cpp.o" "CMakeFiles/utility-test.dir/template_mp.cpp.o" "CMakeFiles/utility-test.dir/textreader.cpp.o" "CMakeFiles/utility-test.dir/textwriter.cpp.o" "CMakeFiles/utility-test.dir/typetraits.cpp.o" "CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/utility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 76%] Built target utility-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests 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/build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/convparm.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/convparm.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/convparm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/convparm.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/pbcutil/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pbcutil-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 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-isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar.cpp.o -MF CMakeFiles/simd-test.dir/scalar.cpp.o.d -o CMakeFiles/simd-test.dir/scalar.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/scalar.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pbcutil-test.dir/link.d "CMakeFiles/pbcutil-test.dir/com.cpp.o" "CMakeFiles/pbcutil-test.dir/mshift.cpp.o" "CMakeFiles/pbcutil-test.dir/pbc.cpp.o" "CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o" "CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pbcutil-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem 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/build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/tests/gmx_chi.cpp [ 76%] Built target pbcutil-test cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include 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src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar_util.cpp.o -MF CMakeFiles/simd-test.dir/scalar_util.cpp.o.d -o CMakeFiles/simd-test.dir/scalar_util.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/scalar_util.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include 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-fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -MF CMakeFiles/random-test.dir/uniformintdistribution.cpp.o.d -o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/random/tests/uniformintdistribution.cpp /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include 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src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/tests/gmx_mindist.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -MF CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o.d -o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/updategroupscog.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/compat/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/compat-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pull-test.dir/link.d "CMakeFiles/pull-test.dir/pull.cpp.o" "CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../CMakeFiles/pulling.dir/output.cpp.o ../CMakeFiles/pulling.dir/pull.cpp.o ../CMakeFiles/pulling.dir/pull_rotation.cpp.o ../CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o ../CMakeFiles/pulling.dir/pullutil.cpp.o ../CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -o ../../../../bin/pull-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lmuparser -lm ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 76%] Built target pull-test cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o -MF CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o.d -o CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/constrtestrunners_gpu.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/compat-test.dir/link.d "CMakeFiles/compat-test.dir/mp11.cpp.o" "CMakeFiles/compat-test.dir/pointers.cpp.o" "CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/compat-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 76%] Built target compat-test cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -MF CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o.d -o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/random/tests/uniformrealdistribution.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/leapfrogtestrunners_gpu.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tables/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/table-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/tests/gmx_traj.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/table-test.dir/link.d "CMakeFiles/table-test.dir/splinetable.cpp.o" "CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/table-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 76%] Built target table-test cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -MF CMakeFiles/topology-test.dir/exclusionblocks.cpp.o.d -o CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/exclusionblocks.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include 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-fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/mdgpugraph.cpp.o -MF CMakeFiles/mdlib-test.dir/mdgpugraph.cpp.o.d -o CMakeFiles/mdlib-test.dir/mdgpugraph.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/mdgpugraph.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include 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-Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/invertmatrix.cpp.o -MF CMakeFiles/math-test.dir/invertmatrix.cpp.o.d -o CMakeFiles/math-test.dir/invertmatrix.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/invertmatrix.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem 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CMakeFiles/simd-test.dir/scalar_math.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/scalar_math.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include 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src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd.cpp.o -MF CMakeFiles/simd-test.dir/simd.cpp.o.d -o CMakeFiles/simd-test.dir/simd.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/simd.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/wholemoleculetransform.cpp.o -MF CMakeFiles/mdlib-test.dir/wholemoleculetransform.cpp.o.d -o CMakeFiles/mdlib-test.dir/wholemoleculetransform.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/wholemoleculetransform.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdtypes-test.dir/link.d "CMakeFiles/mdtypes-test.dir/enerdata.cpp.o" "CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o" "CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o" "CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o" "CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o" "CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdtypes-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 77%] Built target mdtypes-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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-I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 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-Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxana/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxana-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" 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/build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -MF CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o.d -o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/simd_floatingpoint.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmxana-test.dir/link.d "CMakeFiles/gmxana-test.dir/entropy.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o" "CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gmxana-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 77%] Built target gmxana-test /usr/bin/make -f src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build.make 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/build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/tests/builder.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include 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"CMakeFiles/mdlib-test.dir/mdgpugraph.cpp.o" "CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o" "CMakeFiles/mdlib-test.dir/wholemoleculetransform.cpp.o" "CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdlib-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -lmuparser /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 80%] Built target mdlib-test /usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/energyanalysis/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem 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/build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/CMakeFiles/tool-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o -MF CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o.d -o CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/legacyenergy.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem 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/build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/gen_maxwell_velocities.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT 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"CMakeFiles/correlations-test.dir/autocorr.cpp.o" "CMakeFiles/correlations-test.dir/correlationdataset.cpp.o" "CMakeFiles/correlations-test.dir/expfit.cpp.o" "CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o" "CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/correlations-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 81%] Built target correlations-test /usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix 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-o CMakeFiles/topology-test.dir/topsort.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/topsort.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/tool-test-with-leaks.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include 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directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/selection/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/selection/tests/CMakeFiles/selection-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 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pdb2gmx3-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" 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src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include 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src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/densityfittingmodule.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include 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CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/helpwriting.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/nbsearch.cpp.o -MF CMakeFiles/selection-test.dir/nbsearch.cpp.o.d -o CMakeFiles/selection-test.dir/nbsearch.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/tests/nbsearch.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/solvate.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/topdirs.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o -MF CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/outputfiles.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 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/build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -MF CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o.d -o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/simd4_floatingpoint.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/topology/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/topology-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4_math.cpp.o -MF CMakeFiles/simd-test.dir/simd4_math.cpp.o.d -o CMakeFiles/simd-test.dir/simd4_math.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/simd4_math.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/topology-test.dir/link.d "CMakeFiles/topology-test.dir/atoms.cpp.o" "CMakeFiles/topology-test.dir/exclusionblocks.cpp.o" "CMakeFiles/topology-test.dir/idef.cpp.o" "CMakeFiles/topology-test.dir/index.cpp.o" "CMakeFiles/topology-test.dir/mtop.cpp.o" "CMakeFiles/topology-test.dir/symtab.cpp.o" "CMakeFiles/topology-test.dir/topsort.cpp.o" "CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/topology-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 83%] Built target topology-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include 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/build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/tests/setatoms.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include 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/build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -MF CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o.d -o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/simd4_vector_operations.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src 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../../../../bin/gmxpreprocess-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 84%] Built target gmxpreprocess-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/minimize.cpp.o -MF CMakeFiles/minimize-test.dir/minimize.cpp.o.d -o CMakeFiles/minimize-test.dir/minimize.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/minimize.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/simd-test.dir/link.d "CMakeFiles/simd-test.dir/base.cpp.o" "CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o" "CMakeFiles/simd-test.dir/scalar.cpp.o" "CMakeFiles/simd-test.dir/scalar_util.cpp.o" "CMakeFiles/simd-test.dir/scalar_math.cpp.o" "CMakeFiles/simd-test.dir/simd.cpp.o" "CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o" "CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o" "CMakeFiles/simd-test.dir/simd_integer.cpp.o" "CMakeFiles/simd-test.dir/simd_math.cpp.o" "CMakeFiles/simd-test.dir/simd_memory.cpp.o" "CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o" "CMakeFiles/simd-test.dir/simd4.cpp.o" "CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o" "CMakeFiles/simd-test.dir/simd4_math.cpp.o" "CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o" "CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/simd-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 85%] Built target simd-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make 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src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/nonbonded_bench.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tool-test.dir/link.d "CMakeFiles/tool-test.dir/dump.cpp.o" "CMakeFiles/tool-test.dir/helpwriting.cpp.o" "CMakeFiles/tool-test.dir/make_ndx.cpp.o" "CMakeFiles/tool-test.dir/report_methods.cpp.o" "CMakeFiles/tool-test.dir/trjconv.cpp.o" "CMakeFiles/tool-test.dir/convert-tpr.cpp.o" "CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/tool-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 85%] Built target tool-test cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include 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-fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o -MF CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o.d -o CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/ewaldsurfaceterm.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/analysisdata/tests && /usr/bin/cmake -P CMakeFiles/analysisdata-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test-shared.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H 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../../../../lib/libanalysisdata-test-shared.a "CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o" "CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o" "CMakeFiles/analysisdata-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o" /usr/bin/ranlib ../../../../lib/libanalysisdata-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 85%] Built target analysisdata-test-shared /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic 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/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-output-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/testmodule.cpp.o -MF CMakeFiles/coordinateio-test.dir/testmodule.cpp.o.d -o CMakeFiles/coordinateio-test.dir/testmodule.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/tests/testmodule.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY 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-Wl,--dependency-file=CMakeFiles/mdrun-output-test.dir/link.d "CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o" "CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o" "CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o" "CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o" "CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-output-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 87%] Built target mdrun-output-test /usr/bin/make -f 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/build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o -MF CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o.d -o CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/multisim.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" 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/build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/minimize-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/minimize-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 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/build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/simple_mdrun.cpp cd 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/grompp.cpp.o -MF CMakeFiles/mdrun-io-test.dir/grompp.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/grompp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/grompp.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/coordinateio-test.dir/link.d "CMakeFiles/coordinateio-test.dir/builder.cpp.o" "CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o" "CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o" "CMakeFiles/coordinateio-test.dir/register.cpp.o" "CMakeFiles/coordinateio-test.dir/requirements.cpp.o" "CMakeFiles/coordinateio-test.dir/setatoms.cpp.o" "CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o" "CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o" "CMakeFiles/coordinateio-test.dir/settimestep.cpp.o" "CMakeFiles/coordinateio-test.dir/testmodule.cpp.o" "CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/coordinateio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 88%] Built target coordinateio-test cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" 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/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem 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/build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/termination.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-modules-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-single-rank-algorithms-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -MF CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o.d -o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/tabulated_bonded_interactions.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-modules-test.dir/link.d 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-Wl,--dependency-file=CMakeFiles/mdrun-single-rank-algorithms-test.dir/link.d "CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/orires.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-single-rank-algorithms-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 88%] Built target mdrun-modules-test cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/mimic.cpp [ 88%] Built target mdrun-single-rank-algorithms-test cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include 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src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/mrcserializer.cpp.o -MF CMakeFiles/fileio-test.dir/mrcserializer.cpp.o.d -o CMakeFiles/fileio-test.dir/mrcserializer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/mrcserializer.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include 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-Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o -MF CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o.d -o CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/mrcdensitymap.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-tpi-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o -MF CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o.d -o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/mrcdensitymapheader.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/minimize-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-tpi-test.dir/link.d "CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o" "CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-tpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 88%] Built target mdrun-tpi-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build.make 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make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include 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"CMakeFiles/minimize-test.dir/minimize.cpp.o" "CMakeFiles/minimize-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/minimize-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 88%] Built target minimize-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" 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/build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/multisimtest.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem 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/build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem 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/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-non-integrator-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-multisim-test.dir/link.d "CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o" "CMakeFiles/mdrun-multisim-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 88%] Built target mdrun-multisim-test cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include 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-Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o -MF CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o.d -o CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/periodicactions_coupling.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-mpi-test.dir/link.d "CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o" "CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o" "CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 89%] Built target mdrun-mpi-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/build.make 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src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions.cpp.o -MF CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions.cpp.o.d -o CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/periodicactions.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-non-integrator-test.dir/link.d "CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-non-integrator-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 89%] Built target mdrun-non-integrator-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 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/build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/expandedensemble.cpp.o -MF CMakeFiles/mdrun-fep-test.dir/expandedensemble.cpp.o.d -o CMakeFiles/mdrun-fep-test.dir/expandedensemble.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/expandedensemble.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem 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&& /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser 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CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include 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src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/boxdeformation.cpp.o -MF CMakeFiles/mdrun-test.dir/boxdeformation.cpp.o.d -o CMakeFiles/mdrun-test.dir/boxdeformation.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/boxdeformation.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-io-test.dir/link.d "CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o" "CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o" "CMakeFiles/mdrun-io-test.dir/grompp.cpp.o" "CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o" "CMakeFiles/mdrun-io-test.dir/termination.cpp.o" "CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-io-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 89%] Built target mdrun-io-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem 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../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 89%] Built target mdrun-mpi-pme-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests 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-I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-coordination-basic-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-coordination-basic-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/selection/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/selection-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 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89%] Built target selection-test cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include 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CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-multisim-replex-test.dir/link.d "CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o" "CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-replex-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 89%] Built target mdrun-multisim-replex-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/workflow/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/workflow.cpp.o -MF CMakeFiles/workflow-details-test.dir/workflow.cpp.o.d -o CMakeFiles/workflow-details-test.dir/workflow.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/workflow/tests/workflow.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include 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-fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/fileio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileio-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem 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-DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/status.cpp.o -MF CMakeFiles/gmxapi-test.dir/status.cpp.o.d -o CMakeFiles/gmxapi-test.dir/status.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests/status.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/math/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/math-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/fileio-test.dir/link.d "CMakeFiles/fileio-test.dir/checkpoint.cpp.o" "CMakeFiles/fileio-test.dir/confio.cpp.o" "CMakeFiles/fileio-test.dir/filemd5.cpp.o" "CMakeFiles/fileio-test.dir/filetypes.cpp.o" "CMakeFiles/fileio-test.dir/matio.cpp.o" "CMakeFiles/fileio-test.dir/mrcserializer.cpp.o" "CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o" "CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o" "CMakeFiles/fileio-test.dir/readinp.cpp.o" "CMakeFiles/fileio-test.dir/timecontrol.cpp.o" "CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o" "CMakeFiles/fileio-test.dir/tngio.cpp.o" "CMakeFiles/fileio-test.dir/xvgio.cpp.o" "CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/fileio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 90%] Built target fileio-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include 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/build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o -MF CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o.d -o CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tests/integrator.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-coordination-basic-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/math-test.dir/link.d "CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o" "CMakeFiles/math-test.dir/boxmatrix.cpp.o" "CMakeFiles/math-test.dir/complex.cpp.o" "CMakeFiles/math-test.dir/coordinatetransformation.cpp.o" "CMakeFiles/math-test.dir/densityfit.cpp.o" "CMakeFiles/math-test.dir/dofit.cpp.o" "CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o" "CMakeFiles/math-test.dir/functions.cpp.o" "CMakeFiles/math-test.dir/gausstransform.cpp.o" "CMakeFiles/math-test.dir/densityfittingforce.cpp.o" "CMakeFiles/math-test.dir/invertmatrix.cpp.o" "CMakeFiles/math-test.dir/matrix.cpp.o" "CMakeFiles/math-test.dir/multidimarray.cpp.o" "CMakeFiles/math-test.dir/neldermead.cpp.o" "CMakeFiles/math-test.dir/optimization.cpp.o" "CMakeFiles/math-test.dir/paddedvector.cpp.o" "CMakeFiles/math-test.dir/vectypes.cpp.o" "CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/math-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp [ 90%] Built target math-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-setup-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-setup-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests 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-I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem 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-I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT 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../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-coordination-basic-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 90%] Built target mdrun-coordination-basic-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/tests 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-I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem 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CMakeFiles/mdrun-coordination-coupling-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-coordination-constraints-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-coordination-coupling-test.dir/link.d "CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o" "CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o" "CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-coordination-coupling-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 92%] Built target mdrun-coordination-coupling-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integration-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 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-I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem 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/build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/include 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api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o -MF CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o.d -o CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests/stopsignaler.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-coordination-constraints-test.dir/link.d "CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions.cpp.o" "CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions_constraints.cpp.o" "CMakeFiles/mdrun-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-coordination-constraints-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 93%] Built target mdrun-coordination-constraints-test /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/tests /build/reproducible-path/gromacs-2025.0/build/basic 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/build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/interactions.cpp.o -MF CMakeFiles/nblib-setup-test.dir/interactions.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/interactions.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tests/interactions.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/workflow/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/workflow-details-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/workflow-details-test.dir/link.d "CMakeFiles/workflow-details-test.dir/workflow.cpp.o" "CMakeFiles/workflow-details-test.dir/__/__/__/__/__/src/testutils/unittest_main.cpp.o" ../../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../../bin/workflow-details-test ../../../../../lib/libtestutils.a ../../../../../lib/libgmxapi.so.0.4.0 ../../../../../lib/libmdrun_test_infrastructure.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../../lib/libgmock.so.1.13.0 ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 94%] Built target workflow-details-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser 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/build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/tests/gmxcalculator.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api 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/build/reproducible-path/gromacs-2025.0/api/nblib/tests/particletype.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o -MF CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tests/pbcholder.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o -MF CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tests/nbkernelsystem.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/link.d "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o" "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-replex-equivalence-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 94%] Built target mdrun-multisim-replex-equivalence-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem 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/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests/version.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/util/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/util/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/traits.cpp.o -MF CMakeFiles/nblib-util-test.dir/traits.cpp.o.d -o CMakeFiles/nblib-util-test.dir/traits.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/util/tests/traits.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem 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cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-rotation-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-tpr-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src 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/build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-rotation-test.dir/link.d "CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o" "CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-rotation-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 94%] Built target mdrun-rotation-test /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make 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/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/tests/helpers.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-tpr-test.dir/link.d "CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o" "CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-tpr-test ../../../lib/libtestutils.a ../../../lib/libmdrun_test_infrastructure.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 ../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -MF CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/tests/threadaffinity.cpp [ 94%] Built target nblib-tpr-test /usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/moduletest.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/topology.cpp.o -MF CMakeFiles/nblib-setup-test.dir/topology.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/topology.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tests/topology.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-vsites-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-vsites-test.dir/link.d "CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o" "CMakeFiles/mdrun-vsites-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-vsites-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 94%] Built target mdrun-vsites-test cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -MF CMakeFiles/analysisdata-test.dir/arraydata.cpp.o.d -o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/tests/arraydata.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/virials.cpp.o -MF CMakeFiles/nblib-setup-test.dir/virials.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/virials.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tests/virials.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-fep-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/util/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/util/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmxapi-test.dir/link.d "CMakeFiles/gmxapi-test.dir/restraint.cpp.o" "CMakeFiles/gmxapi-test.dir/runner.cpp.o" "CMakeFiles/gmxapi-test.dir/status.cpp.o" "CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o" "CMakeFiles/gmxapi-test.dir/system.cpp.o" "CMakeFiles/gmxapi-test.dir/version.cpp.o" "CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" ../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/gmxapi-test ../../../../lib/libtestutils.a ../../../../lib/libgmxapi.so.0.4.0 ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 94%] Built target gmxapi-test cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/angle.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-fep-test.dir/link.d "CMakeFiles/mdrun-fep-test.dir/expandedensemble.cpp.o" "CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o" "CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-fep-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 94%] Built target mdrun-fep-test cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/tests/listedtesthelpers.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/tests/kernels.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-integrator-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/cmdlinerunner.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-integrator-test.dir/link.d "CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o" "CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-integrator-test ../../../lib/libtestutils.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 ../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 94%] Built target nblib-integrator-test cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/average.cpp.o -MF CMakeFiles/analysisdata-test.dir/average.cpp.o.d -o CMakeFiles/analysisdata-test.dir/average.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/tests/average.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrunutility-mpi-test.dir/link.d "CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o" "CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdrunutility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 94%] Built target mdrunutility-mpi-test cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/convert_trj.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/util/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-util-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/distance.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/tests/typetests.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-util-test.dir/link.d "CMakeFiles/nblib-util-test.dir/setup.cpp.o" "CMakeFiles/nblib-util-test.dir/traits.cpp.o" "CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../../bin/nblib-util-test ../../../../lib/libtestutils.a ../../../../lib/libnblib_test_infrastructure.a ../../../../lib/libnblib_gmx.so.0.1.0 ../../../../lib/libtestutils.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/dssp.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/dssp.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/dssp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/dssp.cpp [ 94%] Built target nblib-util-test cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/histogram.cpp.o -MF CMakeFiles/analysisdata-test.dir/histogram.cpp.o.d -o CMakeFiles/analysisdata-test.dir/histogram.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/tests/histogram.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/lifetime.cpp.o -MF CMakeFiles/analysisdata-test.dir/lifetime.cpp.o.d -o CMakeFiles/analysisdata-test.dir/lifetime.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/tests/lifetime.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-integration-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/extract_cluster.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/tests/calculator.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-integration-test.dir/link.d "CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o" "CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o" "CMakeFiles/nblib-integration-test.dir/simstate.cpp.o" "CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-integration-test ../../../lib/libtestutils.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 ../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 96%] Built target nblib-integration-test cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrunutility-test.dir/link.d "CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o" "CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o" "CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdrunutility-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 96%] Built target mdrunutility-test cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src 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../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 96%] Built target mdrun-pull-test cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/rdf.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include 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/build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem 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/build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/tests/pargs.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/analysisdata-test.dir/link.d "CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o" "CMakeFiles/analysisdata-test.dir/arraydata.cpp.o" "CMakeFiles/analysisdata-test.dir/average.cpp.o" "CMakeFiles/analysisdata-test.dir/histogram.cpp.o" "CMakeFiles/analysisdata-test.dir/lifetime.cpp.o" "CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/analysisdata-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 96%] Built target analysisdata-test cd /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/commandline/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/commandline-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-setup-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/commandline-test.dir/link.d "CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o" "CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o" "CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o" "CMakeFiles/commandline-test.dir/filenm.cpp.o" "CMakeFiles/commandline-test.dir/pargs.cpp.o" "CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 97%] Built target commandline-test /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-setup-test.dir/link.d "CMakeFiles/nblib-setup-test.dir/box.cpp.o" "CMakeFiles/nblib-setup-test.dir/interactions.cpp.o" "CMakeFiles/nblib-setup-test.dir/particletype.cpp.o" "CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o" "CMakeFiles/nblib-setup-test.dir/molecules.cpp.o" "CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o" "CMakeFiles/nblib-setup-test.dir/topology.cpp.o" "CMakeFiles/nblib-setup-test.dir/virials.cpp.o" "CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-setup-test ../../../lib/libtestutils.a ../../../lib/libmdrun_test_infrastructure.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 ../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 98%] Built target nblib-setup-test /usr/bin/make -f api/nblib/CMakeFiles/nblib-tests.dir/build.make api/nblib/CMakeFiles/nblib-tests.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib /build/reproducible-path/gromacs-2025.0/build/basic 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CMakeFiles/trajectoryanalysis-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-listed-forces-test.dir/link.d "CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../../bin/nblib-listed-forces-test ../../../../lib/libtestutils.a ../../../../lib/libnblib_test_infrastructure.a ../../../../lib/libnblib_gmx.so.0.1.0 ../../../../lib/libtestutils.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 98%] Built target nblib-listed-forces-test /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/trajectoryanalysis-test.dir/link.d "CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/dssp.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/gyrate.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/hbond.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/msd.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/scattering.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/trajectoryanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [100%] Built target trajectoryanalysis-test /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/CMakeFiles/tests.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [100%] Built target tests make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.0/build/basic/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[1]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' (cd build/basic; LD_LIBRARY_PATH=/build/reproducible-path/gromacs-2025.0/build/basic/lib ctest -V) UpdateCTestConfiguration from :/build/reproducible-path/gromacs-2025.0/build/basic/DartConfiguration.tcl Parse Config file:/build/reproducible-path/gromacs-2025.0/build/basic/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/gromacs-2025.0/build/basic/DartConfiguration.tcl Parse Config file:/build/reproducible-path/gromacs-2025.0/build/basic/DartConfiguration.tcl Test project /build/reproducible-path/gromacs-2025.0/build/basic Constructing a list of tests Done constructing a list of tests Updating test list for fixtures Added 0 tests to meet fixture requirements Checking test dependency graph... Checking test dependency graph end test 1 Start 1: GmxapiExternalInterfaceTests 1: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/gmxapi-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/GmxapiExternalInterfaceTests.xml" 1: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/tests 1: Test timeout computed to be: 600 1: [==========] Running 9 tests from 1 test suite. 1: [----------] Global test environment set-up. 1: [----------] 9 tests from GmxApiTest 1: [ RUN ] GmxApiTest.ApiRunnerRestrainedMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 1: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to 2109340502 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.100 0.050 199.5 1: (ns/day) (hour/ns) 1: Performance: 10.135 2.368 1: [ OK ] GmxApiTest.ApiRunnerRestrainedMD (1224 ms) 1: [ RUN ] GmxApiTest.RunnerBasicMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 1: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to 1322450429 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.094 0.047 199.5 1: (ns/day) (hour/ns) 1: Performance: 10.691 2.245 1: [ OK ] GmxApiTest.RunnerBasicMD (855 ms) 1: [ RUN ] GmxApiTest.RunnerReinitialize 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 1: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 20 steps, 0.0 ps. 1: 1: 1: Received the remote INT/TERM signal, stopping within 200 steps 1: 1: Setting the LD random seed to 1717425615 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.063 0.032 199.4 1: (ns/day) (hour/ns) 1: Performance: 112.090 0.214 1: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 1: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 20 steps, 0.0 ps. 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.047 0.024 199.1 1: (ns/day) (hour/ns) 1: Performance: 149.404 0.161 1: [ OK ] GmxApiTest.RunnerReinitialize (722 ms) 1: [ RUN ] GmxApiTest.RunnerChainedMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 1: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to -285234691 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.063 0.032 199.4 1: (ns/day) (hour/ns) 1: Performance: 15.943 1.505 1: trr version: GMX_trn_file (single precision) 1: 1: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 1: Setting nsteps to 4 1: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 1: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 1: Input file: 1: Run start step 0 1: Run start time 0 ps 1: Step to be made during run 2 1: Runtime for the run 0.00390625 ps 1: Run end step 2 1: Run end time 0.00390625 ps 1: 1: 1: Output file: 1: Run start step 0 1: Run start time 0 ps 1: Step to be made during run 4 1: Runtime for the run 0.0078125 ps 1: Run end step 4 1: Run end time 0.0078125 ps 1: 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.058 0.029 199.2 1: (ns/day) (hour/ns) 1: Performance: 17.462 1.374 1: 1: [ OK ] GmxApiTest.RunnerChainedMD (771 ms) 1: [ RUN ] GmxApiTest.Status 1: [ OK ] GmxApiTest.Status (0 ms) 1: [ RUN ] GmxApiTest.ApiRunnerStopSignalClient 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 1: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 1: Changing nstlist from 10 to 1, rlist from 1.057 to 1 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps. 1: Setting the LD random seed to -353657 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.058 0.029 199.2 1: (ns/day) (hour/ns) 1: Performance: 28.872 0.831 1: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 1: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 1: Overriding nsteps with value passed on the command line: 4 steps, 0.00781 ps 1: Changing nstlist from 10 to 1, rlist from 1.057 to 1 1: 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.044 0.022 198.9 1: (ns/day) (hour/ns) 1: Performance: 15.381 1.560 1: [ OK ] GmxApiTest.ApiRunnerStopSignalClient (893 ms) 1: [ RUN ] GmxApiTest.SystemConstruction 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Setting the LD random seed to -136677918 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: [ OK ] GmxApiTest.SystemConstruction (625 ms) 1: [ RUN ] GmxApiTest.SaneVersionComparisons 1: [ OK ] GmxApiTest.SaneVersionComparisons (0 ms) 1: [ RUN ] GmxApiTest.VersionNamed0_1_Features 1: [ OK ] GmxApiTest.VersionNamed0_1_Features (0 ms) 1: [----------] 9 tests from GmxApiTest (5094 ms total) 1: 1: [----------] Global test environment tear-down 1: [==========] 9 tests from 1 test suite ran. (5239 ms total) 1: [ PASSED ] 9 tests. 1/90 Test #1: GmxapiExternalInterfaceTests .............. Passed 5.27 sec test 2 Start 2: GmxapiInternalInterfaceTests 2: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/workflow-details-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/GmxapiInternalInterfaceTests.xml" 2: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/workflow/tests 2: Test timeout computed to be: 600 2: [==========] Running 2 tests from 1 test suite. 2: [----------] Global test environment set-up. 2: [----------] 2 tests from GmxApiTest 2: [ RUN ] GmxApiTest.BuildApiWorkflowImpl 2: Generating 1-4 interactions: fudge = 0.5 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: Setting the LD random seed to 1606397822 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: [ OK ] GmxApiTest.BuildApiWorkflowImpl (590 ms) 2: [ RUN ] GmxApiTest.CreateApiWorkflow 2: Generating 1-4 interactions: fudge = 0.5 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: Setting the LD random seed to 2145386239 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: [ OK ] GmxApiTest.CreateApiWorkflow (557 ms) 2: [----------] 2 tests from GmxApiTest (1148 ms total) 2: 2: [----------] Global test environment tear-down 2: [==========] 2 tests from 1 test suite ran. (1273 ms total) 2: [ PASSED ] 2 tests. 2/90 Test #2: GmxapiInternalInterfaceTests .............. Passed 1.30 sec test 3 Start 3: NbLibListedForcesTests 3: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/nblib-listed-forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/NbLibListedForcesTests.xml" 3: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/listed_forces/tests 3: Test timeout computed to be: 600 3: [==========] Running 44 tests from 22 test suites. 3: [----------] Global test environment set-up. 3: [----------] 8 tests from NBlibTest 3: [ RUN ] NBlibTest.BondTypesOperatorEqualWorks 3: [ OK ] NBlibTest.BondTypesOperatorEqualWorks (0 ms) 3: [ RUN ] NBlibTest.BondTypesLessThanWorks 3: [ OK ] NBlibTest.BondTypesLessThanWorks (0 ms) 3: [ RUN ] NBlibTest.CanSplitListedWork 3: [ OK ] NBlibTest.CanSplitListedWork (0 ms) 3: [ RUN ] NBlibTest.ListedForceBuffer 3: [ OK ] NBlibTest.ListedForceBuffer (0 ms) 3: [ RUN ] NBlibTest.ListedForceCalculatorCanConstruct 3: [ OK ] NBlibTest.ListedForceCalculatorCanConstruct (0 ms) 3: [ RUN ] NBlibTest.GmxToNblibConversionAllTypes 3: [ OK ] NBlibTest.GmxToNblibConversionAllTypes (0 ms) 3: [ RUN ] NBlibTest.EndToEndListedComparison 3: [ OK ] NBlibTest.EndToEndListedComparison (0 ms) 3: [ RUN ] NBlibTest.shiftForcesAreCorrect 3: [ OK ] NBlibTest.shiftForcesAreCorrect (25 ms) 3: [----------] 8 tests from NBlibTest (25 ms total) 3: 3: [----------] 1 test from Kernels 3: [ RUN ] Kernels.HarmonicScalarKernelCanCompute 3: [ OK ] Kernels.HarmonicScalarKernelCanCompute (0 ms) 3: [----------] 1 test from Kernels (0 ms total) 3: 3: [----------] 1 test from FourCenter 3: [ RUN ] FourCenter.ListedForcesProperDihedralTest 3: [ OK ] FourCenter.ListedForcesProperDihedralTest (0 ms) 3: [----------] 1 test from FourCenter (0 ms total) 3: 3: [----------] 7 tests from ThreeCenter 3: [ RUN ] ThreeCenter.ListedForcesG96AngleTest 3: [ OK ] ThreeCenter.ListedForcesG96AngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesHarmonicAngleTest 3: [ OK ] ThreeCenter.ListedForcesHarmonicAngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesLinearAngleTest 3: [ OK ] ThreeCenter.ListedForcesLinearAngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesCrossBondBondTest 3: [ OK ] ThreeCenter.ListedForcesCrossBondBondTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesCrossBondAngleTest 3: [ OK ] ThreeCenter.ListedForcesCrossBondAngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesQuarticAngleTest 3: [ OK ] ThreeCenter.ListedForcesQuarticAngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesRestrictedAngleTest 3: [ OK ] ThreeCenter.ListedForcesRestrictedAngleTest (0 ms) 3: [----------] 7 tests from ThreeCenter (0 ms total) 3: 3: [----------] 5 tests from TwoCenter 3: [ RUN ] TwoCenter.ListedForcesHarmonicBondTest 3: [ OK ] TwoCenter.ListedForcesHarmonicBondTest (0 ms) 3: [ RUN ] TwoCenter.ListedForcesG96BondTest 3: [ OK ] TwoCenter.ListedForcesG96BondTest (0 ms) 3: [ RUN ] TwoCenter.ListedForcesCubicBondTest 3: [ OK ] TwoCenter.ListedForcesCubicBondTest (0 ms) 3: [ RUN ] TwoCenter.ListedForcesMorseBondTest 3: [ OK ] TwoCenter.ListedForcesMorseBondTest (0 ms) 3: [ RUN ] TwoCenter.ListedForcesFeneBondTest 3: [ OK ] TwoCenter.ListedForcesFeneBondTest (0 ms) 3: [----------] 5 tests from TwoCenter (0 ms total) 3: 3: [----------] 5 tests from ListedExampleData 3: [ RUN ] ListedExampleData.ComputeHarmonicBondForces 3: [ OK ] ListedExampleData.ComputeHarmonicBondForces (0 ms) 3: [ RUN ] ListedExampleData.ComputeHarmonicBondEnergies 3: [ OK ] ListedExampleData.ComputeHarmonicBondEnergies (0 ms) 3: [ RUN ] ListedExampleData.ComputeHarmonicAngleForces 3: [ OK ] ListedExampleData.ComputeHarmonicAngleForces (0 ms) 3: [ RUN ] ListedExampleData.CanReduceForces 3: [ OK ] ListedExampleData.CanReduceForces (0 ms) 3: [ RUN ] ListedExampleData.CanReduceEnergies 3: [ OK ] ListedExampleData.CanReduceEnergies (0 ms) 3: [----------] 5 tests from ListedExampleData (0 ms total) 3: 3: [----------] 1 test from LinearChainDataFixture 3: [ RUN ] LinearChainDataFixture.Multithreading 3: [ OK ] LinearChainDataFixture.Multithreading (11 ms) 3: [----------] 1 test from LinearChainDataFixture (11 ms total) 3: 3: [----------] 2 tests from ListedShims 3: [ RUN ] ListedShims.ParameterConversion 3: [ OK ] ListedShims.ParameterConversion (0 ms) 3: [ RUN ] ListedShims.GmxToNblibConversion 3: [ OK ] ListedShims.GmxToNblibConversion (0 ms) 3: [----------] 2 tests from ListedShims (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/0, where TypeParam = nblib::TwoParameterInteraction 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/0.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/0.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/0 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/1, where TypeParam = nblib::G96BondType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/1.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/1.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/1 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/2, where TypeParam = nblib::CubicBondType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/2.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/2.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/2 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/3, where TypeParam = nblib::MorseBondType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/3.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/3.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/3 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/4, where TypeParam = nblib::TwoParameterInteraction 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/4.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/4.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/4 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/5, where TypeParam = nblib::AngleInteractionType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/5.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/5.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/5 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/6, where TypeParam = nblib::CosineParamAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/6.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/6.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/6 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/7, where TypeParam = nblib::CosineParamAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/7.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/7.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/7 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/8, where TypeParam = nblib::TwoParameterInteraction 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/8.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/8.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/8 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/9, where TypeParam = nblib::QuarticAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/9.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/9.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/9 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/10, where TypeParam = nblib::CrossBondBond 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/10.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/10.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/10 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/11, where TypeParam = nblib::CrossBondAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/11.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/11.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/11 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/12, where TypeParam = nblib::ProperDihedral 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/12.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/12.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/12 (0 ms total) 3: 3: [----------] 1 test from ListedTransformations 3: [ RUN ] ListedTransformations.SortInteractionIndices 3: [ OK ] ListedTransformations.SortInteractionIndices (0 ms) 3: [----------] 1 test from ListedTransformations (0 ms total) 3: 3: [----------] Global test environment tear-down 3: [==========] 44 tests from 22 test suites ran. (39 ms total) 3: [ PASSED ] 44 tests. 3/90 Test #3: NbLibListedForcesTests .................... Passed 0.06 sec test 4 Start 4: NbLibSamplesTestArgon 4: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/argon-forces-integration 4: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/samples 4: Test timeout computed to be: 1500 4: initial forces on particle 0: x 0.000000 y 0.000000 z 0.000000 4: final forces on particle 0: x -0.412993 y -1.098256 z -0.113191 4: initial position of particle 0: x 0.794000 y 1.439000 z 0.610000 4: final position of particle 0: x 0.789162 y 1.271508 z 0.819867 4/90 Test #4: NbLibSamplesTestArgon ..................... Passed 0.02 sec test 5 Start 5: NbLibSamplesTestMethaneWater 5: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/methane-water-integration 5: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/samples 5: Test timeout computed to be: 1500 5: initial position of particle 0: x 0.005000 y 0.600000 z 0.244000 5: final position of particle 9: x 77.358398 y 5.324913 z -80.600098 5/90 Test #5: NbLibSamplesTestMethaneWater .............. Passed 0.03 sec test 6 Start 6: NbLibUtilTests 6: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/nblib-util-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/NbLibUtilTests.xml" 6: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/util/tests 6: Test timeout computed to be: 30 6: [==========] Running 16 tests from 2 test suites. 6: [----------] Global test environment set-up. 6: [----------] 6 tests from NBlibTest 6: [ RUN ] NBlibTest.isRealValued 6: [ OK ] NBlibTest.isRealValued (0 ms) 6: [ RUN ] NBlibTest.checkNumericValuesHasNan 6: [ OK ] NBlibTest.checkNumericValuesHasNan (0 ms) 6: [ RUN ] NBlibTest.checkNumericValuesHasInf 6: [ OK ] NBlibTest.checkNumericValuesHasInf (0 ms) 6: [ RUN ] NBlibTest.GeneratedVelocitiesAreCorrect 6: Velocities were taken from a Maxwell distribution at 300 K 6: [ OK ] NBlibTest.GeneratedVelocitiesAreCorrect (0 ms) 6: [ RUN ] NBlibTest.generateVelocitySize 6: Velocities were taken from a Maxwell distribution at 300 K 6: [ OK ] NBlibTest.generateVelocitySize (0 ms) 6: [ RUN ] NBlibTest.generateVelocityCheckNumbers 6: Velocities were taken from a Maxwell distribution at 300 K 6: [ OK ] NBlibTest.generateVelocityCheckNumbers (0 ms) 6: [----------] 6 tests from NBlibTest (0 ms total) 6: 6: [----------] 10 tests from NblibTraitsUtils 6: [ RUN ] NblibTraitsUtils.FuseTwo 6: [ OK ] NblibTraitsUtils.FuseTwo (0 ms) 6: [ RUN ] NblibTraitsUtils.Fuse 6: [ OK ] NblibTraitsUtils.Fuse (0 ms) 6: [ RUN ] NblibTraitsUtils.Repeat 6: [ OK ] NblibTraitsUtils.Repeat (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTuple1 6: [ OK ] NblibTraitsUtils.FindIndexTuple1 (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTuple2 6: [ OK ] NblibTraitsUtils.FindIndexTuple2 (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTypeList1 6: [ OK ] NblibTraitsUtils.FindIndexTypeList1 (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTypeList2 6: [ OK ] NblibTraitsUtils.FindIndexTypeList2 (0 ms) 6: [ RUN ] NblibTraitsUtils.Contains 6: [ OK ] NblibTraitsUtils.Contains (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTupleRepeated 6: [ OK ] NblibTraitsUtils.FindIndexTupleRepeated (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTypeListRepeated 6: [ OK ] NblibTraitsUtils.FindIndexTypeListRepeated (0 ms) 6: [----------] 10 tests from NblibTraitsUtils (0 ms total) 6: 6: [----------] Global test environment tear-down 6: [==========] 16 tests from 2 test suites ran. (0 ms total) 6: [ PASSED ] 16 tests. 6/90 Test #6: NbLibUtilTests ............................ Passed 0.02 sec test 7 Start 7: NbLibSetupTests 7: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/nblib-setup-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/NbLibSetupTests.xml" 7: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests 7: Test timeout computed to be: 600 7: [==========] Running 57 tests from 3 test suites. 7: [----------] Global test environment set-up. 7: [----------] 41 tests from NBlibTest 7: [ RUN ] NBlibTest.CubicBoxCannotHaveNaN 7: [ OK ] NBlibTest.CubicBoxCannotHaveNaN (0 ms) 7: [ RUN ] NBlibTest.CubicBoxCannotHaveInf 7: [ OK ] NBlibTest.CubicBoxCannotHaveInf (0 ms) 7: [ RUN ] NBlibTest.RectangularBoxCannotHaveNaN 7: [ OK ] NBlibTest.RectangularBoxCannotHaveNaN (0 ms) 7: [ RUN ] NBlibTest.RectangularBoxCannotHaveInf 7: [ OK ] NBlibTest.RectangularBoxCannotHaveInf (0 ms) 7: [ RUN ] NBlibTest.CubicBoxWorks 7: [ OK ] NBlibTest.CubicBoxWorks (0 ms) 7: [ RUN ] NBlibTest.BoxEqual 7: [ OK ] NBlibTest.BoxEqual (0 ms) 7: [ RUN ] NBlibTest.NonBondedForceParamsCorrect 7: [ OK ] NBlibTest.NonBondedForceParamsCorrect (0 ms) 7: [ RUN ] NBlibTest.CanMergeInteractions 7: [ OK ] NBlibTest.CanMergeInteractions (0 ms) 7: [ RUN ] NBlibTest.ParticleTypeNameCanBeConstructed 7: [ OK ] NBlibTest.ParticleTypeNameCanBeConstructed (0 ms) 7: [ RUN ] NBlibTest.ParticleTypeMassCanBeConstructed 7: [ OK ] NBlibTest.ParticleTypeMassCanBeConstructed (0 ms) 7: [ RUN ] NBlibTest.PbcHolderWorks 7: [ OK ] NBlibTest.PbcHolderWorks (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName (0 ms) 7: [ RUN ] NBlibTest.CanGetNumParticlesInMolecule 7: [ OK ] NBlibTest.CanGetNumParticlesInMolecule (0 ms) 7: [ RUN ] NBlibTest.CanConstructExclusionListFromNames 7: [ OK ] NBlibTest.CanConstructExclusionListFromNames (0 ms) 7: [ RUN ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed 7: [ OK ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed (0 ms) 7: [ RUN ] NBlibTest.AtWorks 7: [ OK ] NBlibTest.AtWorks (0 ms) 7: [ RUN ] NBlibTest.AtThrows 7: [ OK ] NBlibTest.AtThrows (0 ms) 7: [ RUN ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass 7: [ OK ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass (0 ms) 7: [ RUN ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass 7: [ OK ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass (0 ms) 7: [ RUN ] NBlibTest.MoleculeNoThrowsSameParticleTypeName 7: [ OK ] NBlibTest.MoleculeNoThrowsSameParticleTypeName (0 ms) 7: [ RUN ] NBlibTest.CanAddInteractions 7: [ OK ] NBlibTest.CanAddInteractions (0 ms) 7: [ RUN ] NBlibTest.CanAddUreyBradley 7: [ OK ] NBlibTest.CanAddUreyBradley (0 ms) 7: [ RUN ] NBlibTest.TopologyHasNumParticles 7: [ OK ] NBlibTest.TopologyHasNumParticles (0 ms) 7: [ RUN ] NBlibTest.TopologyHasCharges 7: [ OK ] NBlibTest.TopologyHasCharges (0 ms) 7: [ RUN ] NBlibTest.TopologyHasMasses 7: [ OK ] NBlibTest.TopologyHasMasses (0 ms) 7: [ RUN ] NBlibTest.TopologyHasParticleTypes 7: [ OK ] NBlibTest.TopologyHasParticleTypes (0 ms) 7: [ RUN ] NBlibTest.TopologyHasParticleTypeIds 7: [ OK ] NBlibTest.TopologyHasParticleTypeIds (0 ms) 7: [ RUN ] NBlibTest.TopologyThrowsIdenticalParticleType 7: [ OK ] NBlibTest.TopologyThrowsIdenticalParticleType (0 ms) 7: [ RUN ] NBlibTest.TopologyHasExclusions 7: [ OK ] NBlibTest.TopologyHasExclusions (0 ms) 7: [ RUN ] NBlibTest.TopologyHasSequencing 7: [ OK ] NBlibTest.TopologyHasSequencing (0 ms) 7: [ RUN ] NBlibTest.TopologyCanAggregateBonds 7: [ OK ] NBlibTest.TopologyCanAggregateBonds (0 ms) 7: [ RUN ] NBlibTest.TopologyCanSequencePairIDs 7: [ OK ] NBlibTest.TopologyCanSequencePairIDs (0 ms) 7: [ RUN ] NBlibTest.TopologySequenceIdThrows 7: No particle O-Atom in residue SOL in molecule SOL found 7: [ OK ] NBlibTest.TopologySequenceIdThrows (0 ms) 7: [ RUN ] NBlibTest.TopologyCanEliminateDuplicateBonds 7: [ OK ] NBlibTest.TopologyCanEliminateDuplicateBonds (0 ms) 7: [ RUN ] NBlibTest.TopologyListedInteractions 7: [ OK ] NBlibTest.TopologyListedInteractions (0 ms) 7: [ RUN ] NBlibTest.TopologyListedInteractionsMultipleTypes 7: [ OK ] NBlibTest.TopologyListedInteractionsMultipleTypes (0 ms) 7: [ RUN ] NBlibTest.TopologyInvalidParticleInInteractionThrows 7: No particle Iron in residue SOL in molecule SOL found 7: [ OK ] NBlibTest.TopologyInvalidParticleInInteractionThrows (0 ms) 7: [ RUN ] NBlibTest.toGmxExclusionBlockWorks 7: [ OK ] NBlibTest.toGmxExclusionBlockWorks (0 ms) 7: [----------] 41 tests from NBlibTest (2 ms total) 7: 7: [----------] 15 tests from NbnxmSetupTest 7: [ RUN ] NbnxmSetupTest.findNumEnergyGroups 7: [ OK ] NbnxmSetupTest.findNumEnergyGroups (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnumAuto 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnumAuto (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnumNo 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnumNo (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnum2XM 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnum2XM (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnum4XM 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnum4XM (0 ms) 7: [ RUN ] NbnxmSetupTest.CheckKernelSetupThrowsAuto 7: [ OK ] NbnxmSetupTest.CheckKernelSetupThrowsAuto (0 ms) 7: [ RUN ] NbnxmSetupTest.CheckKernelSetupThrowsCount 7: [ OK ] NbnxmSetupTest.CheckKernelSetupThrowsCount (0 ms) 7: [ RUN ] NbnxmSetupTest.canCreateKernelSetupPlain 7: [ OK ] NbnxmSetupTest.canCreateKernelSetupPlain (0 ms) 7: [ RUN ] NbnxmSetupTest.canCreateParticleInfoAllVdv 7: [ OK ] NbnxmSetupTest.canCreateParticleInfoAllVdv (0 ms) 7: [ RUN ] NbnxmSetupTest.ewaldCoeffWorks 7: [ OK ] NbnxmSetupTest.ewaldCoeffWorks (0 ms) 7: [ RUN ] NbnxmSetupTest.updateForcerecWorks 7: [ OK ] NbnxmSetupTest.updateForcerecWorks (0 ms) 7: [ RUN ] NbnxmSetupTest.canCheckKernelSetup 7: [ OK ] NbnxmSetupTest.canCheckKernelSetup (0 ms) 7: [ RUN ] NbnxmSetupTest.cannotCreateKernelSetupCPU2XM 7: [ OK ] NbnxmSetupTest.cannotCreateKernelSetupCPU2XM (0 ms) 7: [ RUN ] NbnxmSetupTest.cannotCreateKernelSetupCPU4XM 7: [ OK ] NbnxmSetupTest.cannotCreateKernelSetupCPU4XM (0 ms) 7: [ RUN ] NbnxmSetupTest.CanCreateNbnxmCPU 7: [ OK ] NbnxmSetupTest.CanCreateNbnxmCPU (0 ms) 7: [----------] 15 tests from NbnxmSetupTest (0 ms total) 7: 7: [----------] 1 test from VirialsTest 7: [ RUN ] VirialsTest.computeVirialTensorWorks 7: [ OK ] VirialsTest.computeVirialTensorWorks (0 ms) 7: [----------] 1 test from VirialsTest (0 ms total) 7: 7: [----------] Global test environment tear-down 7: [==========] 57 tests from 3 test suites ran. (2 ms total) 7: [ PASSED ] 57 tests. 7/90 Test #7: NbLibSetupTests ........................... Passed 0.14 sec test 8 Start 8: NbLibTprTests 8: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/nblib-tpr-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/NbLibTprTests.xml" 8: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests 8: Test timeout computed to be: 30 8: [==========] Running 4 tests from 1 test suite. 8: [----------] Global test environment set-up. 8: [----------] 4 tests from TprReaderTest 8: [ RUN ] TprReaderTest.SimDBTprIsCreated 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 8: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 8: that with the Verlet scheme, nstlist has no effect on the accuracy of 8: your simulation. 8: 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Number of degrees of freedom in T-Coupling group System is 33.00 8: 8: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 8: NVE simulation: will use the initial temperature of 68.810 K for 8: determining the Verlet buffer size 8: 8: 8: There were 3 NOTEs 8: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 8: Generated 1 of the 1 non-bonded parameter combinations 8: 8: Excluding 1 bonded neighbours molecule type 'Argon' 8: 8: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.SimDBTprIsCreated (30 ms) 8: [ RUN ] TprReaderTest.Spc2Reads 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 8: that with the Verlet scheme, nstlist has no effect on the accuracy of 8: your simulation. 8: 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Generating 1-4 interactions: fudge = 0.5 8: Number of degrees of freedom in T-Coupling group System is 9.00 8: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 8: 8: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: NVE simulation: will use the initial temperature of 2573.591 K for 8: determining the Verlet buffer size 8: 8: 8: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: You are using a plain Coulomb cut-off, which might produce artifacts. 8: You might want to consider using PME electrostatics. 8: 8: 8: 8: There were 4 NOTEs 8: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 8: Generated 3 of the 3 non-bonded parameter combinations 8: 8: Generated 3 of the 3 1-4 parameter combinations 8: 8: Excluding 2 bonded neighbours molecule type 'SOL' 8: 8: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.Spc2Reads (15 ms) 8: [ RUN ] TprReaderTest.ArgonImportedDataIsCorrect 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 8: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 8: that with the Verlet scheme, nstlist has no effect on the accuracy of 8: your simulation. 8: 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Number of degrees of freedom in T-Coupling group System is 33.00 8: 8: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 8: NVE simulation: will use the initial temperature of 68.810 K for 8: determining the Verlet buffer size 8: 8: 8: There were 3 NOTEs 8: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 8: Generated 1 of the 1 non-bonded parameter combinations 8: 8: Excluding 1 bonded neighbours molecule type 'Argon' 8: 8: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.ArgonImportedDataIsCorrect (12 ms) 8: [ RUN ] TprReaderTest.FCfromTprDataWorks 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 8: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 8: that with the Verlet scheme, nstlist has no effect on the accuracy of 8: your simulation. 8: 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Number of degrees of freedom in T-Coupling group System is 33.00 8: 8: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 8: NVE simulation: will use the initial temperature of 68.810 K for 8: determining the Verlet buffer size 8: 8: 8: There were 3 NOTEs 8: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 8: Generated 1 of the 1 non-bonded parameter combinations 8: 8: Excluding 1 bonded neighbours molecule type 'Argon' 8: 8: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.FCfromTprDataWorks (15 ms) 8: [----------] 4 tests from TprReaderTest (75 ms total) 8: 8: [----------] Global test environment tear-down 8: [==========] 4 tests from 1 test suite ran. (209 ms total) 8: [ PASSED ] 4 tests. 8/90 Test #8: NbLibTprTests ............................. Passed 0.24 sec test 9 Start 9: NbLibIntegrationTests 9: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/nblib-integration-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/NbLibIntegrationTests.xml" 9: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests 9: Test timeout computed to be: 600 9: [==========] Running 20 tests from 1 test suite. 9: [----------] Global test environment set-up. 9: [----------] 20 tests from NBlibTest 9: [ RUN ] NBlibTest.GmxForceCalculatorCanCompute 9: [ OK ] NBlibTest.GmxForceCalculatorCanCompute (1 ms) 9: [ RUN ] NBlibTest.ArgonVirialsAreCorrect 9: [ OK ] NBlibTest.ArgonVirialsAreCorrect (0 ms) 9: [ RUN ] NBlibTest.ArgonEnergiesAreCorrect 9: [ OK ] NBlibTest.ArgonEnergiesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.SpcMethanolEnergiesAreCorrect 9: [ OK ] NBlibTest.SpcMethanolEnergiesAreCorrect (1 ms) 9: [ RUN ] NBlibTest.SpcMethanolForcesAreCorrect 9: [ OK ] NBlibTest.SpcMethanolForcesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.ExpectedNumberOfForces 9: [ OK ] NBlibTest.ExpectedNumberOfForces (0 ms) 9: [ RUN ] NBlibTest.CanIntegrateSystem 9: [ OK ] NBlibTest.CanIntegrateSystem (0 ms) 9: [ RUN ] NBlibTest.UpdateChangesForces 9: [ OK ] NBlibTest.UpdateChangesForces (0 ms) 9: [ RUN ] NBlibTest.ArgonOplsaForcesAreCorrect 9: [ OK ] NBlibTest.ArgonOplsaForcesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.ArgonGromos43A1ForcesAreCorrect 9: [ OK ] NBlibTest.ArgonGromos43A1ForcesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.CanConstructSimulationState 9: [ OK ] NBlibTest.CanConstructSimulationState (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateNAN 9: [ OK ] NBlibTest.SimulationStateThrowsCoordinateNAN (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateINF 9: [ OK ] NBlibTest.SimulationStateThrowsCoordinateINF (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsVelocityNAN 9: [ OK ] NBlibTest.SimulationStateThrowsVelocityNAN (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsVelocityINF 9: [ OK ] NBlibTest.SimulationStateThrowsVelocityINF (0 ms) 9: [ RUN ] NBlibTest.SimulationStateCanMove 9: [ OK ] NBlibTest.SimulationStateCanMove (0 ms) 9: [ RUN ] NBlibTest.SimulationStateCanAssign 9: [ OK ] NBlibTest.SimulationStateCanAssign (0 ms) 9: [ RUN ] NBlibTest.SimulationStateHasBox 9: [ OK ] NBlibTest.SimulationStateHasBox (0 ms) 9: [ RUN ] NBlibTest.SimulationStateHasCorrectCoordinates 9: [ OK ] NBlibTest.SimulationStateHasCorrectCoordinates (0 ms) 9: [ RUN ] NBlibTest.SimulationStateHasCorrectVelocities 9: [ OK ] NBlibTest.SimulationStateHasCorrectVelocities (0 ms) 9: [----------] 20 tests from NBlibTest (8 ms total) 9: 9: [----------] Global test environment tear-down 9: [==========] 20 tests from 1 test suite ran. (8 ms total) 9: [ PASSED ] 20 tests. 9/90 Test #9: NbLibIntegrationTests ..................... Passed 0.03 sec test 10 Start 10: NbLibIntegratorTests 10: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/nblib-integrator-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/NbLibIntegratorTests.xml" 10: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/api/nblib/tests 10: Test timeout computed to be: 600 10: [==========] Running 1 test from 1 test suite. 10: [----------] Global test environment set-up. 10: [----------] 1 test from NBlibTest 10: [ RUN ] NBlibTest.IntegratorWorks 10: [ OK ] NBlibTest.IntegratorWorks (0 ms) 10: [----------] 1 test from NBlibTest (0 ms total) 10: 10: [----------] Global test environment tear-down 10: [==========] 1 test from 1 test suite ran. (0 ms total) 10: [ PASSED ] 1 test. 10/90 Test #10: NbLibIntegratorTests ...................... Passed 0.02 sec test 11 Start 11: TestUtilsUnitTests 11: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/testutils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/TestUtilsUnitTests.xml" 11: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/testutils/tests 11: Test timeout computed to be: 30 11: [==========] Running 75 tests from 7 test suites. 11: [----------] Global test environment set-up. 11: [----------] 10 tests from InteractiveTestHelperTest 11: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession 11: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (0 ms) 11: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline 11: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (0 ms) 11: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput 11: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput 11: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput 11: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput 11: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (1 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput 11: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput 11: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (2 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput 11: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput 11: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (0 ms) 11: [----------] 10 tests from InteractiveTestHelperTest (7 ms total) 11: 11: [----------] 10 tests from NameOfTestFromTupleTest 11: [ RUN ] NameOfTestFromTupleTest.WorksWithEmptyTuple 11: [ OK ] NameOfTestFromTupleTest.WorksWithEmptyTuple (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFunction 11: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFunction (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFunctionOfEnumVariable 11: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFunctionOfEnumVariable (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.RejectsNullptrFormatFunction 11: [ OK ] NameOfTestFromTupleTest.RejectsNullptrFormatFunction (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatLambda 11: [ OK ] NameOfTestFromTupleTest.WorksWithFormatLambda (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.WorksWithUseStringFormat 11: [ OK ] NameOfTestFromTupleTest.WorksWithUseStringFormat (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.WorksWithPrefixFormatter 11: [ OK ] NameOfTestFromTupleTest.WorksWithPrefixFormatter (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFunctor 11: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFunctor (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFromEnumerationArray 11: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFromEnumerationArray (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.WorksWithMixtureOfFormatters 11: [ OK ] NameOfTestFromTupleTest.WorksWithMixtureOfFormatters (0 ms) 11: [----------] 10 tests from NameOfTestFromTupleTest (0 ms total) 11: 11: [----------] 3 tests from RefDataFilenameMakerTest 11: [ RUN ] RefDataFilenameMakerTest.WorksWithFormatFunction 11: [ OK ] RefDataFilenameMakerTest.WorksWithFormatFunction (0 ms) 11: [ RUN ] RefDataFilenameMakerTest.WorksWithMixtureOfFormatters 11: [ OK ] RefDataFilenameMakerTest.WorksWithMixtureOfFormatters (0 ms) 11: [ RUN ] RefDataFilenameMakerTest.WorksWithToEmpty 11: [ OK ] RefDataFilenameMakerTest.WorksWithToEmpty (0 ms) 11: [----------] 3 tests from RefDataFilenameMakerTest (0 ms total) 11: 11: [----------] 37 tests from ReferenceDataTest 11: [ RUN ] ReferenceDataTest.HandlesSimpleData 11: [ OK ] ReferenceDataTest.HandlesSimpleData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesFloatingPointData 11: [ OK ] ReferenceDataTest.HandlesFloatingPointData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesPresenceChecks 11: [ OK ] ReferenceDataTest.HandlesPresenceChecks (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesStringBlockData 11: [ OK ] ReferenceDataTest.HandlesStringBlockData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesVectorData 11: [ OK ] ReferenceDataTest.HandlesVectorData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesSequenceData 11: [ OK ] ReferenceDataTest.HandlesSequenceData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData 11: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (0 ms) 11: [ RUN ] ReferenceDataTest.CheckSequenceArrayRef 11: [ OK ] ReferenceDataTest.CheckSequenceArrayRef (0 ms) 11: [ RUN ] ReferenceDataTest.CheckSequenceArrayRefHandlesIncorrectData 11: [ OK ] ReferenceDataTest.CheckSequenceArrayRefHandlesIncorrectData (0 ms) 11: [ RUN ] ReferenceDataTest.CheckSequenceArrayRefHandlesSequenceOfCustomData 11: [ OK ] ReferenceDataTest.CheckSequenceArrayRefHandlesSequenceOfCustomData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesIncorrectData 11: [ OK ] ReferenceDataTest.HandlesIncorrectData (2 ms) 11: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType 11: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesMissingData 11: [ OK ] ReferenceDataTest.HandlesMissingData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUncheckedData 11: [ OK ] ReferenceDataTest.HandlesUncheckedData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence 11: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound 11: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesAnys 11: [ OK ] ReferenceDataTest.HandlesAnys (1 ms) 11: [ RUN ] ReferenceDataTest.HandlesKeyValueTree 11: [ OK ] ReferenceDataTest.HandlesKeyValueTree (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey 11: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey 11: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectValue 11: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectValue (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectType 11: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectType (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile 11: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings 11: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace 11: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesEmptyStrings 11: [ OK ] ReferenceDataTest.HandlesEmptyStrings (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock 11: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices 11: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData 11: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds 11: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds 11: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesReadingValues 11: [ OK ] ReferenceDataTest.HandlesReadingValues (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges 11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges 11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges 11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges 11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries 11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (0 ms) 11: [----------] 37 tests from ReferenceDataTest (12 ms total) 11: 11: [----------] 7 tests from FloatingPointDifferenceTest 11: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues 11: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues 11: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign 11: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero 11: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences 11: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero 11: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesNaN 11: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms) 11: [----------] 7 tests from FloatingPointDifferenceTest (0 ms total) 11: 11: [----------] 4 tests from FloatingPointToleranceTest 11: [ RUN ] FloatingPointToleranceTest.UlpTolerance 11: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms) 11: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint 11: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms) 11: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp 11: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms) 11: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance 11: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms) 11: [----------] 4 tests from FloatingPointToleranceTest (0 ms total) 11: 11: [----------] 4 tests from XvgTests 11: [ RUN ] XvgTests.CreateFile 11: [ OK ] XvgTests.CreateFile (0 ms) 11: [ RUN ] XvgTests.CheckMissing 11: [ OK ] XvgTests.CheckMissing (0 ms) 11: [ RUN ] XvgTests.CheckExtra 11: [ OK ] XvgTests.CheckExtra (0 ms) 11: [ RUN ] XvgTests.ReadIncorrect 11: [ OK ] XvgTests.ReadIncorrect (0 ms) 11: [----------] 4 tests from XvgTests (1 ms total) 11: 11: [----------] Global test environment tear-down 11: [==========] 75 tests from 7 test suites ran. (21 ms total) 11: [ PASSED ] 75 tests. 11/90 Test #11: TestUtilsUnitTests ........................ Passed 0.05 sec test 12 Start 12: TestUtilsMpiUnitTests 12: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/testutils-mpi-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/TestUtilsMpiUnitTests.xml" 12: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/testutils/tests 12: Test timeout computed to be: 30 12: [==========] Running 1 test from 1 test suite. 12: [----------] Global test environment set-up. 12: [----------] 1 test from MpiSelfTest 12: [ RUN ] MpiSelfTest.Runs 12: [ OK ] MpiSelfTest.Runs (3 ms) 12: [----------] 1 test from MpiSelfTest (3 ms total) 12: 12: [----------] Global test environment tear-down 12: [==========] 1 test from 1 test suite ran. (3 ms total) 12: [ PASSED ] 1 test. 12/90 Test #12: TestUtilsMpiUnitTests ..................... Passed 0.03 sec test 13 Start 13: UtilityUnitTests 13: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/utility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/UtilityUnitTests.xml" 13: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests 13: Test timeout computed to be: 30 13: [==========] Running 420 tests from 65 test suites. 13: [----------] Global test environment set-up. 13: [----------] 6 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 13: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/0.Move 13: [ OK ] AllocatorTest/0.Move (0 ms) 13: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms) 13: [ RUN ] AllocatorTest/0.Comparison 13: [ OK ] AllocatorTest/0.Comparison (0 ms) 13: [----------] 6 tests from AllocatorTest/0 (0 ms total) 13: 13: [----------] 6 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 13: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/1.Move 13: [ OK ] AllocatorTest/1.Move (0 ms) 13: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms) 13: [ RUN ] AllocatorTest/1.Comparison 13: [ OK ] AllocatorTest/1.Comparison (0 ms) 13: [----------] 6 tests from AllocatorTest/1 (0 ms total) 13: 13: [----------] 6 tests from AllocatorTest/2, where TypeParam = gmx::Allocator 13: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/2.Move 13: [ OK ] AllocatorTest/2.Move (0 ms) 13: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms) 13: [ RUN ] AllocatorTest/2.Comparison 13: [ OK ] AllocatorTest/2.Comparison (0 ms) 13: [----------] 6 tests from AllocatorTest/2 (0 ms total) 13: 13: [----------] 6 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 13: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/3.Move 13: [ OK ] AllocatorTest/3.Move (0 ms) 13: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms) 13: [ RUN ] AllocatorTest/3.Comparison 13: [ OK ] AllocatorTest/3.Comparison (0 ms) 13: [----------] 6 tests from AllocatorTest/3 (0 ms total) 13: 13: [----------] 6 tests from AllocatorTest/4, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 13: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/4.Move 13: [ OK ] AllocatorTest/4.Move (0 ms) 13: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms) 13: [ RUN ] AllocatorTest/4.Comparison 13: [ OK ] AllocatorTest/4.Comparison (0 ms) 13: [----------] 6 tests from AllocatorTest/4 (0 ms total) 13: 13: [----------] 6 tests from AllocatorTest/5, where TypeParam = gmx::Allocator, gmx::PageAlignedAllocationPolicy> 13: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/5.Move 13: [ OK ] AllocatorTest/5.Move (0 ms) 13: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms) 13: [ RUN ] AllocatorTest/5.Comparison 13: [ OK ] AllocatorTest/5.Comparison (0 ms) 13: [----------] 6 tests from AllocatorTest/5 (0 ms total) 13: 13: [----------] 1 test from AllocatorUntypedTest 13: [ RUN ] AllocatorUntypedTest.Comparison 13: [ OK ] AllocatorUntypedTest.Comparison (0 ms) 13: [----------] 1 test from AllocatorUntypedTest (0 ms total) 13: 13: [----------] 4 tests from EmptyArrayRefTest 13: [ RUN ] EmptyArrayRefTest.IsEmpty 13: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 13: [ RUN ] EmptyArrayRefTest.ConstructFromNullptrIsEmpty 13: [ OK ] EmptyArrayRefTest.ConstructFromNullptrIsEmpty (0 ms) 13: [ RUN ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForNullptr 13: [ OK ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForNullptr (0 ms) 13: [ RUN ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForSizeNull 13: [ OK ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForSizeNull (0 ms) 13: [----------] 4 tests from EmptyArrayRefTest (0 ms total) 13: 13: [----------] 1 test from EmptyConstArrayRefTest 13: [ RUN ] EmptyConstArrayRefTest.IsEmpty 13: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms) 13: [----------] 1 test from EmptyConstArrayRefTest (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/0 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/1 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/2 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/3 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/4 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/5 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/6 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/7 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/8 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/9 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/10 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/11 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/12 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/13 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/14 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/15 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/16 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/17 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/18 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/19 (0 ms total) 13: 13: [----------] 8 tests from BoolType 13: [ RUN ] BoolType.ImplicitConversion 13: [ OK ] BoolType.ImplicitConversion (0 ms) 13: [ RUN ] BoolType.FalseByDefault 13: [ OK ] BoolType.FalseByDefault (0 ms) 13: [ RUN ] BoolType.Assignment 13: [ OK ] BoolType.Assignment (0 ms) 13: [ RUN ] BoolType.Copy 13: [ OK ] BoolType.Copy (0 ms) 13: [ RUN ] BoolType.ArrayRefCanBeCreated 13: [ OK ] BoolType.ArrayRefCanBeCreated (0 ms) 13: [ RUN ] BoolType.CanBeCastToBool 13: [ OK ] BoolType.CanBeCastToBool (0 ms) 13: [ RUN ] BoolType.HasSizeOfBool 13: [ OK ] BoolType.HasSizeOfBool (0 ms) 13: [ RUN ] BoolType.HasAlignmentOfBool 13: [ OK ] BoolType.HasAlignmentOfBool (0 ms) 13: [----------] 8 tests from BoolType (0 ms total) 13: 13: [----------] 4 tests from ArrayRefFromBoolTypeVector 13: [ RUN ] ArrayRefFromBoolTypeVector.CanConstructEmpty 13: [ OK ] ArrayRefFromBoolTypeVector.CanConstructEmpty (0 ms) 13: [ RUN ] ArrayRefFromBoolTypeVector.Works 13: [ OK ] ArrayRefFromBoolTypeVector.Works (0 ms) 13: [ RUN ] ArrayRefFromBoolTypeVector.CanConstructConstEmpty 13: [ OK ] ArrayRefFromBoolTypeVector.CanConstructConstEmpty (0 ms) 13: [ RUN ] ArrayRefFromBoolTypeVector.ConstWorks 13: [ OK ] ArrayRefFromBoolTypeVector.ConstWorks (0 ms) 13: [----------] 4 tests from ArrayRefFromBoolTypeVector (0 ms total) 13: 13: [----------] 7 tests from CStringUtilityTest 13: [ RUN ] CStringUtilityTest.CaseInsensitiveComparison 13: [ OK ] CStringUtilityTest.CaseInsensitiveComparison (0 ms) 13: [ RUN ] CStringUtilityTest.CaseInsensitiveComparisonInLength 13: [ OK ] CStringUtilityTest.CaseInsensitiveComparisonInLength (0 ms) 13: [ RUN ] CStringUtilityTest.strip_comment 13: [ OK ] CStringUtilityTest.strip_comment (0 ms) 13: [ RUN ] CStringUtilityTest.upstring 13: [ OK ] CStringUtilityTest.upstring (0 ms) 13: [ RUN ] CStringUtilityTest.ltrim 13: [ OK ] CStringUtilityTest.ltrim (0 ms) 13: [ RUN ] CStringUtilityTest.rtrim 13: [ OK ] CStringUtilityTest.rtrim (0 ms) 13: [ RUN ] CStringUtilityTest.trim 13: [ OK ] CStringUtilityTest.trim (0 ms) 13: [----------] 7 tests from CStringUtilityTest (0 ms total) 13: 13: [----------] 2 tests from DefaultInitializationAllocator 13: [ RUN ] DefaultInitializationAllocator.PerformsValueInitialization 13: [ OK ] DefaultInitializationAllocator.PerformsValueInitialization (0 ms) 13: [ RUN ] DefaultInitializationAllocator.PerformsNoInitialization 13: [ OK ] DefaultInitializationAllocator.PerformsNoInitialization (0 ms) 13: [----------] 2 tests from DefaultInitializationAllocator (0 ms total) 13: 13: [----------] 4 tests from EnumerationHelpersTest 13: [ RUN ] EnumerationHelpersTest.EnumerationWrapperWorks 13: [ OK ] EnumerationHelpersTest.EnumerationWrapperWorks (0 ms) 13: [ RUN ] EnumerationHelpersTest.EnumerationArrayWorks 13: [ OK ] EnumerationHelpersTest.EnumerationArrayWorks (0 ms) 13: [ RUN ] EnumerationHelpersTest.EnumerationArrayCountIsSafe 13: [ OK ] EnumerationHelpersTest.EnumerationArrayCountIsSafe (0 ms) 13: [ RUN ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks 13: [ OK ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks (0 ms) 13: [----------] 4 tests from EnumerationHelpersTest (0 ms total) 13: 13: [----------] 1 test from EnumClassSuitsEnumerationArray 13: [ RUN ] EnumClassSuitsEnumerationArray.Works 13: [ OK ] EnumClassSuitsEnumerationArray.Works (0 ms) 13: [----------] 1 test from EnumClassSuitsEnumerationArray (0 ms total) 13: 13: [----------] 18 tests from FixedCapacityVectorTest 13: [ RUN ] FixedCapacityVectorTest.IsEmpty 13: [ OK ] FixedCapacityVectorTest.IsEmpty (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ConstructorWorks 13: [ OK ] FixedCapacityVectorTest.ConstructorWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.PushWorks 13: [ OK ] FixedCapacityVectorTest.PushWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.PopWorks 13: [ OK ] FixedCapacityVectorTest.PopWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ResizeWorks 13: [ OK ] FixedCapacityVectorTest.ResizeWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ClearWorks 13: [ OK ] FixedCapacityVectorTest.ClearWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.EmplaceBackWorks 13: [ OK ] FixedCapacityVectorTest.EmplaceBackWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.AtThrows 13: [ OK ] FixedCapacityVectorTest.AtThrows (0 ms) 13: [ RUN ] FixedCapacityVectorTest.IteratorWorks 13: [ OK ] FixedCapacityVectorTest.IteratorWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ReverseIteratorWorks 13: [ OK ] FixedCapacityVectorTest.ReverseIteratorWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ZeroCapacityWorks 13: [ OK ] FixedCapacityVectorTest.ZeroCapacityWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.CopyConstructorWorks 13: [ OK ] FixedCapacityVectorTest.CopyConstructorWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.CopyAssignmentWorks 13: [ OK ] FixedCapacityVectorTest.CopyAssignmentWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.MoveConstructorWorks 13: [ OK ] FixedCapacityVectorTest.MoveConstructorWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.MoveAssignmentWorks 13: [ OK ] FixedCapacityVectorTest.MoveAssignmentWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ElementAssignmentWorks 13: [ OK ] FixedCapacityVectorTest.ElementAssignmentWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.DataWorks 13: [ OK ] FixedCapacityVectorTest.DataWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ConstMethodsWork 13: [ OK ] FixedCapacityVectorTest.ConstMethodsWork (0 ms) 13: [----------] 18 tests from FixedCapacityVectorTest (0 ms total) 13: 13: [----------] 5 tests from InMemorySerializerTest 13: [ RUN ] InMemorySerializerTest.Roundtrip 13: [ OK ] InMemorySerializerTest.Roundtrip (0 ms) 13: [ RUN ] InMemorySerializerTest.RoundtripWithEndianessSwap 13: [ OK ] InMemorySerializerTest.RoundtripWithEndianessSwap (0 ms) 13: [ RUN ] InMemorySerializerTest.SerializerExplicitEndianessSwap 13: [ OK ] InMemorySerializerTest.SerializerExplicitEndianessSwap (0 ms) 13: [ RUN ] InMemorySerializerTest.DeserializerExplicitEndianessSwap 13: [ OK ] InMemorySerializerTest.DeserializerExplicitEndianessSwap (0 ms) 13: [ RUN ] InMemorySerializerTest.SizeIsCorrect 13: [ OK ] InMemorySerializerTest.SizeIsCorrect (0 ms) 13: [----------] 5 tests from InMemorySerializerTest (0 ms total) 13: 13: [----------] 4 tests from KeyValueTreeSerializerTest 13: [ RUN ] KeyValueTreeSerializerTest.EmptyTree 13: [ OK ] KeyValueTreeSerializerTest.EmptyTree (0 ms) 13: [ RUN ] KeyValueTreeSerializerTest.SimpleObject 13: [ OK ] KeyValueTreeSerializerTest.SimpleObject (0 ms) 13: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays 13: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (0 ms) 13: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects 13: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (0 ms) 13: [----------] 4 tests from KeyValueTreeSerializerTest (0 ms total) 13: 13: [----------] 7 tests from TreeValueTransformTest 13: [ RUN ] TreeValueTransformTest.SimpleTransforms 13: [ OK ] TreeValueTransformTest.SimpleTransforms (0 ms) 13: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive 13: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (4 ms) 13: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject 13: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (0 ms) 13: [ RUN ] TreeValueTransformTest.ObjectFromString 13: [ OK ] TreeValueTransformTest.ObjectFromString (0 ms) 13: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings 13: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (0 ms) 13: [ RUN ] TreeValueTransformTest.ScopedTransformRules 13: [ OK ] TreeValueTransformTest.ScopedTransformRules (0 ms) 13: [ RUN ] TreeValueTransformTest.CanAssignUserMultiValue 13: [ OK ] TreeValueTransformTest.CanAssignUserMultiValue (0 ms) 13: [----------] 7 tests from TreeValueTransformTest (5 ms total) 13: 13: [----------] 1 test from TreeValueTransformErrorTest 13: [ RUN ] TreeValueTransformErrorTest.ConversionError 13: [ OK ] TreeValueTransformErrorTest.ConversionError (0 ms) 13: [----------] 1 test from TreeValueTransformErrorTest (0 ms total) 13: 13: [----------] 9 tests from ListOfLists 13: [ RUN ] ListOfLists.EmptyListOfListsWorks 13: [ OK ] ListOfLists.EmptyListOfListsWorks (0 ms) 13: [ RUN ] ListOfLists.AppendWorks 13: [ OK ] ListOfLists.AppendWorks (0 ms) 13: [ RUN ] ListOfLists.EmptyListWorks 13: [ OK ] ListOfLists.EmptyListWorks (0 ms) 13: [ RUN ] ListOfLists.AppendAccessWorks 13: [ OK ] ListOfLists.AppendAccessWorks (0 ms) 13: [ RUN ] ListOfLists.ClearWorks 13: [ OK ] ListOfLists.ClearWorks (0 ms) 13: [ RUN ] ListOfLists.OutOfRangeAccessThrows 13: [ OK ] ListOfLists.OutOfRangeAccessThrows (0 ms) 13: [ RUN ] ListOfLists.FrontAndBackWork 13: [ OK ] ListOfLists.FrontAndBackWork (0 ms) 13: [ RUN ] ListOfLists.ExtractsAndRestores 13: [ OK ] ListOfLists.ExtractsAndRestores (0 ms) 13: [ RUN ] ListOfLists.AppendsListOfListsWithOffset 13: [ OK ] ListOfLists.AppendsListOfListsWithOffset (0 ms) 13: [----------] 9 tests from ListOfLists (0 ms total) 13: 13: [----------] 7 tests from LoggerTest 13: [ RUN ] LoggerTest.EmptyLoggerWorks 13: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms) 13: [ RUN ] LoggerTest.LogsToStream 13: [ OK ] LoggerTest.LogsToStream (0 ms) 13: [ RUN ] LoggerTest.LogsToFile 13: [ OK ] LoggerTest.LogsToFile (0 ms) 13: [ RUN ] LoggerTest.LevelFilteringWorks 13: [ OK ] LoggerTest.LevelFilteringWorks (0 ms) 13: [ RUN ] LoggerTest.LogsToMultipleStreams 13: [ OK ] LoggerTest.LogsToMultipleStreams (0 ms) 13: [ RUN ] LoggerTest.LogsToMultipleFiles 13: [ OK ] LoggerTest.LogsToMultipleFiles (0 ms) 13: [ RUN ] LoggerTest.LogsToStreamAndFile 13: [ OK ] LoggerTest.LogsToStreamAndFile (0 ms) 13: [----------] 7 tests from LoggerTest (1 ms total) 13: 13: [----------] 7 tests from MessageStringCollectorTest 13: [ RUN ] MessageStringCollectorTest.CanAddAndClearMessagesNoContext 13: [ OK ] MessageStringCollectorTest.CanAddAndClearMessagesNoContext (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanAddAndClearMessagesWithContext 13: [ OK ] MessageStringCollectorTest.CanAddAndClearMessagesWithContext (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanAddStringMessages 13: [ OK ] MessageStringCollectorTest.CanAddStringMessages (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanAddCharMessagesConditionally 13: [ OK ] MessageStringCollectorTest.CanAddCharMessagesConditionally (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanAddStringMessagesConditionally 13: [ OK ] MessageStringCollectorTest.CanAddStringMessagesConditionally (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanMoveConstruct 13: [ OK ] MessageStringCollectorTest.CanMoveConstruct (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanMoveAssign 13: [ OK ] MessageStringCollectorTest.CanMoveAssign (0 ms) 13: [----------] 7 tests from MessageStringCollectorTest (0 ms total) 13: 13: [----------] 1 test from PathTest 13: [ RUN ] PathTest.StripSourcePrefixWorks 13: [ OK ] PathTest.StripSourcePrefixWorks (0 ms) 13: [----------] 1 test from PathTest (0 ms total) 13: 13: [----------] 2 tests from PhysicalNodeCommunicatorTest 13: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 13: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms) 13: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 13: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) 13: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total) 13: 13: [----------] 5 tests from Range 13: [ RUN ] Range.EmptyRangeWorks 13: [ OK ] Range.EmptyRangeWorks (0 ms) 13: [ RUN ] Range.NonEmptyRangeWorks 13: [ OK ] Range.NonEmptyRangeWorks (0 ms) 13: [ RUN ] Range.BeginEnd 13: [ OK ] Range.BeginEnd (0 ms) 13: [ RUN ] Range.IsInRangeWorks 13: [ OK ] Range.IsInRangeWorks (0 ms) 13: [ RUN ] Range.IteratorWorks 13: [ OK ] Range.IteratorWorks (0 ms) 13: [----------] 5 tests from Range (0 ms total) 13: 13: [----------] 3 tests from ScopeGuardTest 13: [ RUN ] ScopeGuardTest.ScopeGuardExecutesCallbackOnExit 13: [ OK ] ScopeGuardTest.ScopeGuardExecutesCallbackOnExit (0 ms) 13: [ RUN ] ScopeGuardTest.ScopeGuardCanFreePointers 13: [ OK ] ScopeGuardTest.ScopeGuardCanFreePointers (0 ms) 13: [ RUN ] ScopeGuardTest.ScopeGuardsCanBeCreatedByHelperFunctions 13: [ OK ] ScopeGuardTest.ScopeGuardsCanBeCreatedByHelperFunctions (0 ms) 13: [----------] 3 tests from ScopeGuardTest (0 ms total) 13: 13: [----------] 7 tests from StringConvert 13: [ RUN ] StringConvert.NoResultFromEptyString 13: [ OK ] StringConvert.NoResultFromEptyString (0 ms) 13: [ RUN ] StringConvert.ThreeFloatsSuccessfully 13: [ OK ] StringConvert.ThreeFloatsSuccessfully (0 ms) 13: [ RUN ] StringConvert.OneIntSucessfully 13: [ OK ] StringConvert.OneIntSucessfully (0 ms) 13: [ RUN ] StringConvert.FloatAsStringToIntArrayThrows 13: [ OK ] StringConvert.FloatAsStringToIntArrayThrows (0 ms) 13: [ RUN ] StringConvert.ThrowsWhenWrongSize 13: [ OK ] StringConvert.ThrowsWhenWrongSize (0 ms) 13: [ RUN ] StringConvert.StringIdentityTransformWithArrayThrows 13: [ OK ] StringConvert.StringIdentityTransformWithArrayThrows (0 ms) 13: [ RUN ] StringConvert.StringIdentityTransformWithArrayOkay 13: [ OK ] StringConvert.StringIdentityTransformWithArrayOkay (0 ms) 13: [----------] 7 tests from StringConvert (0 ms total) 13: 13: [----------] 7 tests from StringToEnumValueConverterTest 13: [ RUN ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithoutStripping 13: [ OK ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithoutStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithoutStripping 13: [ OK ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithoutStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithoutStripping 13: [ OK ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithoutStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithStripping 13: [ OK ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithStripping 13: [ OK ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithStripping 13: [ OK ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.CustomConverterWorks 13: [ OK ] StringToEnumValueConverterTest.CustomConverterWorks (0 ms) 13: [----------] 7 tests from StringToEnumValueConverterTest (0 ms total) 13: 13: [----------] 9 tests from StringUtilityTest 13: [ RUN ] StringUtilityTest.StartsWith 13: [ OK ] StringUtilityTest.StartsWith (0 ms) 13: [ RUN ] StringUtilityTest.EndsWith 13: [ OK ] StringUtilityTest.EndsWith (0 ms) 13: [ RUN ] StringUtilityTest.StripSuffixIfPresent 13: [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms) 13: [ RUN ] StringUtilityTest.StripString 13: [ OK ] StringUtilityTest.StripString (0 ms) 13: [ RUN ] StringUtilityTest.SplitString 13: [ OK ] StringUtilityTest.SplitString (0 ms) 13: [ RUN ] StringUtilityTest.SplitDelimitedString 13: [ OK ] StringUtilityTest.SplitDelimitedString (0 ms) 13: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString 13: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (0 ms) 13: [ RUN ] StringUtilityTest.CanCompareCaseInsensitive 13: [ OK ] StringUtilityTest.CanCompareCaseInsensitive (0 ms) 13: [ RUN ] StringUtilityTest.CanCompareCaseInsensitiveInLength 13: [ OK ] StringUtilityTest.CanCompareCaseInsensitiveInLength (0 ms) 13: [----------] 9 tests from StringUtilityTest (0 ms total) 13: 13: [----------] 2 tests from FormatStringTest 13: [ RUN ] FormatStringTest.HandlesBasicFormatting 13: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms) 13: [ RUN ] FormatStringTest.HandlesLongStrings 13: [ OK ] FormatStringTest.HandlesLongStrings (0 ms) 13: [----------] 2 tests from FormatStringTest (0 ms total) 13: 13: [----------] 1 test from StringFormatterTest 13: [ RUN ] StringFormatterTest.HandlesBasicFormatting 13: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms) 13: [----------] 1 test from StringFormatterTest (0 ms total) 13: 13: [----------] 1 test from formatAndJoinTest 13: [ RUN ] formatAndJoinTest.Works 13: [ OK ] formatAndJoinTest.Works (0 ms) 13: [----------] 1 test from formatAndJoinTest (0 ms total) 13: 13: [----------] 1 test from JoinStringsTest 13: [ RUN ] JoinStringsTest.Works 13: [ OK ] JoinStringsTest.Works (0 ms) 13: [----------] 1 test from JoinStringsTest (0 ms total) 13: 13: [----------] 6 tests from ReplaceAllTest 13: [ RUN ] ReplaceAllTest.HandlesEmptyStrings 13: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms) 13: [ RUN ] ReplaceAllTest.HandlesNoMatches 13: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms) 13: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds 13: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms) 13: [ RUN ] ReplaceAllTest.HandlesMultipleMatches 13: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms) 13: [ RUN ] ReplaceAllTest.HandlesWordBoundaries 13: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms) 13: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches 13: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms) 13: [----------] 6 tests from ReplaceAllTest (0 ms total) 13: 13: [----------] 10 tests from TextLineWrapperTest 13: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings 13: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace 13: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines 13: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms) 13: [ RUN ] TextLineWrapperTest.WrapsCorrectly 13: [ OK ] TextLineWrapperTest.WrapsCorrectly (0 ms) 13: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks 13: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesIndent 13: [ OK ] TextLineWrapperTest.HandlesIndent (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines 13: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesHangingIndent 13: [ OK ] TextLineWrapperTest.HandlesHangingIndent (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter 13: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (0 ms) 13: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace 13: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (0 ms) 13: [----------] 10 tests from TextLineWrapperTest (1 ms total) 13: 13: [----------] 1 test from CompileTimeStringJoin 13: [ RUN ] CompileTimeStringJoin.Works 13: [ OK ] CompileTimeStringJoin.Works (0 ms) 13: [----------] 1 test from CompileTimeStringJoin (0 ms total) 13: 13: [----------] 3 tests from TemplateMPTest 13: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionEnum 13: [ OK ] TemplateMPTest.DispatchTemplatedFunctionEnum (0 ms) 13: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionBool 13: [ OK ] TemplateMPTest.DispatchTemplatedFunctionBool (0 ms) 13: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionEnumBool 13: [ OK ] TemplateMPTest.DispatchTemplatedFunctionEnumBool (0 ms) 13: [----------] 3 tests from TemplateMPTest (0 ms total) 13: 13: [----------] 6 tests from TextWriterTest 13: [ RUN ] TextWriterTest.WritesLines 13: [ OK ] TextWriterTest.WritesLines (0 ms) 13: [ RUN ] TextWriterTest.WritesLinesInParts 13: [ OK ] TextWriterTest.WritesLinesInParts (0 ms) 13: [ RUN ] TextWriterTest.WritesWrappedLines 13: [ OK ] TextWriterTest.WritesWrappedLines (0 ms) 13: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper 13: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (0 ms) 13: [ RUN ] TextWriterTest.TracksNewlines 13: [ OK ] TextWriterTest.TracksNewlines (0 ms) 13: [ RUN ] TextWriterTest.PreservesTrailingWhitespace 13: [ OK ] TextWriterTest.PreservesTrailingWhitespace (0 ms) 13: [----------] 6 tests from TextWriterTest (0 ms total) 13: 13: [----------] 1 test from TypeTraitsTest 13: [ RUN ] TypeTraitsTest.IsIntegralConstant 13: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms) 13: [----------] 1 test from TypeTraitsTest (0 ms total) 13: 13: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms) 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms) 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms) 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms) 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms) 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms) 13: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (0 ms total) 13: 13: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms) 13: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (0 ms total) 13: 13: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms) 13: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (0 ms total) 13: 13: [----------] 11 tests from WithInputPaths/PathSearchTest 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/0 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/0 (1 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/1 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/1 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/2 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/2 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/3 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/3 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/4 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/4 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/5 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/5 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/6 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/6 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/7 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/7 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/8 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/8 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/9 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/9 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/10 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/10 (0 ms) 13: [----------] 11 tests from WithInputPaths/PathSearchTest (1 ms total) 13: 13: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (0 ms) 13: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (0 ms total) 13: 13: [----------] Global test environment tear-down 13: [==========] 420 tests from 65 test suites ran. (15 ms total) 13: [ PASSED ] 420 tests. 13: 13: YOU HAVE 1 DISABLED TEST 13: 13/90 Test #13: UtilityUnitTests .......................... Passed 0.06 sec test 14 Start 14: UtilityMpiUnitTests 14: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/utility-mpi-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/UtilityMpiUnitTests.xml" 14: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/utility/tests 14: Test timeout computed to be: 30 14: [==========] Running 2 tests from 1 test suite. 14: [----------] Global test environment set-up. 14: [----------] 2 tests from PhysicalNodeCommunicatorTest 14: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 14: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (4 ms) 14: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 14: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) 14: [----------] 2 tests from PhysicalNodeCommunicatorTest (5 ms total) 14: 14: [----------] Global test environment tear-down 14: [==========] 2 tests from 1 test suite ran. (5 ms total) 14: [ PASSED ] 2 tests. 14/90 Test #14: UtilityMpiUnitTests ....................... Passed 0.04 sec test 15 Start 15: GmxlibTests 15: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/nonbonded-fep-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/GmxlibTests.xml" 15: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxlib/nonbonded/tests 15: Test timeout computed to be: 30 15: [==========] Running 78 tests from 2 test suites. 15: [----------] Global test environment set-up. 15: [----------] 72 tests from NBInteraction/NonbondedFepTest 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/0 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/0 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/1 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/1 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/2 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/2 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/3 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/3 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/4 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/4 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/5 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/5 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/6 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/6 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/7 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/7 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/8 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/8 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/9 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/9 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/10 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/10 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/11 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/11 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/12 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/12 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/13 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/13 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/14 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/14 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/15 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/15 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/16 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/16 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/17 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/17 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/18 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/18 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/19 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/19 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/20 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/20 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/21 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/21 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/22 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/22 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/23 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/23 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/24 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/24 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/25 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/25 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/26 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/26 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/27 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/27 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/28 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/28 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/29 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/29 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/30 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/30 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/31 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/31 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/32 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/32 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/33 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/33 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/34 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/34 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/35 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/35 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/36 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/36 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/37 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/37 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/38 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/38 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/39 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/39 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/40 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/40 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/41 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/41 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/42 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/42 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/43 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/43 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/44 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/44 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/45 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/45 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/46 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/46 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/47 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/47 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/48 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/48 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/49 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/49 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/50 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/50 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/51 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/51 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/52 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/52 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/53 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/53 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/54 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/54 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/55 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/55 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/56 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/56 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/57 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/57 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/58 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/58 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/59 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/59 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/60 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/60 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/61 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/61 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/62 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/62 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/63 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/63 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/64 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/64 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/65 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/65 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/66 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/66 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/67 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/67 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/68 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/68 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/69 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/69 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/70 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/70 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/71 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/71 (0 ms) 15: [----------] 72 tests from NBInteraction/NonbondedFepTest (19 ms total) 15: 15: [----------] 6 tests from NBInteractionShortDistance/NonbondedFepTest 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/0 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/0 (0 ms) 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/1 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/1 (0 ms) 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/2 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/2 (0 ms) 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/3 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/3 (0 ms) 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/4 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/4 (0 ms) 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/5 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/5 (0 ms) 15: [----------] 6 tests from NBInteractionShortDistance/NonbondedFepTest (1 ms total) 15: 15: [----------] Global test environment tear-down 15: [==========] 78 tests from 2 test suites ran. (20 ms total) 15: [ PASSED ] 78 tests. 15/90 Test #15: GmxlibTests ............................... Passed 0.06 sec test 16 Start 16: MdlibUnitTest 16: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/mdlib-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/MdlibUnitTest.xml" 16: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests 16: Test timeout computed to be: 30 16: [==========] Running 1032 tests from 27 test suites. 16: [----------] Global test environment set-up. 16: [----------] 3 tests from EffectiveAtomDensity 16: [ RUN ] EffectiveAtomDensity.VolumeIndependence 16: [ OK ] EffectiveAtomDensity.VolumeIndependence (0 ms) 16: [ RUN ] EffectiveAtomDensity.WeightingWorks 16: [ OK ] EffectiveAtomDensity.WeightingWorks (0 ms) 16: [ RUN ] EffectiveAtomDensity.LargeValuesHandledWell 16: [ OK ] EffectiveAtomDensity.LargeValuesHandledWell (0 ms) 16: [----------] 3 tests from EffectiveAtomDensity (0 ms total) 16: 16: [----------] 2 tests from AtomNonbondedAndKineticProperties 16: [ RUN ] AtomNonbondedAndKineticProperties.IsAccurate 16: [ OK ] AtomNonbondedAndKineticProperties.IsAccurate (0 ms) 16: [ RUN ] AtomNonbondedAndKineticProperties.ConstraintsWork 16: [ OK ] AtomNonbondedAndKineticProperties.ConstraintsWork (0 ms) 16: [----------] 2 tests from AtomNonbondedAndKineticProperties (0 ms total) 16: 16: [----------] 1 test from VerletBufferConstraintTest 16: [ RUN ] VerletBufferConstraintTest.EqualMasses 16: [ OK ] VerletBufferConstraintTest.EqualMasses (0 ms) 16: [----------] 1 test from VerletBufferConstraintTest (0 ms total) 16: 16: [----------] 1 test from VerletBufferSize 16: [ RUN ] VerletBufferSize.SizeAboveFourIsEquivalent 16: [ OK ] VerletBufferSize.SizeAboveFourIsEquivalent (0 ms) 16: [----------] 1 test from VerletBufferSize (0 ms total) 16: 16: [----------] 6 tests from CalcvirTest 16: [ RUN ] CalcvirTest.CanCalculateVirialAllAtomsInBox 16: [ OK ] CalcvirTest.CanCalculateVirialAllAtomsInBox (0 ms) 16: [ RUN ] CalcvirTest.CanCalculateVirialAllAtomsInBoxScrew 16: [ OK ] CalcvirTest.CanCalculateVirialAllAtomsInBoxScrew (0 ms) 16: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewX 16: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewX (0 ms) 16: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewY 16: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewY (0 ms) 16: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewZ 16: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewZ (0 ms) 16: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewXYZ 16: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewXYZ (0 ms) 16: [----------] 6 tests from CalcvirTest (0 ms total) 16: 16: [----------] 2 tests from PrEbinTest 16: [ RUN ] PrEbinTest.HandlesAverages 16: [ OK ] PrEbinTest.HandlesAverages (0 ms) 16: [ RUN ] PrEbinTest.HandlesEmptyAverages 16: [ OK ] PrEbinTest.HandlesEmptyAverages (0 ms) 16: [----------] 2 tests from PrEbinTest (0 ms total) 16: 16: [----------] 3 tests from EnergyDriftTracker 16: [ RUN ] EnergyDriftTracker.emptyWorks 16: [ OK ] EnergyDriftTracker.emptyWorks (0 ms) 16: [ RUN ] EnergyDriftTracker.onePointWorks 16: [ OK ] EnergyDriftTracker.onePointWorks (0 ms) 16: [ RUN ] EnergyDriftTracker.manyPointsWorks 16: [ OK ] EnergyDriftTracker.manyPointsWorks (0 ms) 16: [----------] 3 tests from EnergyDriftTracker (0 ms total) 16: 16: [----------] 4 tests from ShakeTest 16: [ RUN ] ShakeTest.ConstrainsOneBond 16: [ OK ] ShakeTest.ConstrainsOneBond (0 ms) 16: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds 16: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms) 16: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom 16: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (0 ms) 16: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms 16: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms) 16: [----------] 4 tests from ShakeTest (0 ms total) 16: 16: [----------] 1 test from NullSignalTest 16: [ RUN ] NullSignalTest.NullSignallerWorks 16: [ OK ] NullSignalTest.NullSignallerWorks (0 ms) 16: [----------] 1 test from NullSignalTest (0 ms total) 16: 16: [----------] 7 tests from SignalTest 16: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace 16: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms) 16: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace 16: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms) 16: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace 16: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms) 16: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace 16: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms) 16: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace 16: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms) 16: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace 16: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms) 16: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace 16: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms) 16: [----------] 7 tests from SignalTest (0 ms total) 16: 16: [----------] 13 tests from UpdateGroupsTest 16: [ RUN ] UpdateGroupsTest.WithEthaneUA 16: [ OK ] UpdateGroupsTest.WithEthaneUA (0 ms) 16: [ RUN ] UpdateGroupsTest.WithMethane 16: [ OK ] UpdateGroupsTest.WithMethane (0 ms) 16: [ RUN ] UpdateGroupsTest.WithEthane 16: [ OK ] UpdateGroupsTest.WithEthane (0 ms) 16: [ RUN ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithEthane 16: [ OK ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithEthane (0 ms) 16: [ RUN ] UpdateGroupsTest.WithButaneUALogsThatUnsuitableForUpdateGroups 16: [ OK ] UpdateGroupsTest.WithButaneUALogsThatUnsuitableForUpdateGroups (0 ms) 16: [ RUN ] UpdateGroupsTest.WithWaterThreeSite 16: [ OK ] UpdateGroupsTest.WithWaterThreeSite (0 ms) 16: [ RUN ] UpdateGroupsTest.WithWaterFourSite 16: [ OK ] UpdateGroupsTest.WithWaterFourSite (0 ms) 16: [ RUN ] UpdateGroupsTest.WithFourAtomsWithSettle 16: [ OK ] UpdateGroupsTest.WithFourAtomsWithSettle (0 ms) 16: [ RUN ] UpdateGroupsTest.WithWaterFlexAngle 16: [ OK ] UpdateGroupsTest.WithWaterFlexAngle (0 ms) 16: [ RUN ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithWaterFlexAngle 16: [ OK ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithWaterFlexAngle (0 ms) 16: [ RUN ] UpdateGroupsTest.WithTwoMoltypes 16: [ OK ] UpdateGroupsTest.WithTwoMoltypes (0 ms) 16: [ RUN ] UpdateGroupsTest.LogsWhenSizesAreInvalid 16: [ OK ] UpdateGroupsTest.LogsWhenSizesAreInvalid (0 ms) 16: [ RUN ] UpdateGroupsTest.LogsWhenUpdateGroupsAreNotUseful 16: [ OK ] UpdateGroupsTest.LogsWhenUpdateGroupsAreNotUseful (0 ms) 16: [----------] 13 tests from UpdateGroupsTest (0 ms total) 16: 16: [----------] 1 test from UpdateGroupsCog 16: [ RUN ] UpdateGroupsCog.ComputesCogs 16: [ OK ] UpdateGroupsCog.ComputesCogs (0 ms) 16: [----------] 1 test from UpdateGroupsCog (0 ms total) 16: 16: [----------] 2 tests from WholeMoleculeTransform 16: [ RUN ] WholeMoleculeTransform.MakesMoleculesWhole 16: [ OK ] WholeMoleculeTransform.MakesMoleculesWhole (0 ms) 16: [ RUN ] WholeMoleculeTransform.HandlesReordering 16: [ OK ] WholeMoleculeTransform.HandlesReordering (0 ms) 16: [----------] 2 tests from WholeMoleculeTransform (0 ms total) 16: 16: [----------] 28 tests from WithParameters/ConstraintsTest 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/0 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/0 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/1 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/1 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/2 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/2 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/3 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/3 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/4 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/4 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/5 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/5 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/6 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/6 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/7 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/7 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/8 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/8 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/9 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/9 (4 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/10 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/10 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/11 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/11 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/12 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/12 (10 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/13 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/13 (8 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/0 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/0 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/1 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/1 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/2 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/2 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/3 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/3 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/4 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/4 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/5 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/5 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/6 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/6 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/7 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/7 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/8 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/8 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/9 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/9 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/10 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/10 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/11 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/11 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/12 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/12 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/13 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/13 (0 ms) 16: [----------] 28 tests from WithParameters/ConstraintsTest (28 ms total) 16: 16: [----------] 11 tests from WithParameters/EnergyOutputTest 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/0 16: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_0.edr as single precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/0 (2 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/1 16: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_1.edr as single precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/1 (1 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/2 16: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_2.edr as single precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/2 (1 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/3 16: [ OK ] WithParameters/EnergyOutputTest.CheckOutput/3 (1 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/4 16: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_4.edr as single precision energy file 16: Reading energy frame 0 time 10.100 Reading energy frame 1 time 27.500 Reading energy frame 2 time 44.900 Reading energy frame 3 time 62.300 Reading energy frame 4 time 79.700 Reading energy frame 5 time 97.100 Reading energy frame 6 time 114.500 Reading energy frame 7 time 131.900 Reading energy frame 8 time 149.300 Reading energy frame 9 time 166.700 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/4 (7 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/5 16: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_5.edr as single precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/5 (3 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/6 16: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_6.edr as single precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/6 (1 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/7 16: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_7.edr as single precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/7 (2 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/8 16: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_8.edr as single precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/8 (3 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/9 16: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_9.edr as single precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/9 (1 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/10 16: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_10.edr as single precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/10 (5 ms) 16: [----------] 11 tests from WithParameters/EnergyOutputTest (35 ms total) 16: 16: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 (0 ms) 16: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple (0 ms total) 16: 16: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 (0 ms) 16: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression (0 ms total) 16: 16: [----------] 23 tests from WithParameters/FreeEnergyParameterTest 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22 (0 ms) 16: [----------] 23 tests from WithParameters/FreeEnergyParameterTest (0 ms total) 16: 16: [----------] 17 tests from WithParameters/LangevinTest 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/0 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/0 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/1 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/1 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/2 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/2 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/3 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/3 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/4 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/4 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/5 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/5 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/6 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/6 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/7 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/7 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/8 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/8 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/9 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/9 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/10 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/10 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/11 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/11 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/12 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/12 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/13 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/13 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/14 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/14 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/15 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/15 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/16 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/16 (0 ms) 16: [----------] 17 tests from WithParameters/LangevinTest (2 ms total) 16: 16: [----------] 16 tests from WithParameters/LeapFrogTest 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/0 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/0 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/1 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/1 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/2 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/2 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/3 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/3 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/4 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/4 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/5 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/5 (1 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/6 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/6 (4 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/7 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/7 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/8 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/8 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/9 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/9 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/10 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/10 (1 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/11 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/11 (1 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/12 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/12 (1 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/13 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/13 (1 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/14 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/14 (1 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/15 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/15 (1 ms) 16: [----------] 16 tests from WithParameters/LeapFrogTest (18 ms total) 16: 16: [----------] 140 tests from Cubic/ParrRahmTest 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 (1 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from Cubic/ParrRahmTest (14 ms total) 16: 16: [----------] 140 tests from Rectilinear/ParrRahmTest 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_100 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from Rectilinear/ParrRahmTest (15 ms total) 16: 16: [----------] 140 tests from RhombDodecXYSquare/ParrRahmTest 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from RhombDodecXYSquare/ParrRahmTest (11 ms total) 16: 16: [----------] 140 tests from RhombDodecXYHex/ParrRahmTest 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 (2 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from RhombDodecXYHex/ParrRahmTest (12 ms total) 16: 16: [----------] 140 tests from TruncOct/ParrRahmTest 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 (1 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_0 (11 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from TruncOct/ParrRahmTest (22 ms total) 16: 16: [----------] 140 tests from Other/ParrRahmTest 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from Other/ParrRahmTest (8 ms total) 16: 16: [----------] 13 tests from WithParameters/SettleTest 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (1 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (0 ms) 16: [----------] 13 tests from WithParameters/SettleTest (6 ms total) 16: 16: [----------] Global test environment tear-down 16: [==========] 1032 tests from 27 test suites ran. (183 ms total) 16: [ PASSED ] 1032 tests. 16/90 Test #16: MdlibUnitTest ............................. Passed 0.46 sec test 17 Start 17: AwhTest 17: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/awh-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/AwhTest.xml" 17: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/awh/tests 17: Test timeout computed to be: 30 17: [==========] Running 27 tests from 10 test suites. 17: [----------] Global test environment set-up. 17: [----------] 3 tests from SerializationTest 17: [ RUN ] SerializationTest.CanSerializeDimParams 17: [ OK ] SerializationTest.CanSerializeDimParams (0 ms) 17: [ RUN ] SerializationTest.CanSerializeBiasParams 17: [ OK ] SerializationTest.CanSerializeBiasParams (0 ms) 17: [ RUN ] SerializationTest.CanSerializeAwhParams 17: [ OK ] SerializationTest.CanSerializeAwhParams (0 ms) 17: [----------] 3 tests from SerializationTest (0 ms total) 17: 17: [----------] 1 test from BiasTest 17: [ RUN ] BiasTest.DetectsCovering 17: [ OK ] BiasTest.DetectsCovering (1 ms) 17: [----------] 1 test from BiasTest (1 ms total) 17: 17: [----------] 1 test from biasGridTest 17: [ RUN ] biasGridTest.neighborhood 17: [ OK ] biasGridTest.neighborhood (1 ms) 17: [----------] 1 test from biasGridTest (1 ms total) 17: 17: [----------] 2 tests from BiasSharingTest 17: [ RUN ] BiasSharingTest.SharingWorks 17: [ OK ] BiasSharingTest.SharingWorks (3 ms) 17: [ RUN ] BiasSharingTest.SharingScalingByMetricWorks 17: [ OK ] BiasSharingTest.SharingScalingByMetricWorks (3 ms) 17: [----------] 2 tests from BiasSharingTest (7 ms total) 17: 17: [----------] 2 tests from BiasFepLambdaStateTest 17: [ RUN ] BiasFepLambdaStateTest.DetectsCovering 17: [ OK ] BiasFepLambdaStateTest.DetectsCovering (3 ms) 17: [ RUN ] BiasFepLambdaStateTest.DetectsLargeNegativeForeignEnergy 17: [ OK ] BiasFepLambdaStateTest.DetectsLargeNegativeForeignEnergy (0 ms) 17: [----------] 2 tests from BiasFepLambdaStateTest (4 ms total) 17: 17: [----------] 8 tests from WithParameters/BiasTest 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/0 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/0 (0 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/1 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/1 (0 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/2 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/2 (0 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/3 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/3 (0 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/4 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/4 (0 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/5 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/5 (0 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/6 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/6 (0 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/7 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/7 (0 ms) 17: [----------] 8 tests from WithParameters/BiasTest (5 ms total) 17: 17: [----------] 2 tests from WithParameters/BiasStateTest 17: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0 17: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (0 ms) 17: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1 17: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (0 ms) 17: [----------] 2 tests from WithParameters/BiasStateTest (0 ms total) 17: 17: [----------] 1 test from WithParameters/UserInputTest 17: [ RUN ] WithParameters/UserInputTest.ParsesUser3DInput/0 17: [ OK ] WithParameters/UserInputTest.ParsesUser3DInput/0 (0 ms) 17: [----------] 1 test from WithParameters/UserInputTest (0 ms total) 17: 17: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest 17: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 17: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 (10 ms) 17: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 17: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 (7 ms) 17: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 17: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 (8 ms) 17: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 17: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 (7 ms) 17: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest (35 ms total) 17: 17: [----------] 3 tests from WithParameters/FrictionMetricTest 17: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/0 17: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/0 (0 ms) 17: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/1 17: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/1 (1 ms) 17: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/2 17: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/2 (30 ms) 17: [----------] 3 tests from WithParameters/FrictionMetricTest (34 ms total) 17: 17: [----------] Global test environment tear-down 17: [==========] 27 tests from 10 test suites ran. (90 ms total) 17: [ PASSED ] 27 tests. 17/90 Test #17: AwhTest ................................... Passed 0.11 sec test 18 Start 18: DensityFittingAppliedForcesUnitTest 18: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/density_fitting_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/DensityFittingAppliedForcesUnitTest.xml" 18: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/densityfitting/tests 18: Test timeout computed to be: 30 18: [==========] Running 18 tests from 4 test suites. 18: [----------] Global test environment set-up. 18: [----------] 2 tests from DensityFittingTest 18: [ RUN ] DensityFittingTest.ForceProviderLackingInputThrows 18: [ OK ] DensityFittingTest.ForceProviderLackingInputThrows (0 ms) 18: [ RUN ] DensityFittingTest.SingleAtom 18: [ OK ] DensityFittingTest.SingleAtom (0 ms) 18: [----------] 2 tests from DensityFittingTest (0 ms total) 18: 18: [----------] 7 tests from DensityFittingAmplitudeLookupTest 18: [ RUN ] DensityFittingAmplitudeLookupTest.Unity 18: [ OK ] DensityFittingAmplitudeLookupTest.Unity (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.Charge 18: [ OK ] DensityFittingAmplitudeLookupTest.Charge (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.Masses 18: [ OK ] DensityFittingAmplitudeLookupTest.Masses (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyAssign 18: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyAssign (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyConstruct 18: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyConstruct (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveAssign 18: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveAssign (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveConstruct 18: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveConstruct (0 ms) 18: [----------] 7 tests from DensityFittingAmplitudeLookupTest (0 ms total) 18: 18: [----------] 1 test from DensityFittingForceProviderState 18: [ RUN ] DensityFittingForceProviderState.RoundTripSaving 18: [ OK ] DensityFittingForceProviderState.RoundTripSaving (0 ms) 18: [----------] 1 test from DensityFittingForceProviderState (0 ms total) 18: 18: [----------] 8 tests from DensityFittingOptionsTest 18: [ RUN ] DensityFittingOptionsTest.DefaultParameters 18: [ OK ] DensityFittingOptionsTest.DefaultParameters (0 ms) 18: [ RUN ] DensityFittingOptionsTest.OptionSetsActive 18: [ OK ] DensityFittingOptionsTest.OptionSetsActive (0 ms) 18: [ RUN ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive 18: [ OK ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 18: [ RUN ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive 18: [ OK ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive (0 ms) 18: [ RUN ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup 18: [ OK ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) 18: [ RUN ] DensityFittingOptionsTest.InternalsToKvt 18: [ OK ] DensityFittingOptionsTest.InternalsToKvt (0 ms) 18: [ RUN ] DensityFittingOptionsTest.KvtToInternal 18: [ OK ] DensityFittingOptionsTest.KvtToInternal (0 ms) 18: [ RUN ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent 18: [ OK ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent (0 ms) 18: [----------] 8 tests from DensityFittingOptionsTest (0 ms total) 18: 18: [----------] Global test environment tear-down 18: [==========] 18 tests from 4 test suites ran. (2 ms total) 18: [ PASSED ] 18 tests. 18/90 Test #18: DensityFittingAppliedForcesUnitTest ....... Passed 0.02 sec test 19 Start 19: QMMMAppliedForcesUnitTest 19: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/qmmm_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/QMMMAppliedForcesUnitTest.xml" 19: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests 19: Test timeout computed to be: 30 19: [==========] Running 21 tests from 5 test suites. 19: [----------] Global test environment set-up. 19: [----------] 3 tests from QMMMInputGeneratorTest 19: [ RUN ] QMMMInputGeneratorTest.CanConstruct 19: [ OK ] QMMMInputGeneratorTest.CanConstruct (0 ms) 19: [ RUN ] QMMMInputGeneratorTest.TwoWatersPBENoLink 19: [ OK ] QMMMInputGeneratorTest.TwoWatersPBENoLink (0 ms) 19: [ RUN ] QMMMInputGeneratorTest.TwoWatersPBEWithLink 19: [ OK ] QMMMInputGeneratorTest.TwoWatersPBEWithLink (0 ms) 19: [----------] 3 tests from QMMMInputGeneratorTest (0 ms total) 19: 19: [----------] 7 tests from QMMMTopologyPreprocessorTest 19: [ RUN ] QMMMTopologyPreprocessorTest.CanConstruct 19: [ OK ] QMMMTopologyPreprocessorTest.CanConstruct (0 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Generating 1-4 interactions: fudge = 0.5 19: Number of degrees of freedom in T-Coupling group rest is 21.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 19: NVE simulation with an initial temperature of zero: will use a Verlet 19: buffer of 10%. Check your energy drift! 19: 19: 19: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 3 NOTEs 19: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 19: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 19: Setting the LD random seed to -554238465 19: 19: Generated 10 of the 10 non-bonded parameter combinations 19: 19: Generated 10 of the 10 1-4 parameter combinations 19: 19: Excluding 2 bonded neighbours molecule type 'SOL' 19: 19: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 19: Analysing residue names: 19: There are: 4 Water residues 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink (6 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Generating 1-4 interactions: fudge = 0.5 19: Number of degrees of freedom in T-Coupling group rest is 21.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 19: NVE simulation with an initial temperature of zero: will use a Verlet 19: buffer of 10%. Check your energy drift! 19: 19: 19: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 3 NOTEs 19: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 19: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 19: Setting the LD random seed to -1135018513 19: 19: Generated 10 of the 10 non-bonded parameter combinations 19: 19: Generated 10 of the 10 1-4 parameter combinations 19: 19: Excluding 2 bonded neighbours molecule type 'SOL' 19: 19: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 19: Analysing residue names: 19: There are: 4 Water residues 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink (4 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Generating 1-4 interactions: fudge = 0.5 19: Number of degrees of freedom in T-Coupling group rest is 21.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 19: NVE simulation with an initial temperature of zero: will use a Verlet 19: buffer of 10%. Check your energy drift! 19: 19: 19: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 3 NOTEs 19: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 19: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 19: Setting the LD random seed to -679503937 19: 19: Generated 10 of the 10 non-bonded parameter combinations 19: 19: Generated 10 of the 10 1-4 parameter combinations 19: 19: Excluding 2 bonded neighbours molecule type 'SOL' 19: 19: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 19: Analysing residue names: 19: There are: 4 Water residues 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink (5 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksNoConstraints 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Generating 1-4 interactions: fudge = 0.5 19: Number of degrees of freedom in T-Coupling group rest is 63.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 19: NVE simulation: will use the initial temperature of 129.093 K for 19: determining the Verlet buffer size 19: 19: 19: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 3 NOTEs 19: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 19: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 19: Setting the LD random seed to -137069729 19: 19: Generated 2145 of the 2145 non-bonded parameter combinations 19: 19: Generated 2145 of the 2145 1-4 parameter combinations 19: 19: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 19: 19: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 19: Analysing residue names: 19: There are: 3 Protein residues 19: Analysing Protein... 19: 19: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 129.093 K 19: 19: Calculated rlist for 1x1 atom pair-list as 1.021 nm, buffer size 0.021 nm 19: 19: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm 19: 19: Note that mdrun will redetermine rlist based on the actual pair-list setup 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksNoConstraints (15 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksWithConstraints 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Generating 1-4 interactions: fudge = 0.5 19: 19: NOTE 2 [file unknown]: 19: You are using constraints on all bonds, whereas the forcefield has been 19: parametrized only with constraints involving hydrogen atoms. We suggest 19: using constraints = h-bonds instead, this will also improve performance. 19: 19: 19: NOTE 3 [file unknown]: 19: For energy conservation with LINCS, lincs_iter should be 2 or larger. 19: 19: 19: Number of degrees of freedom in T-Coupling group rest is 42.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 19: NVE simulation: will use the initial temperature of 193.640 K for 19: determining the Verlet buffer size 19: 19: 19: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 5 NOTEs 19: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 19: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 19: Setting the LD random seed to -405898253 19: 19: Generated 2145 of the 2145 non-bonded parameter combinations 19: 19: Generated 2145 of the 2145 1-4 parameter combinations 19: 19: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 19: 19: turning all bonds into constraints... 19: 19: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 19: Analysing residue names: 19: There are: 3 Protein residues 19: Analysing Protein... 19: 19: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 193.64 K 19: 19: Calculated rlist for 1x1 atom pair-list as 1.023 nm, buffer size 0.023 nm 19: 19: Set rlist, assuming 4x4 atom pair-list, to 1.015 nm, buffer size 0.015 nm 19: 19: Note that mdrun will redetermine rlist based on the actual pair-list setup 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksWithConstraints (16 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.RemovingQMVsites 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Number of degrees of freedom in T-Coupling group rest is 45.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 19: NVE simulation with an initial temperature of zero: will use a Verlet 19: buffer of 10%. Check your energy drift! 19: 19: 19: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 3 NOTEs 19: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 19: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 19: Setting the LD random seed to -2042643987 19: 19: Generated 3 of the 6 non-bonded parameter combinations 19: 19: Excluding 3 bonded neighbours molecule type 'VSTEST' 19: 19: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 19: 19: Cleaning up constraints and constant bonded interactions with virtual sites 19: Analysing residue names: 19: There are: 1 Other residues 19: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.RemovingQMVsites (5 ms) 19: [----------] 7 tests from QMMMTopologyPreprocessorTest (54 ms total) 19: 19: [----------] 9 tests from QMMMOptionsTest 19: [ RUN ] QMMMOptionsTest.DefaultParameters 19: [ OK ] QMMMOptionsTest.DefaultParameters (0 ms) 19: [ RUN ] QMMMOptionsTest.OptionSetsActive 19: [ OK ] QMMMOptionsTest.OptionSetsActive (0 ms) 19: [ RUN ] QMMMOptionsTest.OutputNoDefaultValuesWhenInactive 19: [ OK ] QMMMOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 19: [ RUN ] QMMMOptionsTest.OutputDefaultValuesWhenActive 19: [ OK ] QMMMOptionsTest.OutputDefaultValuesWhenActive (0 ms) 19: [ RUN ] QMMMOptionsTest.CanConvertGroupStringToIndexGroup 19: [ OK ] QMMMOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) 19: [ RUN ] QMMMOptionsTest.NoQMGroupConvertGroupStringToIndexGroup 19: [ OK ] QMMMOptionsTest.NoQMGroupConvertGroupStringToIndexGroup (0 ms) 19: [ RUN ] QMMMOptionsTest.EmptyQMGroupConvertGroupStringToIndexGroup 19: [ OK ] QMMMOptionsTest.EmptyQMGroupConvertGroupStringToIndexGroup (0 ms) 19: [ RUN ] QMMMOptionsTest.InternalsToKvtAndBack 19: [ OK ] QMMMOptionsTest.InternalsToKvtAndBack (0 ms) 19: [ RUN ] QMMMOptionsTest.CP2KInputProcessing 19: [ OK ] QMMMOptionsTest.CP2KInputProcessing (1 ms) 19: [----------] 9 tests from QMMMOptionsTest (2 ms total) 19: 19: [----------] 1 test from QMMMForceProviderTest 19: [ RUN ] QMMMForceProviderTest.CanConstructOrNot 19: [ OK ] QMMMForceProviderTest.CanConstructOrNot (0 ms) 19: [----------] 1 test from QMMMForceProviderTest (0 ms total) 19: 19: [----------] 1 test from QMMMTest 19: [ RUN ] QMMMTest.ForceProviderLackingInputThrows 19: [ OK ] QMMMTest.ForceProviderLackingInputThrows (0 ms) 19: [----------] 1 test from QMMMTest (0 ms total) 19: 19: [----------] Global test environment tear-down 19: [==========] 21 tests from 5 test suites ran. (58 ms total) 19: [ PASSED ] 21 tests. 19/90 Test #19: QMMMAppliedForcesUnitTest ................. Passed 0.08 sec test 20 Start 20: ColvarsAppliedForcesUnitTest 20: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/colvars_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/ColvarsAppliedForcesUnitTest.xml" 20: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests 20: Test timeout computed to be: 30 20: [==========] Running 16 tests from 4 test suites. 20: [----------] Global test environment set-up. 20: [----------] 1 test from ColvarsTest 20: [ RUN ] ColvarsTest.ForceProviderLackingInputThrows 20: [ OK ] ColvarsTest.ForceProviderLackingInputThrows (0 ms) 20: [----------] 1 test from ColvarsTest (0 ms total) 20: 20: [----------] 6 tests from ColvarsOptionsTest 20: [ RUN ] ColvarsOptionsTest.OutputNoDefaultValuesWhenInactive 20: [ OK ] ColvarsOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 20: [ RUN ] ColvarsOptionsTest.OutputDefaultValuesWhenActive 20: [ OK ] ColvarsOptionsTest.OutputDefaultValuesWhenActive (0 ms) 20: [ RUN ] ColvarsOptionsTest.OutputValuesWhenActive 20: [ OK ] ColvarsOptionsTest.OutputValuesWhenActive (0 ms) 20: [ RUN ] ColvarsOptionsTest.OptionSetsActive 20: [ OK ] ColvarsOptionsTest.OptionSetsActive (0 ms) 20: [ RUN ] ColvarsOptionsTest.InternalsToKvtAndBack 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 20: Setting the LD random seed to -67128337 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsOptionsTest.InternalsToKvtAndBack (12 ms) 20: [ RUN ] ColvarsOptionsTest.RetrieveEdrFilename 20: [ OK ] ColvarsOptionsTest.RetrieveEdrFilename (0 ms) 20: [----------] 6 tests from ColvarsOptionsTest (13 ms total) 20: 20: [----------] 4 tests from ColvarsPreProcessorTest 20: [ RUN ] ColvarsPreProcessorTest.CanConstructColvarsPreProcess 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 20: Setting the LD random seed to -186648105 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsPreProcessorTest.CanConstructColvarsPreProcess (8 ms) 20: [ RUN ] ColvarsPreProcessorTest.CheckValuesFourWaters 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 20: Setting the LD random seed to 1037893567 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsPreProcessorTest.CheckValuesFourWaters (11 ms) 20: [ RUN ] ColvarsPreProcessorTest.CheckNestedInputFiles 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 20: Setting the LD random seed to -289949666 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsPreProcessorTest.CheckNestedInputFiles (10 ms) 20: [ RUN ] ColvarsPreProcessorTest.WrongColvarsInput 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 20: Setting the LD random seed to -271194505 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsPreProcessorTest.WrongColvarsInput (7 ms) 20: [----------] 4 tests from ColvarsPreProcessorTest (38 ms total) 20: 20: [----------] 5 tests from ColvarsForceProviderTest 20: [ RUN ] ColvarsForceProviderTest.CanConstructOrNot 20: [ OK ] ColvarsForceProviderTest.CanConstructOrNot (0 ms) 20: [ RUN ] ColvarsForceProviderTest.SimpleInputs 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 20: Setting the LD random seed to 1945026301 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsForceProviderTest.SimpleInputs (8 ms) 20: [ RUN ] ColvarsForceProviderTest.WrongColvarsInput 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 20: Setting the LD random seed to 2130542566 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsForceProviderTest.WrongColvarsInput (6 ms) 20: [ RUN ] ColvarsForceProviderTest.CalculateForces4water 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 20: Setting the LD random seed to 1072430983 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsForceProviderTest.CalculateForces4water (76 ms) 20: [ RUN ] ColvarsForceProviderTest.CalculateForcesAlanine 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 66.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 20: NVE simulation: will use the initial temperature of 300.368 K for 20: determining the Verlet buffer size 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 20: Setting the LD random seed to 1576255473 20: 20: Generated 2211 of the 2211 non-bonded parameter combinations 20: 20: Generated 2211 of the 2211 1-4 parameter combinations 20: 20: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 20: Analysing residue names: 20: There are: 2 Protein residues 20: Analysing Protein... 20: 20: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 20: 20: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 20: 20: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 20: 20: Note that mdrun will redetermine rlist based on the actual pair-list setup 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsForceProviderTest.CalculateForcesAlanine (79 ms) 20: [----------] 5 tests from ColvarsForceProviderTest (173 ms total) 20: 20: [----------] Global test environment tear-down 20: [==========] 16 tests from 4 test suites ran. (226 ms total) 20: [ PASSED ] 16 tests. 20/90 Test #20: ColvarsAppliedForcesUnitTest .............. Passed 0.25 sec test 21 Start 21: NNPotAppliedForcesUnitTest 21: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/nnpot_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/NNPotAppliedForcesUnitTest.xml" 21: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/nnpot/tests 21: Test timeout computed to be: 30 21: [==========] Running 12 tests from 4 test suites. 21: [----------] Global test environment set-up. 21: [----------] 1 test from NNPotTest 21: [ RUN ] NNPotTest.ForceProviderLackingInputThrows 21: [ OK ] NNPotTest.ForceProviderLackingInputThrows (0 ms) 21: [----------] 1 test from NNPotTest (0 ms total) 21: 21: [----------] 5 tests from NNPotOptionsTest 21: [ RUN ] NNPotOptionsTest.DefaultParameters 21: [ OK ] NNPotOptionsTest.DefaultParameters (0 ms) 21: [ RUN ] NNPotOptionsTest.OptionSetsActive 21: [ OK ] NNPotOptionsTest.OptionSetsActive (0 ms) 21: [ RUN ] NNPotOptionsTest.OutputNoDefaultValuesWhenInactive 21: [ OK ] NNPotOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 21: [ RUN ] NNPotOptionsTest.OutputDefaultValuesWhenActive 21: [ OK ] NNPotOptionsTest.OutputDefaultValuesWhenActive (0 ms) 21: [ RUN ] NNPotOptionsTest.InternalsToKvtAndBack 21: [ OK ] NNPotOptionsTest.InternalsToKvtAndBack (0 ms) 21: [----------] 5 tests from NNPotOptionsTest (0 ms total) 21: 21: [----------] 5 tests from NNPotTopologyPreprocessorTest 21: [ RUN ] NNPotTopologyPreprocessorTest.CanConstruct 21: [ OK ] NNPotTopologyPreprocessorTest.CanConstruct (0 ms) 21: [ RUN ] NNPotTopologyPreprocessorTest.FourWatersFirstInQMRegion 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Generating 1-4 interactions: fudge = 0.5 21: Number of degrees of freedom in T-Coupling group rest is 21.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.mdp]: 21: NVE simulation with an initial temperature of zero: will use a Verlet 21: buffer of 10%. Check your energy drift! 21: 21: 21: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.mdp]: 21: You are using a plain Coulomb cut-off, which might produce artifacts. 21: You might want to consider using PME electrostatics. 21: 21: 21: 21: There were 3 NOTEs 21: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 21: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 21: Setting the LD random seed to -538464785 21: 21: Generated 10 of the 10 non-bonded parameter combinations 21: 21: Generated 10 of the 10 1-4 parameter combinations 21: 21: Excluding 2 bonded neighbours molecule type 'SOL' 21: 21: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 21: Analysing residue names: 21: There are: 4 Water residues 21: 21: This run will generate roughly 0 Mb of data 21: [ OK ] NNPotTopologyPreprocessorTest.FourWatersFirstInQMRegion (71 ms) 21: [ RUN ] NNPotTopologyPreprocessorTest.FourWatersSecondAndFourthInQMRegion 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Generating 1-4 interactions: fudge = 0.5 21: Number of degrees of freedom in T-Coupling group rest is 21.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.mdp]: 21: NVE simulation with an initial temperature of zero: will use a Verlet 21: buffer of 10%. Check your energy drift! 21: 21: 21: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.mdp]: 21: You are using a plain Coulomb cut-off, which might produce artifacts. 21: You might want to consider using PME electrostatics. 21: 21: 21: 21: There were 3 NOTEs 21: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 21: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 21: Setting the LD random seed to -570819605 21: 21: Generated 10 of the 10 non-bonded parameter combinations 21: 21: Generated 10 of the 10 1-4 parameter combinations 21: 21: Excluding 2 bonded neighbours molecule type 'SOL' 21: 21: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 21: Analysing residue names: 21: There are: 4 Water residues 21: 21: This run will generate roughly 0 Mb of data 21: [ OK ] NNPotTopologyPreprocessorTest.FourWatersSecondAndFourthInQMRegion (13 ms) 21: [ RUN ] NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsNoConstraints 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Generating 1-4 interactions: fudge = 0.5 21: Number of degrees of freedom in T-Coupling group rest is 63.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.mdp]: 21: NVE simulation: will use the initial temperature of 129.093 K for 21: determining the Verlet buffer size 21: 21: 21: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.mdp]: 21: You are using a plain Coulomb cut-off, which might produce artifacts. 21: You might want to consider using PME electrostatics. 21: 21: 21: 21: There were 3 NOTEs 21: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 21: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 21: Setting the LD random seed to -268697601 21: 21: Generated 2145 of the 2145 non-bonded parameter combinations 21: 21: Generated 2145 of the 2145 1-4 parameter combinations 21: 21: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 21: 21: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 21: Analysing residue names: 21: There are: 3 Protein residues 21: Analysing Protein... 21: 21: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 129.093 K 21: 21: Calculated rlist for 1x1 atom pair-list as 1.021 nm, buffer size 0.021 nm 21: 21: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm 21: 21: Note that mdrun will redetermine rlist based on the actual pair-list setup 21: 21: This run will generate roughly 0 Mb of data 21: [ OK ] NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsNoConstraints (15 ms) 21: [ RUN ] NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsWithConstraints 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Generating 1-4 interactions: fudge = 0.5 21: 21: NOTE 2 [file unknown]: 21: You are using constraints on all bonds, whereas the forcefield has been 21: parametrized only with constraints involving hydrogen atoms. We suggest 21: using constraints = h-bonds instead, this will also improve performance. 21: 21: 21: NOTE 3 [file unknown]: 21: For energy conservation with LINCS, lincs_iter should be 2 or larger. 21: 21: 21: Number of degrees of freedom in T-Coupling group rest is 42.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.mdp]: 21: NVE simulation: will use the initial temperature of 193.640 K for 21: determining the Verlet buffer size 21: 21: 21: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.mdp]: 21: You are using a plain Coulomb cut-off, which might produce artifacts. 21: You might want to consider using PME electrostatics. 21: 21: 21: 21: There were 5 NOTEs 21: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 21: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 21: Setting the LD random seed to -16793941 21: 21: Generated 2145 of the 2145 non-bonded parameter combinations 21: 21: Generated 2145 of the 2145 1-4 parameter combinations 21: 21: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 21: 21: turning all bonds into constraints... 21: 21: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 21: Analysing residue names: 21: There are: 3 Protein residues 21: Analysing Protein... 21: 21: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 193.64 K 21: 21: Calculated rlist for 1x1 atom pair-list as 1.023 nm, buffer size 0.023 nm 21: 21: Set rlist, assuming 4x4 atom pair-list, to 1.015 nm, buffer size 0.015 nm 21: 21: Note that mdrun will redetermine rlist based on the actual pair-list setup 21: 21: This run will generate roughly 0 Mb of data 21: [ OK ] NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsWithConstraints (17 ms) 21: [----------] 5 tests from NNPotTopologyPreprocessorTest (116 ms total) 21: 21: [----------] 1 test from NNPotForceProviderTest 21: [ RUN ] NNPotForceProviderTest.CanConstruct 21: [ OK ] NNPotForceProviderTest.CanConstruct (0 ms) 21: [----------] 1 test from NNPotForceProviderTest (0 ms total) 21: 21: [----------] Global test environment tear-down 21: [==========] 12 tests from 4 test suites ran. (118 ms total) 21: [ PASSED ] 12 tests. 21/90 Test #21: NNPotAppliedForcesUnitTest ................ Passed 0.23 sec test 22 Start 22: AppliedForcesUnitTest 22: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/AppliedForcesUnitTest.xml" 22: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/applied_forces/tests 22: Test timeout computed to be: 30 22: [==========] Running 3 tests from 1 test suite. 22: [----------] Global test environment set-up. 22: [----------] 3 tests from ElectricFieldTest 22: [ RUN ] ElectricFieldTest.Static 22: [ OK ] ElectricFieldTest.Static (0 ms) 22: [ RUN ] ElectricFieldTest.Oscillating 22: [ OK ] ElectricFieldTest.Oscillating (0 ms) 22: [ RUN ] ElectricFieldTest.Pulsed 22: [ OK ] ElectricFieldTest.Pulsed (0 ms) 22: [----------] 3 tests from ElectricFieldTest (0 ms total) 22: 22: [----------] Global test environment tear-down 22: [==========] 3 tests from 1 test suite ran. (0 ms total) 22: [ PASSED ] 3 tests. 22/90 Test #22: AppliedForcesUnitTest ..................... Passed 0.02 sec test 23 Start 23: ListedForcesTest 23: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/listed_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/ListedForcesTest.xml" 23: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/listed_forces/tests 23: Test timeout computed to be: 30 23: [==========] Running 132 tests from 9 test suites. 23: [----------] Global test environment set-up. 23: [----------] 24 tests from Bond/ListedForcesTest 23: [ RUN ] Bond/ListedForcesTest.Ifunc/0 23: [ OK ] Bond/ListedForcesTest.Ifunc/0 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/1 23: [ OK ] Bond/ListedForcesTest.Ifunc/1 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/2 23: [ OK ] Bond/ListedForcesTest.Ifunc/2 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/3 23: [ OK ] Bond/ListedForcesTest.Ifunc/3 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/4 23: [ OK ] Bond/ListedForcesTest.Ifunc/4 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/5 23: [ OK ] Bond/ListedForcesTest.Ifunc/5 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/6 23: [ OK ] Bond/ListedForcesTest.Ifunc/6 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/7 23: [ OK ] Bond/ListedForcesTest.Ifunc/7 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/8 23: [ OK ] Bond/ListedForcesTest.Ifunc/8 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/9 23: [ OK ] Bond/ListedForcesTest.Ifunc/9 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/10 23: [ OK ] Bond/ListedForcesTest.Ifunc/10 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/11 23: [ OK ] Bond/ListedForcesTest.Ifunc/11 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/12 23: [ OK ] Bond/ListedForcesTest.Ifunc/12 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/13 23: [ OK ] Bond/ListedForcesTest.Ifunc/13 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/14 23: [ OK ] Bond/ListedForcesTest.Ifunc/14 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/15 23: [ OK ] Bond/ListedForcesTest.Ifunc/15 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/16 23: [ OK ] Bond/ListedForcesTest.Ifunc/16 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/17 23: [ OK ] Bond/ListedForcesTest.Ifunc/17 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/18 23: [ OK ] Bond/ListedForcesTest.Ifunc/18 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/19 23: [ OK ] Bond/ListedForcesTest.Ifunc/19 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/20 23: [ OK ] Bond/ListedForcesTest.Ifunc/20 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/21 23: [ OK ] Bond/ListedForcesTest.Ifunc/21 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/22 23: [ OK ] Bond/ListedForcesTest.Ifunc/22 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/23 23: [ OK ] Bond/ListedForcesTest.Ifunc/23 (0 ms) 23: [----------] 24 tests from Bond/ListedForcesTest (3 ms total) 23: 23: [----------] 33 tests from Angle/ListedForcesTest 23: [ RUN ] Angle/ListedForcesTest.Ifunc/0 23: [ OK ] Angle/ListedForcesTest.Ifunc/0 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/1 23: [ OK ] Angle/ListedForcesTest.Ifunc/1 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/2 23: [ OK ] Angle/ListedForcesTest.Ifunc/2 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/3 23: [ OK ] Angle/ListedForcesTest.Ifunc/3 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/4 23: [ OK ] Angle/ListedForcesTest.Ifunc/4 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/5 23: [ OK ] Angle/ListedForcesTest.Ifunc/5 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/6 23: [ OK ] Angle/ListedForcesTest.Ifunc/6 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/7 23: [ OK ] Angle/ListedForcesTest.Ifunc/7 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/8 23: [ OK ] Angle/ListedForcesTest.Ifunc/8 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/9 23: [ OK ] Angle/ListedForcesTest.Ifunc/9 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/10 23: [ OK ] Angle/ListedForcesTest.Ifunc/10 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/11 23: [ OK ] Angle/ListedForcesTest.Ifunc/11 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/12 23: [ OK ] Angle/ListedForcesTest.Ifunc/12 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/13 23: [ OK ] Angle/ListedForcesTest.Ifunc/13 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/14 23: [ OK ] Angle/ListedForcesTest.Ifunc/14 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/15 23: [ OK ] Angle/ListedForcesTest.Ifunc/15 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/16 23: [ OK ] Angle/ListedForcesTest.Ifunc/16 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/17 23: [ OK ] Angle/ListedForcesTest.Ifunc/17 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/18 23: [ OK ] Angle/ListedForcesTest.Ifunc/18 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/19 23: [ OK ] Angle/ListedForcesTest.Ifunc/19 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/20 23: [ OK ] Angle/ListedForcesTest.Ifunc/20 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/21 23: [ OK ] Angle/ListedForcesTest.Ifunc/21 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/22 23: [ OK ] Angle/ListedForcesTest.Ifunc/22 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/23 23: [ OK ] Angle/ListedForcesTest.Ifunc/23 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/24 23: [ OK ] Angle/ListedForcesTest.Ifunc/24 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/25 23: [ OK ] Angle/ListedForcesTest.Ifunc/25 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/26 23: [ OK ] Angle/ListedForcesTest.Ifunc/26 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/27 23: [ OK ] Angle/ListedForcesTest.Ifunc/27 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/28 23: [ OK ] Angle/ListedForcesTest.Ifunc/28 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/29 23: [ OK ] Angle/ListedForcesTest.Ifunc/29 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/30 23: [ OK ] Angle/ListedForcesTest.Ifunc/30 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/31 23: [ OK ] Angle/ListedForcesTest.Ifunc/31 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/32 23: [ OK ] Angle/ListedForcesTest.Ifunc/32 (0 ms) 23: [----------] 33 tests from Angle/ListedForcesTest (5 ms total) 23: 23: [----------] 18 tests from Dihedral/ListedForcesTest 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/0 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/0 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/1 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/1 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/2 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/2 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/3 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/3 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/4 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/4 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/5 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/5 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/6 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/6 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/7 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/7 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/8 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/8 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/9 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/9 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/10 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/10 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/11 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/11 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/12 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/12 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/13 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/13 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/14 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/14 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/15 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/15 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/16 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/16 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/17 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/17 (0 ms) 23: [----------] 18 tests from Dihedral/ListedForcesTest (3 ms total) 23: 23: [----------] 12 tests from Polarize/ListedForcesTest 23: [ RUN ] Polarize/ListedForcesTest.Ifunc/0 23: [ OK ] Polarize/ListedForcesTest.Ifunc/0 (0 ms) 23: [ RUN ] Polarize/ListedForcesTest.Ifunc/1 23: [ OK ] Polarize/ListedForcesTest.Ifunc/1 (0 ms) 23: [ RUN ] Polarize/ListedForcesTest.Ifunc/2 23: [ OK ] Polarize/ListedForcesTest.Ifunc/2 (0 ms) 23: [ RUN ] Polarize/ListedForcesTest.Ifunc/3 23: [ OK ] Polarize/ListedForcesTest.Ifunc/3 (0 ms) 23: [ RUN ] Polarize/ListedForcesTest.Ifunc/4 23: [ OK ] Polarize/ListedForcesTest.Ifunc/4 (0 ms) 23: [ RUN ] Polarize/ListedForcesTest.Ifunc/5 23: [ OK ] Polarize/ListedForcesTest.Ifunc/5 (0 ms) 23: [ RUN ] Polarize/ListedForcesTest.Ifunc/6 23: [ OK ] Polarize/ListedForcesTest.Ifunc/6 (0 ms) 23: [ RUN ] Polarize/ListedForcesTest.Ifunc/7 23: [ OK ] Polarize/ListedForcesTest.Ifunc/7 (0 ms) 23: [ RUN ] Polarize/ListedForcesTest.Ifunc/8 23: [ OK ] Polarize/ListedForcesTest.Ifunc/8 (0 ms) 23: [ RUN ] Polarize/ListedForcesTest.Ifunc/9 23: [ OK ] Polarize/ListedForcesTest.Ifunc/9 (0 ms) 23: [ RUN ] Polarize/ListedForcesTest.Ifunc/10 23: [ OK ] Polarize/ListedForcesTest.Ifunc/10 (0 ms) 23: [ RUN ] Polarize/ListedForcesTest.Ifunc/11 23: [ OK ] Polarize/ListedForcesTest.Ifunc/11 (0 ms) 23: [----------] 12 tests from Polarize/ListedForcesTest (1 ms total) 23: 23: [----------] 18 tests from Restraints/ListedForcesTest 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/0 23: [ OK ] Restraints/ListedForcesTest.Ifunc/0 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/1 23: [ OK ] Restraints/ListedForcesTest.Ifunc/1 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/2 23: [ OK ] Restraints/ListedForcesTest.Ifunc/2 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/3 23: [ OK ] Restraints/ListedForcesTest.Ifunc/3 (1 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/4 23: [ OK ] Restraints/ListedForcesTest.Ifunc/4 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/5 23: [ OK ] Restraints/ListedForcesTest.Ifunc/5 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/6 23: [ OK ] Restraints/ListedForcesTest.Ifunc/6 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/7 23: [ OK ] Restraints/ListedForcesTest.Ifunc/7 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/8 23: [ OK ] Restraints/ListedForcesTest.Ifunc/8 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/9 23: [ OK ] Restraints/ListedForcesTest.Ifunc/9 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/10 23: [ OK ] Restraints/ListedForcesTest.Ifunc/10 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/11 23: [ OK ] Restraints/ListedForcesTest.Ifunc/11 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/12 23: [ OK ] Restraints/ListedForcesTest.Ifunc/12 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/13 23: [ OK ] Restraints/ListedForcesTest.Ifunc/13 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/14 23: [ OK ] Restraints/ListedForcesTest.Ifunc/14 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/15 23: [ OK ] Restraints/ListedForcesTest.Ifunc/15 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/16 23: [ OK ] Restraints/ListedForcesTest.Ifunc/16 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/17 23: [ OK ] Restraints/ListedForcesTest.Ifunc/17 (0 ms) 23: [----------] 18 tests from Restraints/ListedForcesTest (5 ms total) 23: 23: [----------] 3 tests from BondZeroLength/ListedForcesTest 23: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/0 23: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/0 (0 ms) 23: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/1 23: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/1 (0 ms) 23: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/2 23: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/2 (0 ms) 23: [----------] 3 tests from BondZeroLength/ListedForcesTest (0 ms total) 23: 23: [----------] 3 tests from AngleZero/ListedForcesTest 23: [ RUN ] AngleZero/ListedForcesTest.Ifunc/0 23: [ OK ] AngleZero/ListedForcesTest.Ifunc/0 (0 ms) 23: [ RUN ] AngleZero/ListedForcesTest.Ifunc/1 23: [ OK ] AngleZero/ListedForcesTest.Ifunc/1 (0 ms) 23: [ RUN ] AngleZero/ListedForcesTest.Ifunc/2 23: [ OK ] AngleZero/ListedForcesTest.Ifunc/2 (0 ms) 23: [----------] 3 tests from AngleZero/ListedForcesTest (1 ms total) 23: 23: [----------] 12 tests from 14Interaction/ListedForcesPairsTest 23: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/0 23: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/0 (0 ms) 23: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/1 23: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/1 (0 ms) 23: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/2 23: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/2 (0 ms) 23: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/3 23: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/3 (0 ms) 23: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/4 23: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/4 (0 ms) 23: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/5 23: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/5 (0 ms) 23: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/6 23: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/6 (0 ms) 23: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/7 23: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/7 (1 ms) 23: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/8 23: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/8 (0 ms) 23: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/9 23: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/9 (0 ms) 23: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/10 23: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/10 (0 ms) 23: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/11 23: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/11 (0 ms) 23: [----------] 12 tests from 14Interaction/ListedForcesPairsTest (3 ms total) 23: 23: [----------] 9 tests from PosResBasicTest/PositionRestraintsTest 23: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/0 23: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/0 (0 ms) 23: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/1 23: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/1 (0 ms) 23: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/2 23: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/2 (0 ms) 23: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/3 23: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/3 (0 ms) 23: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/4 23: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/4 (0 ms) 23: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/5 23: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/5 (0 ms) 23: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/6 23: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/6 (0 ms) 23: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/7 23: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/7 (0 ms) 23: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/8 23: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/8 (0 ms) 23: [----------] 9 tests from PosResBasicTest/PositionRestraintsTest (1 ms total) 23: 23: [----------] Global test environment tear-down 23: [==========] 132 tests from 9 test suites ran. (26 ms total) 23: [ PASSED ] 132 tests. 23/90 Test #23: ListedForcesTest .......................... Passed 0.05 sec test 24 Start 24: NbnxmTests 24: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/nbnxm-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/NbnxmTests.xml" 24: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/nbnxm/tests 24: Test timeout computed to be: 30 24: [==========] Running 383 tests from 4 test suites. 24: [----------] Global test environment set-up. 24: [----------] 18 tests from KernelSetupTest 24: [ RUN ] KernelSetupTest.getCoulombKernelTypeRF 24: [ OK ] KernelSetupTest.getCoulombKernelTypeRF (0 ms) 24: [ RUN ] KernelSetupTest.getCoulombKernelTypeCut 24: [ OK ] KernelSetupTest.getCoulombKernelTypeCut (0 ms) 24: [ RUN ] KernelSetupTest.getCoulombKernelTypeTable 24: [ OK ] KernelSetupTest.getCoulombKernelTypeTable (0 ms) 24: [ RUN ] KernelSetupTest.getCoulombKernelTypeTableTwin 24: [ OK ] KernelSetupTest.getCoulombKernelTypeTableTwin (0 ms) 24: [ RUN ] KernelSetupTest.getCoulombKernelTypeEwald 24: [ OK ] KernelSetupTest.getCoulombKernelTypeEwald (0 ms) 24: [ RUN ] KernelSetupTest.getCoulombKernelTypeEwaldTwin 24: [ OK ] KernelSetupTest.getCoulombKernelTypeEwaldTwin (0 ms) 24: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomNone 24: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomNone (0 ms) 24: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomPotShift 24: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomPotShift (0 ms) 24: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombLBNone 24: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombLBNone (0 ms) 24: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombLBPotShift 24: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombLBPotShift (0 ms) 24: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombNoneNone 24: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombNoneNone (0 ms) 24: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombNonePotShift 24: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombNonePotShift (0 ms) 24: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutThrows 24: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutThrows (0 ms) 24: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutForceSwitch 24: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutForceSwitch (0 ms) 24: [ RUN ] KernelSetupTest.getVdwKernelTypePmeGeom 24: [ OK ] KernelSetupTest.getVdwKernelTypePmeGeom (0 ms) 24: [ RUN ] KernelSetupTest.getVdwKernelTypePmeNone 24: [ OK ] KernelSetupTest.getVdwKernelTypePmeNone (0 ms) 24: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutPotSwitch 24: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutPotSwitch (0 ms) 24: [ RUN ] KernelSetupTest.getVdwKernelTypeAllCountThrows 24: [ OK ] KernelSetupTest.getVdwKernelTypeAllCountThrows (0 ms) 24: [----------] 18 tests from KernelSetupTest (0 ms total) 24: 24: [----------] 2 tests from SimdEnergyAccumulatorTest 24: [ RUN ] SimdEnergyAccumulatorTest.SingleEnergyGroupSimd4xM 24: [ OK ] SimdEnergyAccumulatorTest.SingleEnergyGroupSimd4xM (0 ms) 24: [ RUN ] SimdEnergyAccumulatorTest.EnergyGroupsSimd4xM 24: [ OK ] SimdEnergyAccumulatorTest.EnergyGroupsSimd4xM (0 ms) 24: [----------] 2 tests from SimdEnergyAccumulatorTest (0 ms total) 24: 24: [----------] 3 tests from WithParameters/CpuListDiagonalExclusionsTest 24: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/0 24: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/0 (0 ms) 24: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/1 24: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/1 (0 ms) 24: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/2 24: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/2 (0 ms) 24: [----------] 3 tests from WithParameters/CpuListDiagonalExclusionsTest (0 ms total) 24: 24: [----------] 360 tests from Combinations/NbnxmKernelTest 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (5 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombNone (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwForceSwitch (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwPotSwitch (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombNone (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwForceSwitch (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwPotSwitch (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (5 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombNone (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwForceSwitch (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwPotSwitch (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombNone (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwForceSwitch (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwPotSwitch (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombLB 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombLB (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombNone (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwForceSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwPotSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombLB 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombLB (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombNone (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwForceSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwPotSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombLB 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombLB (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombNone (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwForceSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwPotSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 24: [----------] 360 tests from Combinations/NbnxmKernelTest (583 ms total) 24: 24: [----------] Global test environment tear-down 24: [==========] 383 tests from 4 test suites ran. (584 ms total) 24: [ PASSED ] 185 tests. 24: [ SKIPPED ] 198 tests, listed below: 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 24/90 Test #24: NbnxmTests ................................ Passed 0.62 sec test 25 Start 25: NbnxmGpuTests 25: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/nbnxm-gpu-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/NbnxmGpuTests.xml" 25: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/nbnxm/tests 25: Test timeout computed to be: 30 25: [==========] Running 0 tests from 0 test suites. 25: [==========] 0 tests from 0 test suites ran. (0 ms total) 25: [ PASSED ] 0 tests. 25/90 Test #25: NbnxmGpuTests ............................. Passed 0.16 sec test 26 Start 26: CommandLineUnitTests 26: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/commandline-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/CommandLineUnitTests.xml" 26: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/commandline/tests 26: Test timeout computed to be: 30 26: [==========] Running 60 tests from 7 test suites. 26: [----------] Global test environment set-up. 26: [----------] 3 tests from CommandLineHelpModuleTest 26: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp 26: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (0 ms) 26: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic 26: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (0 ms) 26: [ RUN ] CommandLineHelpModuleTest.ExportsHelp 26: [ OK ] CommandLineHelpModuleTest.ExportsHelp (1 ms) 26: [----------] 3 tests from CommandLineHelpModuleTest (2 ms total) 26: 26: [----------] 7 tests from CommandLineHelpWriterTest 26: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes 26: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (0 ms) 26: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables 26: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (0 ms) 26: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions 26: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (0 ms) 26: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions 26: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (0 ms) 26: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups 26: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (0 ms) 26: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText 26: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (0 ms) 26: [ RUN ] CommandLineHelpWriterTest.HandlesKnownIssues 26: [ OK ] CommandLineHelpWriterTest.HandlesKnownIssues (0 ms) 26: [----------] 7 tests from CommandLineHelpWriterTest (1 ms total) 26: 26: [----------] 6 tests from CommandLineModuleManagerTest 26: [ RUN ] CommandLineModuleManagerTest.RunsModule 26: [ OK ] CommandLineModuleManagerTest.RunsModule (0 ms) 26: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp 26: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (0 ms) 26: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet 26: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (0 ms) 26: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH 26: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (0 ms) 26: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule 26: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (0 ms) 26: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames 26: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (0 ms) 26: [----------] 6 tests from CommandLineModuleManagerTest (1 ms total) 26: 26: [----------] 13 tests from CommandLineParserTest 26: [ RUN ] CommandLineParserTest.HandlesSingleValues 26: [ OK ] CommandLineParserTest.HandlesSingleValues (0 ms) 26: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument 26: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms) 26: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument 26: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms) 26: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument 26: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (0 ms) 26: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers 26: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (0 ms) 26: [ RUN ] CommandLineParserTest.HandlesString 26: [ OK ] CommandLineParserTest.HandlesString (0 ms) 26: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues 26: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (0 ms) 26: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix 26: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms) 26: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers 26: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms) 26: [ RUN ] CommandLineParserTest.HandlesSkipUnknown 26: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms) 26: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault 26: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms) 26: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments 26: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms) 26: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions 26: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (0 ms) 26: [----------] 13 tests from CommandLineParserTest (1 ms total) 26: 26: [----------] 6 tests from CommandLineProgramContextTest 26: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath 26: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (0 ms) 26: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath 26: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms) 26: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath 26: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (0 ms) 26: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory 26: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms) 26: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink 26: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (0 ms) 26: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink 26: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (0 ms) 26: [----------] 6 tests from CommandLineProgramContextTest (0 ms total) 26: 26: [----------] 3 tests from OutputNamesTest 26: [ RUN ] OutputNamesTest.CanBeSuffixed 26: [ OK ] OutputNamesTest.CanBeSuffixed (0 ms) 26: [ RUN ] OutputNamesTest.HasSuffixFromNoAppend 26: [ OK ] OutputNamesTest.HasSuffixFromNoAppend (0 ms) 26: [ RUN ] OutputNamesTest.CanHavePartNumberAdded 26: [ OK ] OutputNamesTest.CanHavePartNumberAdded (0 ms) 26: [----------] 3 tests from OutputNamesTest (0 ms total) 26: 26: [----------] 22 tests from ParseCommonArgsTest 26: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs 26: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesInt64Args 26: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesRealArgs 26: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesStringArgs 26: [ OK ] ParseCommonArgsTest.ParsesStringArgs (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs 26: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgsToValuesOfSuitableEnum 26: [ OK ] ParseCommonArgsTest.ParsesBooleanArgsToValuesOfSuitableEnum (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs 26: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs 26: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit 26: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs 26: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesFileArgs 26: [ OK ] ParseCommonArgsTest.ParsesFileArgs (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults 26: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName 26: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension 26: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms) 26: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles 26: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (0 ms) 26: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles 26: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (0 ms) 26: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified 26: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (0 ms) 26: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles 26: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (0 ms) 26: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension 26: Value is /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/commandline/tests/Testing/Temporary/ParseCommonArgsTest_AcceptsUnknownTrajectoryExtension.foo 26: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (0 ms) 26: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile 26: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (0 ms) 26: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName 26: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (270 ms) 26: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs 26: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (0 ms) 26: [----------] 22 tests from ParseCommonArgsTest (273 ms total) 26: 26: [----------] Global test environment tear-down 26: [==========] 60 tests from 7 test suites ran. (280 ms total) 26: [ PASSED ] 60 tests. 26/90 Test #26: CommandLineUnitTests ...................... Passed 0.32 sec test 27 Start 27: DomDecTests 27: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/domdec-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/DomDecTests.xml" 27: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/domdec/tests 27: Test timeout computed to be: 30 27: [==========] Running 9 tests from 2 test suites. 27: [----------] Global test environment set-up. 27: [----------] 7 tests from HashedMap 27: [ RUN ] HashedMap.InsertsFinds 27: [ OK ] HashedMap.InsertsFinds (0 ms) 27: [ RUN ] HashedMap.NegativeKeysWork 27: [ OK ] HashedMap.NegativeKeysWork (0 ms) 27: [ RUN ] HashedMap.InsertsErases 27: [ OK ] HashedMap.InsertsErases (0 ms) 27: [ RUN ] HashedMap.InsertsOrAssigns 27: [ OK ] HashedMap.InsertsOrAssigns (0 ms) 27: [ RUN ] HashedMap.Clears 27: [ OK ] HashedMap.Clears (0 ms) 27: [ RUN ] HashedMap.LinkedEntries 27: [ OK ] HashedMap.LinkedEntries (0 ms) 27: [ RUN ] HashedMap.ResizesTable 27: [ OK ] HashedMap.ResizesTable (0 ms) 27: [----------] 7 tests from HashedMap (0 ms total) 27: 27: [----------] 2 tests from LocalAtomSetManager 27: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet 27: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms) 27: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices 27: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms) 27: [----------] 2 tests from LocalAtomSetManager (0 ms total) 27: 27: [----------] Global test environment tear-down 27: [==========] 9 tests from 2 test suites ran. (0 ms total) 27: [ PASSED ] 9 tests. 27/90 Test #27: DomDecTests ............................... Passed 0.03 sec test 28 Start 28: DomDecMpiTests 28: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/domdec-mpi-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/DomDecMpiTests.xml" 28: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/domdec/tests 28: Test timeout computed to be: 30 28: [==========] Running 4 tests from 1 test suite. 28: [----------] Global test environment set-up. 28: [----------] 4 tests from HaloExchangeTest 28: [ RUN ] HaloExchangeTest.Coordinates1dHaloWith1Pulse 28: [ OK ] HaloExchangeTest.Coordinates1dHaloWith1Pulse (23 ms) 28: [ RUN ] HaloExchangeTest.Coordinates1dHaloWith2Pulses 28: [ OK ] HaloExchangeTest.Coordinates1dHaloWith2Pulses (27 ms) 28: [ RUN ] HaloExchangeTest.Coordinates2dHaloWith1PulseInEachDim 28: [ OK ] HaloExchangeTest.Coordinates2dHaloWith1PulseInEachDim (35 ms) 28: [ RUN ] HaloExchangeTest.Coordinates2dHaloWith2PulsesInDim1 28: [ OK ] HaloExchangeTest.Coordinates2dHaloWith2PulsesInDim1 (27 ms) 28: [----------] 4 tests from HaloExchangeTest (115 ms total) 28: 28: [----------] Global test environment tear-down 28: [==========] 4 tests from 1 test suite ran. (115 ms total) 28: [ PASSED ] 4 tests. 28/90 Test #28: DomDecMpiTests ............................ Passed 0.28 sec test 29 Start 29: EwaldUnitTests 29: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/ewald-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/EwaldUnitTests.xml" 29: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/ewald/tests 29: Test timeout computed to be: 30 29: [==========] Running 407 tests from 9 test suites. 29: [----------] Global test environment set-up. 29: [----------] 6 tests from SeparatePmeRanksPermittedTest 29: [ RUN ] SeparatePmeRanksPermittedTest.ZeroPmeDisableReasons 29: [ OK ] SeparatePmeRanksPermittedTest.ZeroPmeDisableReasons (0 ms) 29: [ RUN ] SeparatePmeRanksPermittedTest.CanBeDisabled 29: [ OK ] SeparatePmeRanksPermittedTest.CanBeDisabled (0 ms) 29: [ RUN ] SeparatePmeRanksPermittedTest.OneDisableReasonFlag 29: [ OK ] SeparatePmeRanksPermittedTest.OneDisableReasonFlag (0 ms) 29: [ RUN ] SeparatePmeRanksPermittedTest.OneDisableReasonText 29: [ OK ] SeparatePmeRanksPermittedTest.OneDisableReasonText (0 ms) 29: [ RUN ] SeparatePmeRanksPermittedTest.TwoDisableReasonText 29: [ OK ] SeparatePmeRanksPermittedTest.TwoDisableReasonText (0 ms) 29: [ RUN ] SeparatePmeRanksPermittedTest.EmptyDisableReasonText 29: [ OK ] SeparatePmeRanksPermittedTest.EmptyDisableReasonText (0 ms) 29: [----------] 6 tests from SeparatePmeRanksPermittedTest (0 ms total) 29: 29: [----------] 108 tests from Pme_SplineAndSpreadTest 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spline (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spline (3 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spline (16 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spline (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spread (14 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_fused spline and spread (6 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spline (2 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spread (10 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_fused spline and spread (5 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spline (2 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spread (3 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_fused spline and spread (11 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spline (4 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_fused spline and spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spline (7 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spread (13 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_fused spline and spread (4 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spline (5 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_fused spline and spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spline (12 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spread (5 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_fused spline and spread (4 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spline (9 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spline (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_fused spline and spread (6 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spread (4 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spline (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_fused spline and spread (2 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spline (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spline (5 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spline (2 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spread (6 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_fused spline and spread (3 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spread (5 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_fused spline and spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spline (7 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spread (3 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_fused spline and spread (10 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spline (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_fused spline and spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spline (12 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spread (7 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_fused spline and spread (4 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spread (9 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_fused spline and spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spline (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_fused spline and spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spline (8 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spread (8 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_fused spline and spread (4 ms) 29: [----------] 108 tests from Pme_SplineAndSpreadTest (359 ms total) 29: 29: [----------] 64 tests from Pme_SolveTest 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (9 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (1 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (1 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (5 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (8 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (1 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (3 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [----------] 64 tests from Pme_SolveTest (46 ms total) 29: 29: [----------] 32 tests from PmeDiffEwaldQ_SolveTest 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (7 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [----------] 32 tests from PmeDiffEwaldQ_SolveTest (14 ms total) 29: 29: [----------] 32 tests from PmeDiffEwaldLJ_SolveTest 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (5 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (9 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 29: [----------] 32 tests from PmeDiffEwaldLJ_SolveTest (23 ms total) 29: 29: [----------] 64 tests from PmeDiffEps_SolveTest 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (5 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (5 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (6 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [----------] 64 tests from PmeDiffEps_SolveTest (33 ms total) 29: 29: [----------] 72 tests from Pme_GatherTest 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_1_atom (4 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_13_atoms (5 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_13_atoms (4 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_1_atom (4 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_13_atoms (4 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_13_atoms (7 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 29: [----------] 72 tests from Pme_GatherTest (53 ms total) 29: 29: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest 29: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 29: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (0 ms) 29: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 29: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms) 29: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 29: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (0 ms) 29: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 29: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (7 ms) 29: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 29: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (0 ms) 29: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (7 ms total) 29: 29: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (3 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (7 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (8 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (3 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (12 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (4 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (8 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (7 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (3 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (11 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (4 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (6 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (7 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (2 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (2 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (2 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (1 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (1 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (3 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (3 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (2 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (2 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (2 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (2 ms) 29: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (118 ms total) 29: 29: [----------] Global test environment tear-down 29: [==========] 407 tests from 9 test suites ran. (657 ms total) 29: [ PASSED ] 311 tests. 29: [ SKIPPED ] 96 tests, listed below: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29/90 Test #29: EwaldUnitTests ............................ Passed 0.87 sec test 30 Start 30: FFTUnitTests 30: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/fft-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/FFTUnitTests.xml" 30: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/fft/tests 30: Test timeout computed to be: 1920 30: [==========] Running 15 tests from 4 test suites. 30: [----------] Global test environment set-up. 30: [----------] 2 tests from ManyFFTTest 30: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test 30: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (6 ms) 30: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test 30: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (22 ms) 30: [----------] 2 tests from ManyFFTTest (29 ms total) 30: 30: [----------] 1 test from FFTTest 30: [ RUN ] FFTTest.Real2DLength18_15Test 30: [ OK ] FFTTest.Real2DLength18_15Test (5 ms) 30: [----------] 1 test from FFTTest (5 ms total) 30: 30: [----------] 10 tests from 7_8_25_36_60/FFTTest1D 30: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0 30: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (0 ms) 30: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1 30: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (0 ms) 30: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2 30: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (1 ms) 30: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3 30: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (3 ms) 30: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4 30: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (1 ms) 30: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0 30: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (0 ms) 30: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1 30: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (0 ms) 30: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2 30: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (1 ms) 30: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3 30: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (10 ms) 30: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4 30: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (18 ms) 30: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (40 ms total) 30: 30: [----------] 2 tests from Works/ParameterizedFFTTest3D 30: [ RUN ] Works/ParameterizedFFTTest3D.RunsOnHost/5_6_9 30: [ OK ] Works/ParameterizedFFTTest3D.RunsOnHost/5_6_9 (1 ms) 30: [ RUN ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 30: [ OK ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 (1 ms) 30: [----------] 2 tests from Works/ParameterizedFFTTest3D (2 ms total) 30: 30: [----------] Global test environment tear-down 30: [==========] 15 tests from 4 test suites ran. (78 ms total) 30: [ PASSED ] 15 tests. 30/90 Test #30: FFTUnitTests .............................. Passed 0.27 sec test 31 Start 31: GpuUtilsUnitTests 31: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/gpu_utils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/GpuUtilsUnitTests.xml" 31: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gpu_utils/tests 31: Test timeout computed to be: 30 31: [==========] Running 67 tests from 22 test suites. 31: [----------] Global test environment set-up. 31: [----------] 2 tests from ClfftInitializer 31: [ RUN ] ClfftInitializer.SingleInitializationWorks 31: [ OK ] ClfftInitializer.SingleInitializationWorks (0 ms) 31: [ RUN ] ClfftInitializer.TwoInitializationsWork 31: [ OK ] ClfftInitializer.TwoInitializationsWork (0 ms) 31: [----------] 2 tests from ClfftInitializer (0 ms total) 31: 31: [----------] 1 test from DevicesAvailable 31: [ RUN ] DevicesAvailable.ShouldBeAbleToRunOnDevice 31: [ OK ] DevicesAvailable.ShouldBeAbleToRunOnDevice (0 ms) 31: [----------] 1 test from DevicesAvailable (0 ms total) 31: 31: [----------] 1 test from DeviceStreamManagerTest 31: [ RUN ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice 31: [ OK ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice (0 ms) 31: [----------] 1 test from DeviceStreamManagerTest (0 ms total) 31: 31: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int 31: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks 31: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms) 31: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory 31: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms) 31: [----------] 2 tests from HostAllocatorTest/0 (0 ms total) 31: 31: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = float 31: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks 31: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms) 31: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory 31: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms) 31: [----------] 2 tests from HostAllocatorTest/1 (0 ms total) 31: 31: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector 31: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks 31: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms) 31: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory 31: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms) 31: [----------] 2 tests from HostAllocatorTest/2 (0 ms total) 31: 31: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly 31: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks 31: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms) 31: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory 31: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms) 31: [----------] 2 tests from HostAllocatorTest/3 (0 ms total) 31: 31: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int 31: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks 31: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 31: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork 31: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms) 31: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve 31: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms) 31: [----------] 3 tests from HostAllocatorTestCopyable/0 (0 ms total) 31: 31: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = float 31: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks 31: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 31: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork 31: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms) 31: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve 31: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms) 31: [----------] 3 tests from HostAllocatorTestCopyable/1 (0 ms total) 31: 31: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector 31: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks 31: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 31: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork 31: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms) 31: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve 31: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms) 31: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total) 31: 31: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int 31: [ RUN ] HostAllocatorTestNoMem/0.CreateVector 31: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment 31: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction 31: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/0.Swap 31: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/0.Comparison 31: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms) 31: [----------] 5 tests from HostAllocatorTestNoMem/0 (0 ms total) 31: 31: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = float 31: [ RUN ] HostAllocatorTestNoMem/1.CreateVector 31: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment 31: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction 31: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/1.Swap 31: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/1.Comparison 31: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms) 31: [----------] 5 tests from HostAllocatorTestNoMem/1 (0 ms total) 31: 31: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector 31: [ RUN ] HostAllocatorTestNoMem/2.CreateVector 31: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment 31: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction 31: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/2.Swap 31: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/2.Comparison 31: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms) 31: [----------] 5 tests from HostAllocatorTestNoMem/2 (0 ms total) 31: 31: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly 31: [ RUN ] HostAllocatorTestNoMem/3.CreateVector 31: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment 31: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction 31: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/3.Swap 31: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/3.Comparison 31: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms) 31: [----------] 5 tests from HostAllocatorTestNoMem/3 (0 ms total) 31: 31: [----------] 3 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int 31: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment 31: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms) 31: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction 31: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms) 31: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator 31: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator (0 ms) 31: [----------] 3 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total) 31: 31: [----------] 3 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = float 31: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment 31: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms) 31: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction 31: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms) 31: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator 31: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator (0 ms) 31: [----------] 3 tests from HostAllocatorTestNoMemCopyable/1 (0 ms total) 31: 31: [----------] 3 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector 31: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment 31: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms) 31: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction 31: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms) 31: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator 31: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator (0 ms) 31: [----------] 3 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total) 31: 31: [----------] 1 test from HostAllocatorUntypedTest 31: [ RUN ] HostAllocatorUntypedTest.Comparison 31: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms) 31: [----------] 1 test from HostAllocatorUntypedTest (0 ms total) 31: 31: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 31: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 31: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 31: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 31: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/0.Move 31: [ OK ] AllocatorTest/0.Move (0 ms) 31: [----------] 4 tests from AllocatorTest/0 (0 ms total) 31: 31: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 31: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 31: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 31: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 31: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/1.Move 31: [ OK ] AllocatorTest/1.Move (0 ms) 31: [----------] 4 tests from AllocatorTest/1 (0 ms total) 31: 31: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator, gmx::HostAllocationPolicy> 31: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 31: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 31: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 31: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/2.Move 31: [ OK ] AllocatorTest/2.Move (0 ms) 31: [----------] 4 tests from AllocatorTest/2 (0 ms total) 31: 31: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 31: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 31: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 31: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 31: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/3.Move 31: [ OK ] AllocatorTest/3.Move (0 ms) 31: [----------] 4 tests from AllocatorTest/3 (0 ms total) 31: 31: [----------] Global test environment tear-down 31: [==========] 67 tests from 22 test suites ran. (1 ms total) 31: [ PASSED ] 67 tests. 31/90 Test #31: GpuUtilsUnitTests ......................... Passed 0.22 sec test 32 Start 32: HardwareUnitTests 32: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/hardware-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/HardwareUnitTests.xml" 32: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/hardware/tests 32: Test timeout computed to be: 30 32: [==========] Running 22 tests from 10 test suites. 32: [----------] Global test environment set-up. 32: [----------] 1 test from CpuInfoTest 32: [ RUN ] CpuInfoTest.SupportLevel 32: [ OK ] CpuInfoTest.SupportLevel (53 ms) 32: [----------] 1 test from CpuInfoTest (53 ms total) 32: 32: [----------] 4 tests from HardwareTopologyTest 32: [ RUN ] HardwareTopologyTest.Execute 32: [ OK ] HardwareTopologyTest.Execute (95 ms) 32: [ RUN ] HardwareTopologyTest.HwlocExecute 32: [ OK ] HardwareTopologyTest.HwlocExecute (83 ms) 32: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency 32: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (88 ms) 32: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency 32: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (89 ms) 32: [----------] 4 tests from HardwareTopologyTest (356 ms total) 32: 32: [----------] 1 test from DevicesManagerTest 32: [ RUN ] DevicesManagerTest.Serialization 32: [ OK ] DevicesManagerTest.Serialization (0 ms) 32: [ DISABLED ] DevicesManagerTest.DISABLED_DetectsUuid 32: [----------] 1 test from DevicesManagerTest (0 ms total) 32: 32: [----------] 1 test from UuidStringTest 32: [ RUN ] UuidStringTest.Works 32: [ OK ] UuidStringTest.Works (0 ms) 32: [----------] 1 test from UuidStringTest (0 ms total) 32: 32: [----------] 5 tests from XeonE52620/MockHardwareTopologyTest 32: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/0 32: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/0 (1 ms) 32: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/1 32: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/1 (0 ms) 32: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/2 32: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/2 (0 ms) 32: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/3 32: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/3 (0 ms) 32: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/4 32: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/4 (0 ms) 32: [----------] 5 tests from XeonE52620/MockHardwareTopologyTest (3 ms total) 32: 32: [----------] 5 tests from Xeon4116/MockHardwareTopologyTest 32: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/0 32: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/0 (1 ms) 32: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/1 32: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/1 (0 ms) 32: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/2 32: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/2 (0 ms) 32: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/3 32: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/3 (0 ms) 32: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/4 32: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/4 (1 ms) 32: [----------] 5 tests from Xeon4116/MockHardwareTopologyTest (5 ms total) 32: 32: [----------] 2 tests from Core12900K/MockHardwareTopologyTest 32: [ RUN ] Core12900K/MockHardwareTopologyTest.DetectsHardware/0 32: [ OK ] Core12900K/MockHardwareTopologyTest.DetectsHardware/0 (1 ms) 32: [ RUN ] Core12900K/MockHardwareTopologyTest.DetectsHardware/1 32: [ OK ] Core12900K/MockHardwareTopologyTest.DetectsHardware/1 (1 ms) 32: [----------] 2 tests from Core12900K/MockHardwareTopologyTest (2 ms total) 32: 32: [----------] 1 test from Core12900K/MockHardwareTopologySpecialSystemTest 32: [ RUN ] Core12900K/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 32: [ OK ] Core12900K/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (2 ms) 32: [----------] 1 test from Core12900K/MockHardwareTopologySpecialSystemTest (2 ms total) 32: 32: [----------] 1 test from Power9/MockHardwareTopologySpecialSystemTest 32: [ RUN ] Power9/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 32: [ OK ] Power9/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (3 ms) 32: [----------] 1 test from Power9/MockHardwareTopologySpecialSystemTest (3 ms total) 32: 32: [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest 32: [ RUN ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 32: [ OK ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (6 ms) 32: [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest (6 ms total) 32: 32: [----------] Global test environment tear-down 32: [==========] 22 tests from 10 test suites ran. (434 ms total) 32: [ PASSED ] 22 tests. 32: 32: YOU HAVE 1 DISABLED TEST 32: 32/90 Test #32: HardwareUnitTests ......................... Passed 0.49 sec test 33 Start 33: MathUnitTests 33: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/math-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/MathUnitTests.xml" 33: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/math/tests 33: Test timeout computed to be: 30 33: [==========] Running 328 tests from 41 test suites. 33: [----------] Global test environment set-up. 33: [----------] 1 test from EmptyArrayRefWithPaddingTest 33: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty 33: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms) 33: [----------] 1 test from EmptyArrayRefWithPaddingTest (0 ms total) 33: 33: [----------] 1 test from EmptyConstArrayRefWithPaddingTest 33: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty 33: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms) 33: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total) 33: 33: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding 33: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks 33: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms) 33: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks 33: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms) 33: [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total) 33: 33: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding 33: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks 33: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms) 33: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks 33: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms) 33: [----------] 2 tests from ArrayRefWithPaddingTest/1 (0 ms total) 33: 33: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding 33: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks 33: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms) 33: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks 33: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms) 33: [----------] 2 tests from ArrayRefWithPaddingTest/2 (0 ms total) 33: 33: [----------] 2 tests from InvertBoxMatrixTest 33: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent 33: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms) 33: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace 33: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms) 33: [----------] 2 tests from InvertBoxMatrixTest (0 ms total) 33: 33: [----------] 8 tests from ComplexNumberTest 33: [ RUN ] ComplexNumberTest.RealComplexMultiply 33: [ OK ] ComplexNumberTest.RealComplexMultiply (0 ms) 33: [ RUN ] ComplexNumberTest.RealComplexExp 33: [ OK ] ComplexNumberTest.RealComplexExp (0 ms) 33: [ RUN ] ComplexNumberTest.ComplexAdd 33: [ OK ] ComplexNumberTest.ComplexAdd (0 ms) 33: [ RUN ] ComplexNumberTest.ComplexSubtract 33: [ OK ] ComplexNumberTest.ComplexSubtract (0 ms) 33: [ RUN ] ComplexNumberTest.ComplexMultiply 33: [ OK ] ComplexNumberTest.ComplexMultiply (0 ms) 33: [ RUN ] ComplexNumberTest.ComplexDivision 33: [ OK ] ComplexNumberTest.ComplexDivision (0 ms) 33: [ RUN ] ComplexNumberTest.ComplexConjugate 33: [ OK ] ComplexNumberTest.ComplexConjugate (0 ms) 33: [ RUN ] ComplexNumberTest.ComplexAbs2 33: [ OK ] ComplexNumberTest.ComplexAbs2 (0 ms) 33: [----------] 8 tests from ComplexNumberTest (0 ms total) 33: 33: [----------] 11 tests from TranslateAndScaleTest 33: [ RUN ] TranslateAndScaleTest.identityTransformation 33: [ OK ] TranslateAndScaleTest.identityTransformation (0 ms) 33: [ RUN ] TranslateAndScaleTest.translationWithIdentityScaling 33: [ OK ] TranslateAndScaleTest.translationWithIdentityScaling (0 ms) 33: [ RUN ] TranslateAndScaleTest.scalingWithZeroTranslation 33: [ OK ] TranslateAndScaleTest.scalingWithZeroTranslation (0 ms) 33: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivial 33: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivial (0 ms) 33: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector 33: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector (0 ms) 33: [ RUN ] TranslateAndScaleTest.scalingIdentity 33: [ OK ] TranslateAndScaleTest.scalingIdentity (0 ms) 33: [ RUN ] TranslateAndScaleTest.scalingNonTrivial 33: [ OK ] TranslateAndScaleTest.scalingNonTrivial (0 ms) 33: [ RUN ] TranslateAndScaleTest.scalingNonTrivialSingleVector 33: [ OK ] TranslateAndScaleTest.scalingNonTrivialSingleVector (0 ms) 33: [ RUN ] TranslateAndScaleTest.scalingInverseNoZero 33: [ OK ] TranslateAndScaleTest.scalingInverseNoZero (0 ms) 33: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero 33: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero (0 ms) 33: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector 33: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector (0 ms) 33: [----------] 11 tests from TranslateAndScaleTest (0 ms total) 33: 33: [----------] 3 tests from AffineTransformationTest 33: [ RUN ] AffineTransformationTest.identityTransformYieldsSameVectors 33: [ OK ] AffineTransformationTest.identityTransformYieldsSameVectors (0 ms) 33: [ RUN ] AffineTransformationTest.applyTransformationToVectors 33: [ OK ] AffineTransformationTest.applyTransformationToVectors (0 ms) 33: [ RUN ] AffineTransformationTest.retrieveGradient 33: [ OK ] AffineTransformationTest.retrieveGradient (0 ms) 33: [----------] 3 tests from AffineTransformationTest (0 ms total) 33: 33: [----------] 14 tests from DensitySimilarityTest 33: [ RUN ] DensitySimilarityTest.InnerProductIsCorrect 33: [ OK ] DensitySimilarityTest.InnerProductIsCorrect (0 ms) 33: [ RUN ] DensitySimilarityTest.InnerProductGradientIsCorrect 33: [ OK ] DensitySimilarityTest.InnerProductGradientIsCorrect (0 ms) 33: [ RUN ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch 33: [ OK ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch (0 ms) 33: [ RUN ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch 33: [ OK ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch (0 ms) 33: [ RUN ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect 33: [ OK ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect (0 ms) 33: [ RUN ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero 33: [ OK ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero (0 ms) 33: [ RUN ] DensitySimilarityTest.RelativeEntropyIsCorrect 33: [ OK ] DensitySimilarityTest.RelativeEntropyIsCorrect (0 ms) 33: [ RUN ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect 33: [ OK ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect (0 ms) 33: [ RUN ] DensitySimilarityTest.CrossCorrelationIsOne 33: [ OK ] DensitySimilarityTest.CrossCorrelationIsOne (81 ms) 33: [ RUN ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated 33: [ OK ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated (72 ms) 33: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated 33: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated (6 ms) 33: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect 33: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect (0 ms) 33: [ RUN ] DensitySimilarityTest.NormalizationCorrect 33: [ OK ] DensitySimilarityTest.NormalizationCorrect (0 ms) 33: [ RUN ] DensitySimilarityTest.NormalizationAllNonPositive 33: [ OK ] DensitySimilarityTest.NormalizationAllNonPositive (0 ms) 33: [----------] 14 tests from DensitySimilarityTest (161 ms total) 33: 33: [----------] 6 tests from StructureSimilarityTest 33: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD 33: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms) 33: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho 33: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms) 33: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD 33: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms) 33: [ RUN ] StructureSimilarityTest.YieldsCorrectRho 33: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms) 33: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex 33: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms) 33: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex 33: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms) 33: [----------] 6 tests from StructureSimilarityTest (0 ms total) 33: 33: [----------] 8 tests from ExponentialMovingAverage 33: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero 33: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero (0 ms) 33: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative 33: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative (0 ms) 33: [ RUN ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue 33: [ OK ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue (0 ms) 33: [ RUN ] ExponentialMovingAverage.YieldsCorrectValue 33: [ OK ] ExponentialMovingAverage.YieldsCorrectValue (0 ms) 33: [ RUN ] ExponentialMovingAverage.SetAverageCorrectly 33: [ OK ] ExponentialMovingAverage.SetAverageCorrectly (0 ms) 33: [ RUN ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing 33: [ OK ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing (0 ms) 33: [ RUN ] ExponentialMovingAverage.InverseLagTimeCorrect 33: [ OK ] ExponentialMovingAverage.InverseLagTimeCorrect (0 ms) 33: [ RUN ] ExponentialMovingAverage.RoundTripAsKeyValueTree 33: [ OK ] ExponentialMovingAverage.RoundTripAsKeyValueTree (0 ms) 33: [----------] 8 tests from ExponentialMovingAverage (0 ms total) 33: 33: [----------] 21 tests from FunctionTest 33: [ RUN ] FunctionTest.StaticLog2 33: [ OK ] FunctionTest.StaticLog2 (0 ms) 33: [ RUN ] FunctionTest.Log2I32Bit 33: [ OK ] FunctionTest.Log2I32Bit (0 ms) 33: [ RUN ] FunctionTest.Log2I64Bit 33: [ OK ] FunctionTest.Log2I64Bit (0 ms) 33: [ RUN ] FunctionTest.GreatestCommonDivisor 33: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms) 33: [ RUN ] FunctionTest.InvsqrtFloat 33: [ OK ] FunctionTest.InvsqrtFloat (0 ms) 33: [ RUN ] FunctionTest.InvsqrtDouble 33: [ OK ] FunctionTest.InvsqrtDouble (0 ms) 33: [ RUN ] FunctionTest.InvsqrtInteger 33: [ OK ] FunctionTest.InvsqrtInteger (0 ms) 33: [ RUN ] FunctionTest.InvcbrtFloat 33: [ OK ] FunctionTest.InvcbrtFloat (0 ms) 33: [ RUN ] FunctionTest.InvcbrtDouble 33: [ OK ] FunctionTest.InvcbrtDouble (0 ms) 33: [ RUN ] FunctionTest.InvcbrtInteger 33: [ OK ] FunctionTest.InvcbrtInteger (0 ms) 33: [ RUN ] FunctionTest.SixthrootFloat 33: [ OK ] FunctionTest.SixthrootFloat (0 ms) 33: [ RUN ] FunctionTest.SixthrootDouble 33: [ OK ] FunctionTest.SixthrootDouble (0 ms) 33: [ RUN ] FunctionTest.SixthrootInteger 33: [ OK ] FunctionTest.SixthrootInteger (0 ms) 33: [ RUN ] FunctionTest.InvsixthrootFloat 33: [ OK ] FunctionTest.InvsixthrootFloat (0 ms) 33: [ RUN ] FunctionTest.InvsixthrootDouble 33: [ OK ] FunctionTest.InvsixthrootDouble (0 ms) 33: [ RUN ] FunctionTest.InvsixthrootInteger 33: [ OK ] FunctionTest.InvsixthrootInteger (0 ms) 33: [ RUN ] FunctionTest.Powers 33: [ OK ] FunctionTest.Powers (0 ms) 33: [ RUN ] FunctionTest.ErfInvFloat 33: [ OK ] FunctionTest.ErfInvFloat (0 ms) 33: [ RUN ] FunctionTest.ErfInvDouble 33: [ OK ] FunctionTest.ErfInvDouble (0 ms) 33: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat 33: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (0 ms) 33: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble 33: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (0 ms) 33: [----------] 21 tests from FunctionTest (2 ms total) 33: 33: [----------] 2 tests from FunctionTestIntegerTypes/0, where TypeParam = signed char 33: [ RUN ] FunctionTestIntegerTypes/0.IsPowerOfTwo 33: [ OK ] FunctionTestIntegerTypes/0.IsPowerOfTwo (0 ms) 33: [ RUN ] FunctionTestIntegerTypes/0.DivideRoundUp 33: [ OK ] FunctionTestIntegerTypes/0.DivideRoundUp (0 ms) 33: [----------] 2 tests from FunctionTestIntegerTypes/0 (0 ms total) 33: 33: [----------] 2 tests from FunctionTestIntegerTypes/1, where TypeParam = unsigned char 33: [ RUN ] FunctionTestIntegerTypes/1.IsPowerOfTwo 33: [ OK ] FunctionTestIntegerTypes/1.IsPowerOfTwo (0 ms) 33: [ RUN ] FunctionTestIntegerTypes/1.DivideRoundUp 33: [ OK ] FunctionTestIntegerTypes/1.DivideRoundUp (0 ms) 33: [----------] 2 tests from FunctionTestIntegerTypes/1 (0 ms total) 33: 33: [----------] 2 tests from FunctionTestIntegerTypes/2, where TypeParam = short 33: [ RUN ] FunctionTestIntegerTypes/2.IsPowerOfTwo 33: [ OK ] FunctionTestIntegerTypes/2.IsPowerOfTwo (0 ms) 33: [ RUN ] FunctionTestIntegerTypes/2.DivideRoundUp 33: [ OK ] FunctionTestIntegerTypes/2.DivideRoundUp (0 ms) 33: [----------] 2 tests from FunctionTestIntegerTypes/2 (0 ms total) 33: 33: [----------] 2 tests from FunctionTestIntegerTypes/3, where TypeParam = unsigned short 33: [ RUN ] FunctionTestIntegerTypes/3.IsPowerOfTwo 33: [ OK ] FunctionTestIntegerTypes/3.IsPowerOfTwo (0 ms) 33: [ RUN ] FunctionTestIntegerTypes/3.DivideRoundUp 33: [ OK ] FunctionTestIntegerTypes/3.DivideRoundUp (0 ms) 33: [----------] 2 tests from FunctionTestIntegerTypes/3 (0 ms total) 33: 33: [----------] 2 tests from FunctionTestIntegerTypes/4, where TypeParam = int 33: [ RUN ] FunctionTestIntegerTypes/4.IsPowerOfTwo 33: [ OK ] FunctionTestIntegerTypes/4.IsPowerOfTwo (0 ms) 33: [ RUN ] FunctionTestIntegerTypes/4.DivideRoundUp 33: [ OK ] FunctionTestIntegerTypes/4.DivideRoundUp (0 ms) 33: [----------] 2 tests from FunctionTestIntegerTypes/4 (0 ms total) 33: 33: [----------] 2 tests from FunctionTestIntegerTypes/5, where TypeParam = unsigned int 33: [ RUN ] FunctionTestIntegerTypes/5.IsPowerOfTwo 33: [ OK ] FunctionTestIntegerTypes/5.IsPowerOfTwo (0 ms) 33: [ RUN ] FunctionTestIntegerTypes/5.DivideRoundUp 33: [ OK ] FunctionTestIntegerTypes/5.DivideRoundUp (0 ms) 33: [----------] 2 tests from FunctionTestIntegerTypes/5 (0 ms total) 33: 33: [----------] 2 tests from FunctionTestIntegerTypes/6, where TypeParam = long 33: [ RUN ] FunctionTestIntegerTypes/6.IsPowerOfTwo 33: [ OK ] FunctionTestIntegerTypes/6.IsPowerOfTwo (0 ms) 33: [ RUN ] FunctionTestIntegerTypes/6.DivideRoundUp 33: [ OK ] FunctionTestIntegerTypes/6.DivideRoundUp (0 ms) 33: [----------] 2 tests from FunctionTestIntegerTypes/6 (0 ms total) 33: 33: [----------] 2 tests from FunctionTestIntegerTypes/7, where TypeParam = unsigned long 33: [ RUN ] FunctionTestIntegerTypes/7.IsPowerOfTwo 33: [ OK ] FunctionTestIntegerTypes/7.IsPowerOfTwo (0 ms) 33: [ RUN ] FunctionTestIntegerTypes/7.DivideRoundUp 33: [ OK ] FunctionTestIntegerTypes/7.DivideRoundUp (0 ms) 33: [----------] 2 tests from FunctionTestIntegerTypes/7 (0 ms total) 33: 33: [----------] 4 tests from GaussianOn1DLattice 33: [ RUN ] GaussianOn1DLattice.sumsCloseToOne 33: [ OK ] GaussianOn1DLattice.sumsCloseToOne (0 ms) 33: [ RUN ] GaussianOn1DLattice.isCorrect 33: [ OK ] GaussianOn1DLattice.isCorrect (0 ms) 33: [ RUN ] GaussianOn1DLattice.complementaryAmplitudesSumToZero 33: [ OK ] GaussianOn1DLattice.complementaryAmplitudesSumToZero (0 ms) 33: [ RUN ] GaussianOn1DLattice.doesNotOverflowForLargeRange 33: [ OK ] GaussianOn1DLattice.doesNotOverflowForLargeRange (0 ms) 33: [----------] 4 tests from GaussianOn1DLattice (0 ms total) 33: 33: [----------] 9 tests from GaussTransformTest 33: [ RUN ] GaussTransformTest.isZeroUponConstruction 33: [ OK ] GaussTransformTest.isZeroUponConstruction (0 ms) 33: [ RUN ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss 33: [ OK ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss (0 ms) 33: [ RUN ] GaussTransformTest.isZeroAfterSettingZero 33: [ OK ] GaussTransformTest.isZeroAfterSettingZero (0 ms) 33: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinX 33: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinX (0 ms) 33: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinY 33: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinY (0 ms) 33: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinZ 33: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinZ (0 ms) 33: [ RUN ] GaussTransformTest.complementaryGaussAddToZero 33: [ OK ] GaussTransformTest.complementaryGaussAddToZero (0 ms) 33: [ RUN ] GaussTransformTest.centerGaussianInCubeHasExpectedValues 33: [ OK ] GaussTransformTest.centerGaussianInCubeHasExpectedValues (0 ms) 33: [ RUN ] GaussTransformTest.view 33: [ OK ] GaussTransformTest.view (0 ms) 33: [----------] 9 tests from GaussTransformTest (0 ms total) 33: 33: [----------] 3 tests from DensityFittingForce 33: [ RUN ] DensityFittingForce.isZeroWhenMatchingDensity 33: [ OK ] DensityFittingForce.isZeroWhenMatchingDensity (0 ms) 33: [ RUN ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections 33: [ OK ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections (0 ms) 33: [ RUN ] DensityFittingForce.pullsTowardsDerivative 33: [ OK ] DensityFittingForce.pullsTowardsDerivative (0 ms) 33: [----------] 3 tests from DensityFittingForce (0 ms total) 33: 33: [----------] 2 tests from InvertMatrixTest 33: [ RUN ] InvertMatrixTest.IdentityIsImpotent 33: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms) 33: [ RUN ] InvertMatrixTest.ComputesInverse 33: [ OK ] InvertMatrixTest.ComputesInverse (0 ms) 33: [----------] 2 tests from InvertMatrixTest (0 ms total) 33: 33: [----------] 22 tests from MatrixTest 33: [ RUN ] MatrixTest.canSetFromArray 33: [ OK ] MatrixTest.canSetFromArray (0 ms) 33: [ RUN ] MatrixTest.canSetStaticallyFromList 33: [ OK ] MatrixTest.canSetStaticallyFromList (0 ms) 33: [ RUN ] MatrixTest.canConstructAndFill 33: [ OK ] MatrixTest.canConstructAndFill (0 ms) 33: [ RUN ] MatrixTest.canSetValues 33: [ OK ] MatrixTest.canSetValues (0 ms) 33: [ RUN ] MatrixTest.canCopyAssign 33: [ OK ] MatrixTest.canCopyAssign (0 ms) 33: [ RUN ] MatrixTest.canSwap 33: [ OK ] MatrixTest.canSwap (0 ms) 33: [ RUN ] MatrixTest.staticMultiDimArrayExtent 33: [ OK ] MatrixTest.staticMultiDimArrayExtent (0 ms) 33: [ RUN ] MatrixTest.canAddMatrix 33: [ OK ] MatrixTest.canAddMatrix (0 ms) 33: [ RUN ] MatrixTest.canSubstractMatrix 33: [ OK ] MatrixTest.canSubstractMatrix (0 ms) 33: [ RUN ] MatrixTest.canNegateMatrix 33: [ OK ] MatrixTest.canNegateMatrix (0 ms) 33: [ RUN ] MatrixTest.determinantWorks 33: [ OK ] MatrixTest.determinantWorks (0 ms) 33: [ RUN ] MatrixTest.noninvertableDeterminantIsZero 33: [ OK ] MatrixTest.noninvertableDeterminantIsZero (0 ms) 33: [ RUN ] MatrixTest.determinantOfDiagonalMatrix 33: [ OK ] MatrixTest.determinantOfDiagonalMatrix (0 ms) 33: [ RUN ] MatrixTest.traceWorks 33: [ OK ] MatrixTest.traceWorks (0 ms) 33: [ RUN ] MatrixTest.transposeWorks 33: [ OK ] MatrixTest.transposeWorks (0 ms) 33: [ RUN ] MatrixTest.transposeOfSymmetricMatrix 33: [ OK ] MatrixTest.transposeOfSymmetricMatrix (0 ms) 33: [ RUN ] MatrixTest.canCreateFromLegacyMatrix 33: [ OK ] MatrixTest.canCreateFromLegacyMatrix (0 ms) 33: [ RUN ] MatrixTest.canFillLegacyMatrix 33: [ OK ] MatrixTest.canFillLegacyMatrix (0 ms) 33: [ RUN ] MatrixTest.IdentityMatrix 33: [ OK ] MatrixTest.IdentityMatrix (0 ms) 33: [ RUN ] MatrixTest.MatrixMatrixInnerProduct 33: [ OK ] MatrixTest.MatrixMatrixInnerProduct (0 ms) 33: [ RUN ] MatrixTest.MatrixMatrixMultiplication 33: [ OK ] MatrixTest.MatrixMatrixMultiplication (0 ms) 33: [ RUN ] MatrixTest.MatrixVectorMultiplication 33: [ OK ] MatrixTest.MatrixVectorMultiplication (0 ms) 33: [----------] 22 tests from MatrixTest (0 ms total) 33: 33: [----------] 25 tests from MultiDimArrayTest 33: [ RUN ] MultiDimArrayTest.canConstructAndFillStatic 33: [ OK ] MultiDimArrayTest.canConstructAndFillStatic (0 ms) 33: [ RUN ] MultiDimArrayTest.canConstructAndFillDynamic 33: [ OK ] MultiDimArrayTest.canConstructAndFillDynamic (0 ms) 33: [ RUN ] MultiDimArrayTest.canSetValuesInStatic 33: [ OK ] MultiDimArrayTest.canSetValuesInStatic (0 ms) 33: [ RUN ] MultiDimArrayTest.canSetValuesInDynamic 33: [ OK ] MultiDimArrayTest.canSetValuesInDynamic (0 ms) 33: [ RUN ] MultiDimArrayTest.canMoveConstructStatic 33: [ OK ] MultiDimArrayTest.canMoveConstructStatic (0 ms) 33: [ RUN ] MultiDimArrayTest.canMoveConstructDynamic 33: [ OK ] MultiDimArrayTest.canMoveConstructDynamic (0 ms) 33: [ RUN ] MultiDimArrayTest.canMoveAssignStatic 33: [ OK ] MultiDimArrayTest.canMoveAssignStatic (0 ms) 33: [ RUN ] MultiDimArrayTest.canMoveAssignDynamic 33: [ OK ] MultiDimArrayTest.canMoveAssignDynamic (0 ms) 33: [ RUN ] MultiDimArrayTest.canCopyConstructStatic 33: [ OK ] MultiDimArrayTest.canCopyConstructStatic (0 ms) 33: [ RUN ] MultiDimArrayTest.canCopyConstructDynamic 33: [ OK ] MultiDimArrayTest.canCopyConstructDynamic (0 ms) 33: [ RUN ] MultiDimArrayTest.canCopyAssignStatic 33: [ OK ] MultiDimArrayTest.canCopyAssignStatic (0 ms) 33: [ RUN ] MultiDimArrayTest.canCopyAssignDynamic 33: [ OK ] MultiDimArrayTest.canCopyAssignDynamic (0 ms) 33: [ RUN ] MultiDimArrayTest.canSwapStatic 33: [ OK ] MultiDimArrayTest.canSwapStatic (0 ms) 33: [ RUN ] MultiDimArrayTest.canSwapDynamic 33: [ OK ] MultiDimArrayTest.canSwapDynamic (0 ms) 33: [ RUN ] MultiDimArrayTest.staticMultiDimArrayExtent 33: [ OK ] MultiDimArrayTest.staticMultiDimArrayExtent (0 ms) 33: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayExtent 33: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayExtent (0 ms) 33: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent 33: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent (0 ms) 33: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue 33: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue (0 ms) 33: [ RUN ] MultiDimArrayTest.staticMultiDimArrayFromArray 33: [ OK ] MultiDimArrayTest.staticMultiDimArrayFromArray (0 ms) 33: [ RUN ] MultiDimArrayTest.conversionToView 33: [ OK ] MultiDimArrayTest.conversionToView (0 ms) 33: [ RUN ] MultiDimArrayTest.conversionToConstView 33: [ OK ] MultiDimArrayTest.conversionToConstView (0 ms) 33: [ RUN ] MultiDimArrayTest.viewBegin 33: [ OK ] MultiDimArrayTest.viewBegin (0 ms) 33: [ RUN ] MultiDimArrayTest.viewEnd 33: [ OK ] MultiDimArrayTest.viewEnd (0 ms) 33: [ RUN ] MultiDimArrayTest.constViewConstBegin 33: [ OK ] MultiDimArrayTest.constViewConstBegin (0 ms) 33: [ RUN ] MultiDimArrayTest.constViewConstEnd 33: [ OK ] MultiDimArrayTest.constViewConstEnd (0 ms) 33: [----------] 25 tests from MultiDimArrayTest (0 ms total) 33: 33: [----------] 4 tests from MultiDimArrayToMdSpanTest 33: [ RUN ] MultiDimArrayToMdSpanTest.convertsToMdSpan 33: [ OK ] MultiDimArrayToMdSpanTest.convertsToMdSpan (0 ms) 33: [ RUN ] MultiDimArrayToMdSpanTest.constArrayToMdSpan 33: [ OK ] MultiDimArrayToMdSpanTest.constArrayToMdSpan (0 ms) 33: [ RUN ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan 33: [ OK ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan (0 ms) 33: [ RUN ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan 33: [ OK ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan (0 ms) 33: [----------] 4 tests from MultiDimArrayToMdSpanTest (0 ms total) 33: 33: [----------] 9 tests from NelderMeadSimplexTest 33: [ RUN ] NelderMeadSimplexTest.BestVertex 33: [ OK ] NelderMeadSimplexTest.BestVertex (0 ms) 33: [ RUN ] NelderMeadSimplexTest.WorstVertex 33: [ OK ] NelderMeadSimplexTest.WorstVertex (0 ms) 33: [ RUN ] NelderMeadSimplexTest.SecondWorstValue 33: [ OK ] NelderMeadSimplexTest.SecondWorstValue (0 ms) 33: [ RUN ] NelderMeadSimplexTest.ReflectionPoint 33: [ OK ] NelderMeadSimplexTest.ReflectionPoint (0 ms) 33: [ RUN ] NelderMeadSimplexTest.EvaluateExpansionPoint 33: [ OK ] NelderMeadSimplexTest.EvaluateExpansionPoint (0 ms) 33: [ RUN ] NelderMeadSimplexTest.EvaluateContractionPoint 33: [ OK ] NelderMeadSimplexTest.EvaluateContractionPoint (0 ms) 33: [ RUN ] NelderMeadSimplexTest.SwapOutWorst 33: [ OK ] NelderMeadSimplexTest.SwapOutWorst (0 ms) 33: [ RUN ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest 33: [ OK ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest (0 ms) 33: [ RUN ] NelderMeadSimplexTest.OrientedLength 33: [ OK ] NelderMeadSimplexTest.OrientedLength (0 ms) 33: [----------] 9 tests from NelderMeadSimplexTest (0 ms total) 33: 33: [----------] 2 tests from NelderMead 33: [ RUN ] NelderMead.Optimizes2DFunctionCorrectly 33: [ OK ] NelderMead.Optimizes2DFunctionCorrectly (0 ms) 33: [ RUN ] NelderMead.Optimizes3DFunctorCorrectly 33: [ OK ] NelderMead.Optimizes3DFunctorCorrectly (0 ms) 33: [----------] 2 tests from NelderMead (0 ms total) 33: 33: [----------] 11 tests from PaddedVectorTest/0, where TypeParam = std::allocator 33: [ RUN ] PaddedVectorTest/0.DefaultConstructorWorks 33: [ OK ] PaddedVectorTest/0.DefaultConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/0.ResizeWorks 33: [ OK ] PaddedVectorTest/0.ResizeWorks (0 ms) 33: [ RUN ] PaddedVectorTest/0.ReserveWorks 33: [ OK ] PaddedVectorTest/0.ReserveWorks (0 ms) 33: [ RUN ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve 33: [ OK ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve (0 ms) 33: [ RUN ] PaddedVectorTest/0.MoveConstructorWorks 33: [ OK ] PaddedVectorTest/0.MoveConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks 33: [ OK ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/0.MoveAssignmentWorks 33: [ OK ] PaddedVectorTest/0.MoveAssignmentWorks (0 ms) 33: [ RUN ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical 33: [ OK ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical (0 ms) 33: [ RUN ] PaddedVectorTest/0.CanCopyAssign 33: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms) 33: [ RUN ] PaddedVectorTest/0.CanMoveAssign 33: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms) 33: [ RUN ] PaddedVectorTest/0.CanSwap 33: [ OK ] PaddedVectorTest/0.CanSwap (0 ms) 33: [----------] 11 tests from PaddedVectorTest/0 (0 ms total) 33: 33: [----------] 11 tests from PaddedVectorTest/1, where TypeParam = std::allocator 33: [ RUN ] PaddedVectorTest/1.DefaultConstructorWorks 33: [ OK ] PaddedVectorTest/1.DefaultConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/1.ResizeWorks 33: [ OK ] PaddedVectorTest/1.ResizeWorks (0 ms) 33: [ RUN ] PaddedVectorTest/1.ReserveWorks 33: [ OK ] PaddedVectorTest/1.ReserveWorks (0 ms) 33: [ RUN ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve 33: [ OK ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve (0 ms) 33: [ RUN ] PaddedVectorTest/1.MoveConstructorWorks 33: [ OK ] PaddedVectorTest/1.MoveConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks 33: [ OK ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/1.MoveAssignmentWorks 33: [ OK ] PaddedVectorTest/1.MoveAssignmentWorks (0 ms) 33: [ RUN ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical 33: [ OK ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical (0 ms) 33: [ RUN ] PaddedVectorTest/1.CanCopyAssign 33: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms) 33: [ RUN ] PaddedVectorTest/1.CanMoveAssign 33: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms) 33: [ RUN ] PaddedVectorTest/1.CanSwap 33: [ OK ] PaddedVectorTest/1.CanSwap (0 ms) 33: [----------] 11 tests from PaddedVectorTest/1 (0 ms total) 33: 33: [----------] 11 tests from PaddedVectorTest/2, where TypeParam = std::allocator 33: [ RUN ] PaddedVectorTest/2.DefaultConstructorWorks 33: [ OK ] PaddedVectorTest/2.DefaultConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/2.ResizeWorks 33: [ OK ] PaddedVectorTest/2.ResizeWorks (0 ms) 33: [ RUN ] PaddedVectorTest/2.ReserveWorks 33: [ OK ] PaddedVectorTest/2.ReserveWorks (0 ms) 33: [ RUN ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve 33: [ OK ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve (0 ms) 33: [ RUN ] PaddedVectorTest/2.MoveConstructorWorks 33: [ OK ] PaddedVectorTest/2.MoveConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks 33: [ OK ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/2.MoveAssignmentWorks 33: [ OK ] PaddedVectorTest/2.MoveAssignmentWorks (0 ms) 33: [ RUN ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical 33: [ OK ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical (0 ms) 33: [ RUN ] PaddedVectorTest/2.CanCopyAssign 33: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms) 33: [ RUN ] PaddedVectorTest/2.CanMoveAssign 33: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms) 33: [ RUN ] PaddedVectorTest/2.CanSwap 33: [ OK ] PaddedVectorTest/2.CanSwap (0 ms) 33: [----------] 11 tests from PaddedVectorTest/2 (0 ms total) 33: 33: [----------] 11 tests from PaddedVectorTest/3, where TypeParam = std::allocator > 33: [ RUN ] PaddedVectorTest/3.DefaultConstructorWorks 33: [ OK ] PaddedVectorTest/3.DefaultConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/3.ResizeWorks 33: [ OK ] PaddedVectorTest/3.ResizeWorks (0 ms) 33: [ RUN ] PaddedVectorTest/3.ReserveWorks 33: [ OK ] PaddedVectorTest/3.ReserveWorks (0 ms) 33: [ RUN ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve 33: [ OK ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve (0 ms) 33: [ RUN ] PaddedVectorTest/3.MoveConstructorWorks 33: [ OK ] PaddedVectorTest/3.MoveConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks 33: [ OK ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/3.MoveAssignmentWorks 33: [ OK ] PaddedVectorTest/3.MoveAssignmentWorks (0 ms) 33: [ RUN ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical 33: [ OK ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical (0 ms) 33: [ RUN ] PaddedVectorTest/3.CanCopyAssign 33: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms) 33: [ RUN ] PaddedVectorTest/3.CanMoveAssign 33: [ OK ] PaddedVectorTest/3.CanMoveAssign (0 ms) 33: [ RUN ] PaddedVectorTest/3.CanSwap 33: [ OK ] PaddedVectorTest/3.CanSwap (0 ms) 33: [----------] 11 tests from PaddedVectorTest/3 (0 ms total) 33: 33: [----------] 11 tests from PaddedVectorTest/4, where TypeParam = std::allocator > 33: [ RUN ] PaddedVectorTest/4.DefaultConstructorWorks 33: [ OK ] PaddedVectorTest/4.DefaultConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/4.ResizeWorks 33: [ OK ] PaddedVectorTest/4.ResizeWorks (0 ms) 33: [ RUN ] PaddedVectorTest/4.ReserveWorks 33: [ OK ] PaddedVectorTest/4.ReserveWorks (0 ms) 33: [ RUN ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve 33: [ OK ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve (0 ms) 33: [ RUN ] PaddedVectorTest/4.MoveConstructorWorks 33: [ OK ] PaddedVectorTest/4.MoveConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks 33: [ OK ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/4.MoveAssignmentWorks 33: [ OK ] PaddedVectorTest/4.MoveAssignmentWorks (0 ms) 33: [ RUN ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical 33: [ OK ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical (0 ms) 33: [ RUN ] PaddedVectorTest/4.CanCopyAssign 33: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms) 33: [ RUN ] PaddedVectorTest/4.CanMoveAssign 33: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms) 33: [ RUN ] PaddedVectorTest/4.CanSwap 33: [ OK ] PaddedVectorTest/4.CanSwap (0 ms) 33: [----------] 11 tests from PaddedVectorTest/4 (0 ms total) 33: 33: [----------] 11 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator 33: [ RUN ] PaddedVectorTest/5.DefaultConstructorWorks 33: [ OK ] PaddedVectorTest/5.DefaultConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/5.ResizeWorks 33: [ OK ] PaddedVectorTest/5.ResizeWorks (0 ms) 33: [ RUN ] PaddedVectorTest/5.ReserveWorks 33: [ OK ] PaddedVectorTest/5.ReserveWorks (0 ms) 33: [ RUN ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve 33: [ OK ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve (0 ms) 33: [ RUN ] PaddedVectorTest/5.MoveConstructorWorks 33: [ OK ] PaddedVectorTest/5.MoveConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks 33: [ OK ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/5.MoveAssignmentWorks 33: [ OK ] PaddedVectorTest/5.MoveAssignmentWorks (0 ms) 33: [ RUN ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical 33: [ OK ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical (0 ms) 33: [ RUN ] PaddedVectorTest/5.CanCopyAssign 33: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms) 33: [ RUN ] PaddedVectorTest/5.CanMoveAssign 33: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms) 33: [ RUN ] PaddedVectorTest/5.CanSwap 33: [ OK ] PaddedVectorTest/5.CanSwap (0 ms) 33: [----------] 11 tests from PaddedVectorTest/5 (0 ms total) 33: 33: [----------] 11 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator 33: [ RUN ] PaddedVectorTest/6.DefaultConstructorWorks 33: [ OK ] PaddedVectorTest/6.DefaultConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/6.ResizeWorks 33: [ OK ] PaddedVectorTest/6.ResizeWorks (0 ms) 33: [ RUN ] PaddedVectorTest/6.ReserveWorks 33: [ OK ] PaddedVectorTest/6.ReserveWorks (0 ms) 33: [ RUN ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve 33: [ OK ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve (0 ms) 33: [ RUN ] PaddedVectorTest/6.MoveConstructorWorks 33: [ OK ] PaddedVectorTest/6.MoveConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks 33: [ OK ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/6.MoveAssignmentWorks 33: [ OK ] PaddedVectorTest/6.MoveAssignmentWorks (0 ms) 33: [ RUN ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical 33: [ OK ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical (0 ms) 33: [ RUN ] PaddedVectorTest/6.CanCopyAssign 33: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms) 33: [ RUN ] PaddedVectorTest/6.CanMoveAssign 33: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms) 33: [ RUN ] PaddedVectorTest/6.CanSwap 33: [ OK ] PaddedVectorTest/6.CanSwap (0 ms) 33: [----------] 11 tests from PaddedVectorTest/6 (0 ms total) 33: 33: [----------] 11 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator 33: [ RUN ] PaddedVectorTest/7.DefaultConstructorWorks 33: [ OK ] PaddedVectorTest/7.DefaultConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/7.ResizeWorks 33: [ OK ] PaddedVectorTest/7.ResizeWorks (0 ms) 33: [ RUN ] PaddedVectorTest/7.ReserveWorks 33: [ OK ] PaddedVectorTest/7.ReserveWorks (0 ms) 33: [ RUN ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve 33: [ OK ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve (0 ms) 33: [ RUN ] PaddedVectorTest/7.MoveConstructorWorks 33: [ OK ] PaddedVectorTest/7.MoveConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks 33: [ OK ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/7.MoveAssignmentWorks 33: [ OK ] PaddedVectorTest/7.MoveAssignmentWorks (0 ms) 33: [ RUN ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical 33: [ OK ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical (0 ms) 33: [ RUN ] PaddedVectorTest/7.CanCopyAssign 33: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms) 33: [ RUN ] PaddedVectorTest/7.CanMoveAssign 33: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms) 33: [ RUN ] PaddedVectorTest/7.CanSwap 33: [ OK ] PaddedVectorTest/7.CanSwap (0 ms) 33: [----------] 11 tests from PaddedVectorTest/7 (0 ms total) 33: 33: [----------] 11 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 33: [ RUN ] PaddedVectorTest/8.DefaultConstructorWorks 33: [ OK ] PaddedVectorTest/8.DefaultConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/8.ResizeWorks 33: [ OK ] PaddedVectorTest/8.ResizeWorks (0 ms) 33: [ RUN ] PaddedVectorTest/8.ReserveWorks 33: [ OK ] PaddedVectorTest/8.ReserveWorks (0 ms) 33: [ RUN ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve 33: [ OK ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve (0 ms) 33: [ RUN ] PaddedVectorTest/8.MoveConstructorWorks 33: [ OK ] PaddedVectorTest/8.MoveConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks 33: [ OK ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/8.MoveAssignmentWorks 33: [ OK ] PaddedVectorTest/8.MoveAssignmentWorks (0 ms) 33: [ RUN ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical 33: [ OK ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical (0 ms) 33: [ RUN ] PaddedVectorTest/8.CanCopyAssign 33: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms) 33: [ RUN ] PaddedVectorTest/8.CanMoveAssign 33: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms) 33: [ RUN ] PaddedVectorTest/8.CanSwap 33: [ OK ] PaddedVectorTest/8.CanSwap (0 ms) 33: [----------] 11 tests from PaddedVectorTest/8 (0 ms total) 33: 33: [----------] 11 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 33: [ RUN ] PaddedVectorTest/9.DefaultConstructorWorks 33: [ OK ] PaddedVectorTest/9.DefaultConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/9.ResizeWorks 33: [ OK ] PaddedVectorTest/9.ResizeWorks (0 ms) 33: [ RUN ] PaddedVectorTest/9.ReserveWorks 33: [ OK ] PaddedVectorTest/9.ReserveWorks (0 ms) 33: [ RUN ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve 33: [ OK ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve (0 ms) 33: [ RUN ] PaddedVectorTest/9.MoveConstructorWorks 33: [ OK ] PaddedVectorTest/9.MoveConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks 33: [ OK ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/9.MoveAssignmentWorks 33: [ OK ] PaddedVectorTest/9.MoveAssignmentWorks (0 ms) 33: [ RUN ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical 33: [ OK ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical (0 ms) 33: [ RUN ] PaddedVectorTest/9.CanCopyAssign 33: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms) 33: [ RUN ] PaddedVectorTest/9.CanMoveAssign 33: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms) 33: [ RUN ] PaddedVectorTest/9.CanSwap 33: [ OK ] PaddedVectorTest/9.CanSwap (0 ms) 33: [----------] 11 tests from PaddedVectorTest/9 (0 ms total) 33: 33: [----------] 41 tests from RVecTest 33: [ RUN ] RVecTest.CanBeStoredInVector 33: [ OK ] RVecTest.CanBeStoredInVector (0 ms) 33: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec 33: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms) 33: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec 33: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms) 33: [ RUN ] RVecTest.WorksAsMutable_rvec 33: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms) 33: [ RUN ] RVecTest.WorksAs_rvec_Array 33: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms) 33: [ RUN ] RVecTest.ComparesEqual 33: [ OK ] RVecTest.ComparesEqual (0 ms) 33: [ RUN ] RVecTest.ComparesUnequal 33: [ OK ] RVecTest.ComparesUnequal (0 ms) 33: [ RUN ] RVecTest.CanAddRVecToRvec 33: [ OK ] RVecTest.CanAddRVecToRvec (0 ms) 33: [ RUN ] RVecTest.CanAddAssignRVecToRvec 33: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms) 33: [ RUN ] RVecTest.CanSubtractRVecFromRvec 33: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms) 33: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec 33: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms) 33: [ RUN ] RVecTest.CanDotProductRVecByRvec 33: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms) 33: [ RUN ] RVecTest.CanCrossProductRVecByRvec 33: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms) 33: [ RUN ] RVecTest.CanDivideRVecInplace 33: [ OK ] RVecTest.CanDivideRVecInplace (0 ms) 33: [ RUN ] RVecTest.CanScaleRVec 33: [ OK ] RVecTest.CanScaleRVec (0 ms) 33: [ RUN ] RVecTest.CanDivideRVec 33: [ OK ] RVecTest.CanDivideRVec (0 ms) 33: [ RUN ] RVecTest.CanDoUnitvFromRVec 33: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms) 33: [ RUN ] RVecTest.CanSqLengthOfRVec 33: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms) 33: [ RUN ] RVecTest.CanLengthOfRVec 33: [ OK ] RVecTest.CanLengthOfRVec (0 ms) 33: [ RUN ] RVecTest.CanCastToRVec 33: [ OK ] RVecTest.CanCastToRVec (0 ms) 33: [ RUN ] RVecTest.CanCastToDVec 33: [ OK ] RVecTest.CanCastToDVec (0 ms) 33: [ RUN ] RVecTest.CanLeftScalarMultiply 33: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms) 33: [ RUN ] RVecTest.CanRightScalarMultiply 33: [ OK ] RVecTest.CanRightScalarMultiply (0 ms) 33: [ RUN ] RVecTest.CanGetUnitvFromRVec 33: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms) 33: [ RUN ] RVecTest.CanGetSqLengthOfRVec 33: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms) 33: [ RUN ] RVecTest.CanGetLengthOfRVec 33: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms) 33: [ RUN ] RVecTest.CanDoCrossProductOfRVec 33: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms) 33: [ RUN ] RVecTest.CanDoDotProductOfRVec 33: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms) 33: [ RUN ] RVecTest.CanScaleByVector 33: [ OK ] RVecTest.CanScaleByVector (0 ms) 33: [ RUN ] RVecTest.CanNegate 33: [ OK ] RVecTest.CanNegate (0 ms) 33: [ RUN ] RVecTest.asIVec 33: [ OK ] RVecTest.asIVec (0 ms) 33: [ RUN ] RVecTest.elementWiseMin 33: [ OK ] RVecTest.elementWiseMin (0 ms) 33: [ RUN ] RVecTest.elementWiseMax 33: [ OK ] RVecTest.elementWiseMax (0 ms) 33: [ RUN ] RVecTest.WorksAs_dvec_Reference 33: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms) 33: [ RUN ] RVecTest.WorksAs_ivec_Reference 33: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms) 33: [ RUN ] RVecTest.WorksAs_rvec_Reference 33: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms) 33: [ RUN ] RVecTest.CopyConstructorWorks 33: [ OK ] RVecTest.CopyConstructorWorks (0 ms) 33: [ RUN ] RVecTest.CopyAssignmentWorks 33: [ OK ] RVecTest.CopyAssignmentWorks (0 ms) 33: [ RUN ] RVecTest.MoveConstructorWorks 33: [ OK ] RVecTest.MoveConstructorWorks (0 ms) 33: [ RUN ] RVecTest.MoveAssignmentWorks 33: [ OK ] RVecTest.MoveAssignmentWorks (0 ms) 33: [ RUN ] RVecTest.UsableInConstexpr 33: [ OK ] RVecTest.UsableInConstexpr (0 ms) 33: [----------] 41 tests from RVecTest (1 ms total) 33: 33: [----------] Global test environment tear-down 33: [==========] 328 tests from 41 test suites ran. (169 ms total) 33: [ PASSED ] 328 tests. 33/90 Test #33: MathUnitTests ............................. Passed 0.25 sec test 34 Start 34: MdrunUtilityUnitTests 34: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/mdrunutility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/MdrunUtilityUnitTests.xml" 34: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdrunutility/tests 34: Test timeout computed to be: 30 34: [==========] Running 21 tests from 2 test suites. 34: [----------] Global test environment set-up. 34: [----------] 4 tests from MDModulesNotifierTest 34: [ RUN ] MDModulesNotifierTest.AddConsumer 34: [ OK ] MDModulesNotifierTest.AddConsumer (0 ms) 34: [ RUN ] MDModulesNotifierTest.AddConsumerWithPointerParameter 34: [ OK ] MDModulesNotifierTest.AddConsumerWithPointerParameter (0 ms) 34: [ RUN ] MDModulesNotifierTest.AddTwoDifferentConsumers 34: [ OK ] MDModulesNotifierTest.AddTwoDifferentConsumers (0 ms) 34: [ RUN ] MDModulesNotifierTest.AddConsumerOfTwoResources 34: [ OK ] MDModulesNotifierTest.AddConsumerOfTwoResources (0 ms) 34: [----------] 4 tests from MDModulesNotifierTest (0 ms total) 34: 34: [----------] 17 tests from ThreadAffinityTest 34: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled 34: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (0 ms) 34: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported 34: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms) 34: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads 34: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (0 ms) 34: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads 34: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (0 ms) 34: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads 34: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (0 ms) 34: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware 34: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (0 ms) 34: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads 34: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (0 ms) 34: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset 34: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (0 ms) 34: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride 34: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (0 ms) 34: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto 34: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (0 ms) 34: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced 34: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (0 ms) 34: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced 34: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (0 ms) 34: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread 34: NOTE: Affinity setting failed. 34: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (0 ms) 34: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto 34: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (9 ms) 34: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced 34: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (0 ms) 34: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads 34: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (0 ms) 34: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing 34: NOTE: Affinity setting for 1/2 threads failed. 34: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (0 ms) 34: [----------] 17 tests from ThreadAffinityTest (17 ms total) 34: 34: [----------] Global test environment tear-down 34: [==========] 21 tests from 2 test suites ran. (17 ms total) 34: [ PASSED ] 21 tests. 34/90 Test #34: MdrunUtilityUnitTests ..................... Passed 0.06 sec test 35 Start 35: MdrunUtilityMpiUnitTests 35: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/mdrunutility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/MdrunUtilityMpiUnitTests.xml" 35: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdrunutility/tests 35: Test timeout computed to be: 30 35: [==========] Running 13 tests from 2 test suites. 35: [----------] Global test environment set-up. 35: [----------] 6 tests from ThreadAffinityMultiRankTest 35: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode 35: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (57 ms) 35: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride 35: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (135 ms) 35: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes 35: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (49 ms) 35: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled 35: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (37 ms) 35: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto 35: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (64 ms) 35: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce 35: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (83 ms) 35: [----------] 6 tests from ThreadAffinityMultiRankTest (429 ms total) 35: 35: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest 35: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMainOnly 35: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMainOnly (68 ms) 35: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMainOnly 35: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMainOnly (52 ms) 35: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMain 35: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMain (8 ms) 35: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMainOnly 35: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMainOnly (30 ms) 35: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMainOnly 35: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMainOnly (1 ms) 35: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMainOnly 35: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMainOnly (11 ms) 35: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMainOnly 35: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMainOnly (1 ms) 35: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (174 ms total) 35: 35: [----------] Global test environment tear-down 35: [==========] 13 tests from 2 test suites ran. (603 ms total) 35: [ PASSED ] 13 tests. 35/90 Test #35: MdrunUtilityMpiUnitTests .................. Passed 0.72 sec test 36 Start 36: MDSpanTests 36: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/mdspan-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/MDSpanTests.xml" 36: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdspan/tests 36: Test timeout computed to be: 30 36: [==========] Running 32 tests from 7 test suites. 36: [----------] Global test environment set-up. 36: [----------] 4 tests from BasicAccessorPolicy 36: [ RUN ] BasicAccessorPolicy.Decay 36: [ OK ] BasicAccessorPolicy.Decay (0 ms) 36: [ RUN ] BasicAccessorPolicy.Access 36: [ OK ] BasicAccessorPolicy.Access (0 ms) 36: [ RUN ] BasicAccessorPolicy.Offset 36: [ OK ] BasicAccessorPolicy.Offset (0 ms) 36: [ RUN ] BasicAccessorPolicy.CopyAccessor 36: [ OK ] BasicAccessorPolicy.CopyAccessor (0 ms) 36: [----------] 4 tests from BasicAccessorPolicy (0 ms total) 36: 36: [----------] 4 tests from ExtentsTest 36: [ RUN ] ExtentsTest.Construction 36: [ OK ] ExtentsTest.Construction (0 ms) 36: [ RUN ] ExtentsTest.PurelyStatic 36: [ OK ] ExtentsTest.PurelyStatic (0 ms) 36: [ RUN ] ExtentsTest.RankNought 36: [ OK ] ExtentsTest.RankNought (0 ms) 36: [ RUN ] ExtentsTest.Assignment 36: [ OK ] ExtentsTest.Assignment (0 ms) 36: [----------] 4 tests from ExtentsTest (0 ms total) 36: 36: [----------] 8 tests from MdSpanExtension 36: [ RUN ] MdSpanExtension.SlicingAllStatic 36: [ OK ] MdSpanExtension.SlicingAllStatic (0 ms) 36: [ RUN ] MdSpanExtension.SlicingDynamic 36: [ OK ] MdSpanExtension.SlicingDynamic (0 ms) 36: [ RUN ] MdSpanExtension.SlicingAllStatic3D 36: [ OK ] MdSpanExtension.SlicingAllStatic3D (0 ms) 36: [ RUN ] MdSpanExtension.SlicingEqualsView3D 36: [ OK ] MdSpanExtension.SlicingEqualsView3D (0 ms) 36: [ RUN ] MdSpanExtension.additionWorks 36: [ OK ] MdSpanExtension.additionWorks (0 ms) 36: [ RUN ] MdSpanExtension.subtractionWorks 36: [ OK ] MdSpanExtension.subtractionWorks (0 ms) 36: [ RUN ] MdSpanExtension.multiplicationWorks 36: [ OK ] MdSpanExtension.multiplicationWorks (0 ms) 36: [ RUN ] MdSpanExtension.divisionWorks 36: [ OK ] MdSpanExtension.divisionWorks (0 ms) 36: [----------] 8 tests from MdSpanExtension (0 ms total) 36: 36: [----------] 3 tests from LayoutTests 36: [ RUN ] LayoutTests.LayoutRightConstruction 36: [ OK ] LayoutTests.LayoutRightConstruction (0 ms) 36: [ RUN ] LayoutTests.LayoutRightProperties 36: [ OK ] LayoutTests.LayoutRightProperties (0 ms) 36: [ RUN ] LayoutTests.LayoutRightOperator 36: [ OK ] LayoutTests.LayoutRightOperator (0 ms) 36: [----------] 3 tests from LayoutTests (0 ms total) 36: 36: [----------] 1 test from MdSpanTest 36: [ RUN ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly 36: [ OK ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly (0 ms) 36: [----------] 1 test from MdSpanTest (0 ms total) 36: 36: [----------] 6 tests from MdSpanTest/0, where TypeParam = gmx::basic_mdspan, gmx::layout_right, gmx::accessor_basic > 36: [ RUN ] MdSpanTest/0.Rank 36: [ OK ] MdSpanTest/0.Rank (0 ms) 36: [ RUN ] MdSpanTest/0.DynamicRank 36: [ OK ] MdSpanTest/0.DynamicRank (0 ms) 36: [ RUN ] MdSpanTest/0.Extents 36: [ OK ] MdSpanTest/0.Extents (0 ms) 36: [ RUN ] MdSpanTest/0.Strides 36: [ OK ] MdSpanTest/0.Strides (0 ms) 36: [ RUN ] MdSpanTest/0.Properties 36: [ OK ] MdSpanTest/0.Properties (0 ms) 36: [ RUN ] MdSpanTest/0.Operator 36: [ OK ] MdSpanTest/0.Operator (0 ms) 36: [----------] 6 tests from MdSpanTest/0 (0 ms total) 36: 36: [----------] 6 tests from MdSpanTest/1, where TypeParam = gmx::basic_mdspan, gmx::layout_right, gmx::accessor_basic > 36: [ RUN ] MdSpanTest/1.Rank 36: [ OK ] MdSpanTest/1.Rank (0 ms) 36: [ RUN ] MdSpanTest/1.DynamicRank 36: [ OK ] MdSpanTest/1.DynamicRank (0 ms) 36: [ RUN ] MdSpanTest/1.Extents 36: [ OK ] MdSpanTest/1.Extents (0 ms) 36: [ RUN ] MdSpanTest/1.Strides 36: [ OK ] MdSpanTest/1.Strides (0 ms) 36: [ RUN ] MdSpanTest/1.Properties 36: [ OK ] MdSpanTest/1.Properties (0 ms) 36: [ RUN ] MdSpanTest/1.Operator 36: [ OK ] MdSpanTest/1.Operator (0 ms) 36: [----------] 6 tests from MdSpanTest/1 (0 ms total) 36: 36: [----------] Global test environment tear-down 36: [==========] 32 tests from 7 test suites ran. (0 ms total) 36: [ PASSED ] 32 tests. 36/90 Test #36: MDSpanTests ............................... Passed 0.21 sec test 37 Start 37: MdtypesUnitTest 37: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/mdtypes-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/MdtypesUnitTest.xml" 37: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/mdtypes/tests 37: Test timeout computed to be: 30 37: [==========] Running 97 tests from 7 test suites. 37: [----------] Global test environment set-up. 37: [----------] 4 tests from ForeingLambdaTermsDhdl 37: [ RUN ] ForeingLambdaTermsDhdl.RateCheckWorks 37: [ OK ] ForeingLambdaTermsDhdl.RateCheckWorks (0 ms) 37: [ RUN ] ForeingLambdaTermsDhdl.AllLinear 37: [ OK ] ForeingLambdaTermsDhdl.AllLinear (0 ms) 37: [ RUN ] ForeingLambdaTermsDhdl.AllLinearNegative 37: [ OK ] ForeingLambdaTermsDhdl.AllLinearNegative (0 ms) 37: [ RUN ] ForeingLambdaTermsDhdl.SeparateVdwCoul 37: [ OK ] ForeingLambdaTermsDhdl.SeparateVdwCoul (0 ms) 37: [----------] 4 tests from ForeingLambdaTermsDhdl (0 ms total) 37: 37: [----------] 4 tests from ObservablesReducerTest 37: [ RUN ] ObservablesReducerTest.CanMoveAssign 37: [ OK ] ObservablesReducerTest.CanMoveAssign (0 ms) 37: [ RUN ] ObservablesReducerTest.CanMoveConstruct 37: [ OK ] ObservablesReducerTest.CanMoveConstruct (0 ms) 37: [ RUN ] ObservablesReducerTest.CanBuildAndUseWithNoSubscribers 37: [ OK ] ObservablesReducerTest.CanBuildAndUseWithNoSubscribers (0 ms) 37: [ RUN ] ObservablesReducerTest.CanBuildAndUseWithOneSubscriber 37: [ OK ] ObservablesReducerTest.CanBuildAndUseWithOneSubscriber (0 ms) 37: [----------] 4 tests from ObservablesReducerTest (0 ms total) 37: 37: [----------] 2 tests from CheckpointDataTest 37: [ RUN ] CheckpointDataTest.SingleDataTest 37: [ OK ] CheckpointDataTest.SingleDataTest (850 ms) 37: [ RUN ] CheckpointDataTest.MultiDataTest 37: [ OK ] CheckpointDataTest.MultiDataTest (607 ms) 37: [----------] 2 tests from CheckpointDataTest (1458 ms total) 37: 37: [----------] 7 tests from ForceBuffers 37: [ RUN ] ForceBuffers.ConstructsUnpinned 37: [ OK ] ForceBuffers.ConstructsUnpinned (0 ms) 37: [ RUN ] ForceBuffers.ConstructsPinned 37: [ OK ] ForceBuffers.ConstructsPinned (0 ms) 37: [ RUN ] ForceBuffers.ConstructsEmpty 37: [ OK ] ForceBuffers.ConstructsEmpty (0 ms) 37: [ RUN ] ForceBuffers.ResizeWorks 37: [ OK ] ForceBuffers.ResizeWorks (0 ms) 37: [ RUN ] ForceBuffers.PaddingWorks 37: [ OK ] ForceBuffers.PaddingWorks (0 ms) 37: [ RUN ] ForceBuffers.CopyWorks 37: [ OK ] ForceBuffers.CopyWorks (0 ms) 37: [ RUN ] ForceBuffers.CopyDoesNotPin 37: [ OK ] ForceBuffers.CopyDoesNotPin (0 ms) 37: [----------] 7 tests from ForceBuffers (0 ms total) 37: 37: [----------] 5 tests from MultipleTimeStepping 37: [ RUN ] MultipleTimeStepping.ChecksNumLevels 37: [ OK ] MultipleTimeStepping.ChecksNumLevels (0 ms) 37: [ RUN ] MultipleTimeStepping.SelectsForceGroups 37: [ OK ] MultipleTimeStepping.SelectsForceGroups (0 ms) 37: [ RUN ] MultipleTimeStepping.ChecksStepFactor 37: [ OK ] MultipleTimeStepping.ChecksStepFactor (0 ms) 37: [ RUN ] MultipleTimeStepping.ChecksPmeIsAtLastLevel 37: [ OK ] MultipleTimeStepping.ChecksPmeIsAtLastLevel (0 ms) 37: [ RUN ] MultipleTimeStepping.ChecksIntegrator 37: [ OK ] MultipleTimeStepping.ChecksIntegrator (0 ms) 37: [----------] 5 tests from MultipleTimeStepping (0 ms total) 37: 37: [----------] 60 tests from WithVariousSubscriberCounts/ObservablesReducerIntegrationTest 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks3 (0 ms) 37: [----------] 60 tests from WithVariousSubscriberCounts/ObservablesReducerIntegrationTest (1 ms total) 37: 37: [----------] 15 tests from ChecksStepInterval/MtsIntervalTest 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/0 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/0 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/1 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/1 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/2 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/2 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/3 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/3 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/4 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/4 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/5 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/5 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/6 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/6 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/7 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/7 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/8 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/8 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/9 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/9 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/10 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/10 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/11 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/11 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/12 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/12 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/13 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/13 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/14 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/14 (0 ms) 37: [----------] 15 tests from ChecksStepInterval/MtsIntervalTest (0 ms total) 37: 37: [----------] Global test environment tear-down 37: [==========] 97 tests from 7 test suites ran. (1460 ms total) 37: [ PASSED ] 97 tests. 37/90 Test #37: MdtypesUnitTest ........................... Passed 1.53 sec test 38 Start 38: OnlineHelpUnitTests 38: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/onlinehelp-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/OnlineHelpUnitTests.xml" 38: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/onlinehelp/tests 38: Test timeout computed to be: 30 38: [==========] Running 22 tests from 4 test suites. 38: [----------] Global test environment set-up. 38: [----------] 6 tests from TextTableFormatterTest 38: [ RUN ] TextTableFormatterTest.HandlesBasicCase 38: [ OK ] TextTableFormatterTest.HandlesBasicCase (0 ms) 38: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles 38: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (0 ms) 38: [ RUN ] TextTableFormatterTest.HandlesIndentation 38: [ OK ] TextTableFormatterTest.HandlesIndentation (0 ms) 38: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines 38: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (0 ms) 38: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding 38: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (0 ms) 38: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns 38: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (0 ms) 38: [----------] 6 tests from TextTableFormatterTest (0 ms total) 38: 38: [----------] 3 tests from HelpManagerTest 38: [ RUN ] HelpManagerTest.HandlesRootTopic 38: [ OK ] HelpManagerTest.HandlesRootTopic (0 ms) 38: [ RUN ] HelpManagerTest.HandlesSubTopics 38: [ OK ] HelpManagerTest.HandlesSubTopics (0 ms) 38: [ RUN ] HelpManagerTest.HandlesInvalidTopics 38: [ OK ] HelpManagerTest.HandlesInvalidTopics (0 ms) 38: [----------] 3 tests from HelpManagerTest (0 ms total) 38: 38: [----------] 2 tests from HelpTopicFormattingTest 38: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic 38: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (0 ms) 38: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics 38: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (0 ms) 38: [----------] 2 tests from HelpTopicFormattingTest (0 ms total) 38: 38: [----------] 11 tests from HelpWriterContextTest 38: [ RUN ] HelpWriterContextTest.FormatsParagraphs 38: [ OK ] HelpWriterContextTest.FormatsParagraphs (0 ms) 38: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs 38: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (0 ms) 38: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace 38: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (0 ms) 38: [ RUN ] HelpWriterContextTest.FormatsLiteralText 38: [ OK ] HelpWriterContextTest.FormatsLiteralText (0 ms) 38: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning 38: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (0 ms) 38: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation 38: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (0 ms) 38: [ RUN ] HelpWriterContextTest.FormatsBulletList 38: [ OK ] HelpWriterContextTest.FormatsBulletList (0 ms) 38: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList 38: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (0 ms) 38: [ RUN ] HelpWriterContextTest.FormatsSimpleTable 38: [ OK ] HelpWriterContextTest.FormatsSimpleTable (0 ms) 38: [ RUN ] HelpWriterContextTest.FormatsGridTable 38: [ OK ] HelpWriterContextTest.FormatsGridTable (0 ms) 38: [ RUN ] HelpWriterContextTest.FormatsTitles 38: [ OK ] HelpWriterContextTest.FormatsTitles (0 ms) 38: [----------] 11 tests from HelpWriterContextTest (1 ms total) 38: 38: [----------] Global test environment tear-down 38: [==========] 22 tests from 4 test suites ran. (2 ms total) 38: [ PASSED ] 22 tests. 38/90 Test #38: OnlineHelpUnitTests ....................... Passed 0.06 sec test 39 Start 39: OptionsUnitTests 39: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/options-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/OptionsUnitTests.xml" 39: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/options/tests 39: Test timeout computed to be: 30 39: [==========] Running 112 tests from 18 test suites. 39: [----------] Global test environment set-up. 39: [----------] 5 tests from AbstractOptionStorageTest 39: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish 39: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (0 ms) 39: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval 39: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (0 ms) 39: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition 39: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (0 ms) 39: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition 39: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (0 ms) 39: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues 39: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (0 ms) 39: [----------] 5 tests from AbstractOptionStorageTest (0 ms total) 39: 39: [----------] 10 tests from FileNameOptionTest 39: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension 39: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (0 ms) 39: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue 39: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms) 39: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption 39: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms) 39: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension 39: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms) 39: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension 39: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms) 39: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension 39: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms) 39: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix 39: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (0 ms) 39: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix 39: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms) 39: [ RUN ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension 39: [ OK ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension (0 ms) 39: [ RUN ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue 39: [ OK ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue (0 ms) 39: [----------] 10 tests from FileNameOptionTest (0 ms total) 39: 39: [----------] 16 tests from FileNameOptionManagerTest 39: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension 39: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms) 39: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension 39: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms) 39: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile 39: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (0 ms) 39: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile 39: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (0 ms) 39: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile 39: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (0 ms) 39: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile 39: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms) 39: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified 39: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms) 39: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified 39: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms) 39: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified 39: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms) 39: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile 39: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms) 39: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile 39: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms) 39: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile 39: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms) 39: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile 39: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms) 39: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile 39: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms) 39: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking 39: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms) 39: [ RUN ] FileNameOptionManagerTest.AcceptsCompressedInputFile 39: [ OK ] FileNameOptionManagerTest.AcceptsCompressedInputFile (0 ms) 39: [----------] 16 tests from FileNameOptionManagerTest (0 ms total) 39: 39: [----------] 1 test from OptionsTest 39: [ RUN ] OptionsTest.FailsOnNonsafeStorage 39: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms) 39: [----------] 1 test from OptionsTest (0 ms total) 39: 39: [----------] 9 tests from OptionsAssignerTest 39: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter 39: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms) 39: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue 39: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms) 39: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter 39: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (0 ms) 39: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter 39: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms) 39: [ RUN ] OptionsAssignerTest.HandlesMissingValue 39: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms) 39: [ RUN ] OptionsAssignerTest.HandlesExtraValue 39: [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms) 39: [ RUN ] OptionsAssignerTest.HandlesGroups 39: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms) 39: [ RUN ] OptionsAssignerTest.HandlesSections 39: [ OK ] OptionsAssignerTest.HandlesSections (0 ms) 39: [ RUN ] OptionsAssignerTest.HandlesMultipleSources 39: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms) 39: [----------] 9 tests from OptionsAssignerTest (0 ms total) 39: 39: [----------] 4 tests from OptionsAssignerBooleanTest 39: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue 39: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms) 39: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue 39: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms) 39: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo 39: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms) 39: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue 39: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms) 39: [----------] 4 tests from OptionsAssignerBooleanTest (0 ms total) 39: 39: [----------] 13 tests from OptionsAssignerIntegerTest 39: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue 39: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue 39: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue 39: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow 39: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue 39: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet 39: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet 39: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues 39: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.StoresToVector 39: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors 39: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue 39: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue 39: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment 39: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms) 39: [----------] 13 tests from OptionsAssignerIntegerTest (0 ms total) 39: 39: [----------] 5 tests from OptionsAssignerDoubleTest 39: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue 39: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms) 39: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat 39: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms) 39: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue 39: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (0 ms) 39: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue 39: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms) 39: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue 39: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms) 39: [----------] 5 tests from OptionsAssignerDoubleTest (0 ms total) 39: 39: [----------] 9 tests from OptionsAssignerStringTest 39: [ RUN ] OptionsAssignerStringTest.StoresSingleValue 39: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms) 39: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue 39: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms) 39: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray 39: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms) 39: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue 39: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms) 39: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue 39: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms) 39: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue 39: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms) 39: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue 39: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms) 39: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable 39: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms) 39: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector 39: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms) 39: [----------] 9 tests from OptionsAssignerStringTest (0 ms total) 39: 39: [----------] 6 tests from OptionsAssignerEnumTest 39: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue 39: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms) 39: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues 39: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms) 39: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange 39: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms) 39: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue 39: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms) 39: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable 39: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms) 39: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector 39: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms) 39: [----------] 6 tests from OptionsAssignerEnumTest (0 ms total) 39: 39: [----------] 8 tests from RepeatingOptionSectionTest 39: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance 39: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms) 39: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption 39: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms) 39: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance 39: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms) 39: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue 39: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms) 39: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances 39: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms) 39: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault 39: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms) 39: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault 39: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms) 39: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections 39: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms) 39: [----------] 8 tests from RepeatingOptionSectionTest (0 ms total) 39: 39: [----------] 1 test from TimeUnitManagerTest 39: [ RUN ] TimeUnitManagerTest.BasicOperations 39: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms) 39: [----------] 1 test from TimeUnitManagerTest (0 ms total) 39: 39: [----------] 4 tests from TimeUnitBehaviorTest 39: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue 39: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms) 39: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues 39: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms) 39: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources 39: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms) 39: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks 39: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms) 39: [----------] 4 tests from TimeUnitBehaviorTest (0 ms total) 39: 39: [----------] 2 tests from TreeValueSupportAssignTest 39: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree 39: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (0 ms) 39: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays 39: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (4 ms) 39: [----------] 2 tests from TreeValueSupportAssignTest (4 ms total) 39: 39: [----------] 1 test from TreeValueSupportAssignErrorTest 39: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue 39: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (0 ms) 39: [----------] 1 test from TreeValueSupportAssignErrorTest (0 ms total) 39: 39: [----------] 5 tests from TreeValueSupportCheckTest 39: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty 39: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms) 39: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree 39: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms) 39: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1 39: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms) 39: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2 39: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms) 39: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue 39: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms) 39: [----------] 5 tests from TreeValueSupportCheckTest (0 ms total) 39: 39: [----------] 6 tests from TreeValueSupportAdjustTest 39: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues 39: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (0 ms) 39: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues 39: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (0 ms) 39: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues 39: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (0 ms) 39: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues 39: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (0 ms) 39: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues 39: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (0 ms) 39: [ RUN ] TreeValueSupportAdjustTest.OrdersValues 39: [ OK ] TreeValueSupportAdjustTest.OrdersValues (0 ms) 39: [----------] 6 tests from TreeValueSupportAdjustTest (1 ms total) 39: 39: [----------] 7 tests from TreeValueSupportTest 39: [ RUN ] TreeValueSupportTest.SupportsBooleanOption 39: [ OK ] TreeValueSupportTest.SupportsBooleanOption (0 ms) 39: [ RUN ] TreeValueSupportTest.SupportsIntegerOption 39: [ OK ] TreeValueSupportTest.SupportsIntegerOption (0 ms) 39: [ RUN ] TreeValueSupportTest.SupportsInt64Option 39: [ OK ] TreeValueSupportTest.SupportsInt64Option (0 ms) 39: [ RUN ] TreeValueSupportTest.SupportsStringOption 39: [ OK ] TreeValueSupportTest.SupportsStringOption (0 ms) 39: [ RUN ] TreeValueSupportTest.SupportsFloatOption 39: [ OK ] TreeValueSupportTest.SupportsFloatOption (0 ms) 39: [ RUN ] TreeValueSupportTest.SupportsDoubleOption 39: [ OK ] TreeValueSupportTest.SupportsDoubleOption (0 ms) 39: [ RUN ] TreeValueSupportTest.SupportsEnumOption 39: [ OK ] TreeValueSupportTest.SupportsEnumOption (0 ms) 39: [----------] 7 tests from TreeValueSupportTest (1 ms total) 39: 39: [----------] Global test environment tear-down 39: [==========] 112 tests from 18 test suites ran. (9 ms total) 39: [ PASSED ] 112 tests. 39/90 Test #39: OptionsUnitTests .......................... Passed 0.07 sec test 40 Start 40: PbcutilUnitTest 40: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/pbcutil-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/PbcutilUnitTest.xml" 40: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/pbcutil/tests 40: Test timeout computed to be: 30 40: [==========] Running 37 tests from 5 test suites. 40: [----------] Global test environment set-up. 40: [----------] 1 test from ShiftTest 40: [ RUN ] ShiftTest.CoordinateShiftWorks 40: [ OK ] ShiftTest.CoordinateShiftWorks (0 ms) 40: [----------] 1 test from ShiftTest (0 ms total) 40: 40: [----------] 2 tests from MShift 40: [ RUN ] MShift.shiftsAndUnshifts 40: [ OK ] MShift.shiftsAndUnshifts (0 ms) 40: [ RUN ] MShift.shiftsAndUnshiftsSelf 40: [ OK ] MShift.shiftsAndUnshiftsSelf (0 ms) 40: [----------] 2 tests from MShift (0 ms total) 40: 40: [----------] 5 tests from PbcTest 40: [ RUN ] PbcTest.CalcShiftsWorks 40: [ OK ] PbcTest.CalcShiftsWorks (7 ms) 40: [ RUN ] PbcTest.PutAtomsInCubicBoxAlreadyInBox 40: [ OK ] PbcTest.PutAtomsInCubicBoxAlreadyInBox (0 ms) 40: [ RUN ] PbcTest.PutAtomsInCubicBoxFromOutsideBox 40: [ OK ] PbcTest.PutAtomsInCubicBoxFromOutsideBox (0 ms) 40: [ RUN ] PbcTest.PutAtomsInTriclinicBoxFromOutsideBox 40: [ OK ] PbcTest.PutAtomsInTriclinicBoxFromOutsideBox (0 ms) 40: [ RUN ] PbcTest.PutAtomsInBoxHandlesInf 40: [ OK ] PbcTest.PutAtomsInBoxHandlesInf (0 ms) 40: [----------] 5 tests from PbcTest (7 ms total) 40: 40: [----------] 2 tests from PbcEnumsTest 40: [ RUN ] PbcEnumsTest.CenteringTypeNamesAreCorrect 40: [ OK ] PbcEnumsTest.CenteringTypeNamesAreCorrect (0 ms) 40: [ RUN ] PbcEnumsTest.UnitCellTypeNamesAreCorrect 40: [ OK ] PbcEnumsTest.UnitCellTypeNamesAreCorrect (0 ms) 40: [----------] 2 tests from PbcEnumsTest (0 ms total) 40: 40: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 (5 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 (4 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 (0 ms) 40: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest (16 ms total) 40: 40: [----------] Global test environment tear-down 40: [==========] 37 tests from 5 test suites ran. (24 ms total) 40: [ PASSED ] 37 tests. 40/90 Test #40: PbcutilUnitTest ........................... Passed 0.08 sec test 41 Start 41: RandomUnitTests 41: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/random-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/RandomUnitTests.xml" 41: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/random/tests 41: Test timeout computed to be: 30 41: [==========] Running 44 tests from 10 test suites. 41: [----------] Global test environment set-up. 41: [----------] 4 tests from ExponentialDistributionTest 41: [ RUN ] ExponentialDistributionTest.Output 41: [ OK ] ExponentialDistributionTest.Output (0 ms) 41: [ RUN ] ExponentialDistributionTest.Logical 41: [ OK ] ExponentialDistributionTest.Logical (0 ms) 41: [ RUN ] ExponentialDistributionTest.Reset 41: [ OK ] ExponentialDistributionTest.Reset (0 ms) 41: [ RUN ] ExponentialDistributionTest.AltParam 41: [ OK ] ExponentialDistributionTest.AltParam (0 ms) 41: [----------] 4 tests from ExponentialDistributionTest (0 ms total) 41: 41: [----------] 4 tests from GammaDistributionTest 41: [ RUN ] GammaDistributionTest.Output 41: [ OK ] GammaDistributionTest.Output (0 ms) 41: [ RUN ] GammaDistributionTest.Logical 41: [ OK ] GammaDistributionTest.Logical (0 ms) 41: [ RUN ] GammaDistributionTest.Reset 41: [ OK ] GammaDistributionTest.Reset (0 ms) 41: [ RUN ] GammaDistributionTest.AltParam 41: [ OK ] GammaDistributionTest.AltParam (0 ms) 41: [----------] 4 tests from GammaDistributionTest (0 ms total) 41: 41: [----------] 4 tests from NormalDistributionTest 41: [ RUN ] NormalDistributionTest.Output 41: [ OK ] NormalDistributionTest.Output (0 ms) 41: [ RUN ] NormalDistributionTest.Logical 41: [ OK ] NormalDistributionTest.Logical (0 ms) 41: [ RUN ] NormalDistributionTest.Reset 41: [ OK ] NormalDistributionTest.Reset (0 ms) 41: [ RUN ] NormalDistributionTest.AltParam 41: [ OK ] NormalDistributionTest.AltParam (0 ms) 41: [----------] 4 tests from NormalDistributionTest (0 ms total) 41: 41: [----------] 1 test from SeedTest 41: [ RUN ] SeedTest.makeRandomSeed 41: [ OK ] SeedTest.makeRandomSeed (0 ms) 41: [----------] 1 test from SeedTest (0 ms total) 41: 41: [----------] 6 tests from TabulatedNormalDistributionTest 41: [ RUN ] TabulatedNormalDistributionTest.Output14 41: [ OK ] TabulatedNormalDistributionTest.Output14 (0 ms) 41: [ RUN ] TabulatedNormalDistributionTest.Output16 41: [ OK ] TabulatedNormalDistributionTest.Output16 (0 ms) 41: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14 41: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (0 ms) 41: [ RUN ] TabulatedNormalDistributionTest.Logical 41: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms) 41: [ RUN ] TabulatedNormalDistributionTest.Reset 41: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms) 41: [ RUN ] TabulatedNormalDistributionTest.AltParam 41: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms) 41: [----------] 6 tests from TabulatedNormalDistributionTest (0 ms total) 41: 41: [----------] 1 test from TabulatedNormalDistributionTableTest 41: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties 41: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (0 ms) 41: [----------] 1 test from TabulatedNormalDistributionTableTest (0 ms total) 41: 41: [----------] 6 tests from ThreeFry2x64Test 41: [ RUN ] ThreeFry2x64Test.Logical 41: [ OK ] ThreeFry2x64Test.Logical (0 ms) 41: [ RUN ] ThreeFry2x64Test.InternalCounterSequence 41: [ OK ] ThreeFry2x64Test.InternalCounterSequence (0 ms) 41: [ RUN ] ThreeFry2x64Test.Reseed 41: [ OK ] ThreeFry2x64Test.Reseed (0 ms) 41: [ RUN ] ThreeFry2x64Test.Discard 41: [ OK ] ThreeFry2x64Test.Discard (0 ms) 41: [ RUN ] ThreeFry2x64Test.InvalidCounter 41: [ OK ] ThreeFry2x64Test.InvalidCounter (0 ms) 41: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter 41: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms) 41: [----------] 6 tests from ThreeFry2x64Test (0 ms total) 41: 41: [----------] 4 tests from UniformIntDistributionTest 41: [ RUN ] UniformIntDistributionTest.Output 41: [ OK ] UniformIntDistributionTest.Output (0 ms) 41: [ RUN ] UniformIntDistributionTest.Logical 41: [ OK ] UniformIntDistributionTest.Logical (0 ms) 41: [ RUN ] UniformIntDistributionTest.Reset 41: [ OK ] UniformIntDistributionTest.Reset (0 ms) 41: [ RUN ] UniformIntDistributionTest.AltParam 41: [ OK ] UniformIntDistributionTest.AltParam (0 ms) 41: [----------] 4 tests from UniformIntDistributionTest (0 ms total) 41: 41: [----------] 5 tests from UniformRealDistributionTest 41: [ RUN ] UniformRealDistributionTest.GenerateCanonical 41: [ OK ] UniformRealDistributionTest.GenerateCanonical (0 ms) 41: [ RUN ] UniformRealDistributionTest.Output 41: [ OK ] UniformRealDistributionTest.Output (0 ms) 41: [ RUN ] UniformRealDistributionTest.Logical 41: [ OK ] UniformRealDistributionTest.Logical (0 ms) 41: [ RUN ] UniformRealDistributionTest.Reset 41: [ OK ] UniformRealDistributionTest.Reset (0 ms) 41: [ RUN ] UniformRealDistributionTest.AltParam 41: [ OK ] UniformRealDistributionTest.AltParam (0 ms) 41: [----------] 5 tests from UniformRealDistributionTest (0 ms total) 41: 41: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test 41: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0 41: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (0 ms) 41: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1 41: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (0 ms) 41: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2 41: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (0 ms) 41: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 41: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (0 ms) 41: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 41: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (0 ms) 41: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 41: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (0 ms) 41: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 41: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (0 ms) 41: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 41: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (0 ms) 41: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 41: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (0 ms) 41: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (0 ms total) 41: 41: [----------] Global test environment tear-down 41: [==========] 44 tests from 10 test suites ran. (3 ms total) 41: [ PASSED ] 44 tests. 41/90 Test #41: RandomUnitTests ........................... Passed 0.07 sec test 42 Start 42: RestraintTests 42: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/restraintpotential-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/RestraintTests.xml" 42: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/restraint/tests 42: Test timeout computed to be: 30 42: [==========] Running 1 test from 1 test suite. 42: [----------] Global test environment set-up. 42: [----------] 1 test from RestraintManager 42: [ RUN ] RestraintManager.restraintList 42: [ OK ] RestraintManager.restraintList (0 ms) 42: [----------] 1 test from RestraintManager (0 ms total) 42: 42: [----------] Global test environment tear-down 42: [==========] 1 test from 1 test suite ran. (0 ms total) 42: [ PASSED ] 1 test. 42/90 Test #42: RestraintTests ............................ Passed 0.06 sec test 43 Start 43: TableUnitTests 43: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/table-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/TableUnitTests.xml" 43: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tables/tests 43: Test timeout computed to be: 30 43: [==========] Running 20 tests from 2 test suites. 43: [----------] Global test environment set-up. 43: [----------] 10 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable 43: [ RUN ] SplineTableTest/0.HandlesIncorrectInput 43: [ OK ] SplineTableTest/0.HandlesIncorrectInput (1 ms) 43: [ RUN ] SplineTableTest/0.Sinc 43: [ OK ] SplineTableTest/0.Sinc (1 ms) 43: [ RUN ] SplineTableTest/0.LJ12 43: [ OK ] SplineTableTest/0.LJ12 (33 ms) 43: [ RUN ] SplineTableTest/0.PmeCorrection 43: [ OK ] SplineTableTest/0.PmeCorrection (1 ms) 43: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput 43: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (0 ms) 43: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr 43: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (1 ms) 43: [ RUN ] SplineTableTest/0.TwoFunctions 43: [ OK ] SplineTableTest/0.TwoFunctions (48 ms) 43: [ RUN ] SplineTableTest/0.ThreeFunctions 43: [ OK ] SplineTableTest/0.ThreeFunctions (60 ms) 43: [ RUN ] SplineTableTest/0.Simd 43: [ OK ] SplineTableTest/0.Simd (14 ms) 43: [ RUN ] SplineTableTest/0.SimdTwoFunctions 43: [ OK ] SplineTableTest/0.SimdTwoFunctions (48 ms) 43: [----------] 10 tests from SplineTableTest/0 (210 ms total) 43: 43: [----------] 10 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable 43: [ RUN ] SplineTableTest/1.HandlesIncorrectInput 43: [ OK ] SplineTableTest/1.HandlesIncorrectInput (1 ms) 43: [ RUN ] SplineTableTest/1.Sinc 43: [ OK ] SplineTableTest/1.Sinc (0 ms) 43: [ RUN ] SplineTableTest/1.LJ12 43: [ OK ] SplineTableTest/1.LJ12 (6 ms) 43: [ RUN ] SplineTableTest/1.PmeCorrection 43: [ OK ] SplineTableTest/1.PmeCorrection (1 ms) 43: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput 43: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (0 ms) 43: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr 43: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (0 ms) 43: [ RUN ] SplineTableTest/1.TwoFunctions 43: [ OK ] SplineTableTest/1.TwoFunctions (4 ms) 43: [ RUN ] SplineTableTest/1.ThreeFunctions 43: [ OK ] SplineTableTest/1.ThreeFunctions (12 ms) 43: [ RUN ] SplineTableTest/1.Simd 43: [ OK ] SplineTableTest/1.Simd (1 ms) 43: [ RUN ] SplineTableTest/1.SimdTwoFunctions 43: [ OK ] SplineTableTest/1.SimdTwoFunctions (8 ms) 43: [----------] 10 tests from SplineTableTest/1 (36 ms total) 43: 43: [----------] Global test environment tear-down 43: [==========] 20 tests from 2 test suites ran. (247 ms total) 43: [ PASSED ] 20 tests. 43/90 Test #43: TableUnitTests ............................ Passed 0.31 sec test 44 Start 44: TaskAssignmentUnitTests 44: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/taskassignment-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/TaskAssignmentUnitTests.xml" 44: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/taskassignment/tests 44: Test timeout computed to be: 30 44: [==========] Running 3 tests from 2 test suites. 44: [----------] Global test environment set-up. 44: [----------] 2 tests from UserTaskAssignmentStringHandlingTest 44: [ RUN ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork 44: [ OK ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork (0 ms) 44: [ RUN ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid 44: [ OK ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid (0 ms) 44: [----------] 2 tests from UserTaskAssignmentStringHandlingTest (0 ms total) 44: 44: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest 44: [ RUN ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow 44: [ OK ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow (0 ms) 44: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest (0 ms total) 44: 44: [----------] Global test environment tear-down 44: [==========] 3 tests from 2 test suites ran. (0 ms total) 44: [ PASSED ] 3 tests. 44/90 Test #44: TaskAssignmentUnitTests ................... Passed 0.06 sec test 45 Start 45: GmxTimingTests 45: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/timing-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/GmxTimingTests.xml" 45: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/timing/tests 45: Test timeout computed to be: 30 45: [==========] Running 6 tests from 1 test suite. 45: [----------] Global test environment set-up. 45: [----------] 6 tests from TimingTest 45: [ RUN ] TimingTest.ElementCountingWorks 45: [ OK ] TimingTest.ElementCountingWorks (0 ms) 45: [ RUN ] TimingTest.ElementNoCountingWorks 45: [ OK ] TimingTest.ElementNoCountingWorks (0 ms) 45: [ RUN ] TimingTest.SubElementCountingWorks 45: [ OK ] TimingTest.SubElementCountingWorks (0 ms) 45: [ RUN ] TimingTest.SubElementNoCountingWorks 45: [ OK ] TimingTest.SubElementNoCountingWorks (0 ms) 45: [ RUN ] TimingTest.RunWallCycle 45: [ OK ] TimingTest.RunWallCycle (5 ms) 45: [ RUN ] TimingTest.RunWallCycleSub 45: [ OK ] TimingTest.RunWallCycleSub (0 ms) 45: [----------] 6 tests from TimingTest (5 ms total) 45: 45: [----------] Global test environment tear-down 45: [==========] 6 tests from 1 test suite ran. (5 ms total) 45: [ PASSED ] 6 tests. 45/90 Test #45: GmxTimingTests ............................ Passed 0.05 sec test 46 Start 46: TopologyTest 46: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/topology-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/TopologyTest.xml" 46: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/topology/tests 46: Test timeout computed to be: 30 46: [==========] Running 153 tests from 10 test suites. 46: [----------] Global test environment set-up. 46: [----------] 3 tests from PdbAtomEntryTest 46: [ RUN ] PdbAtomEntryTest.CanCreateBasicEntry 46: [ OK ] PdbAtomEntryTest.CanCreateBasicEntry (0 ms) 46: [ RUN ] PdbAtomEntryTest.CanCreateEntryWithOccupAndBfac 46: [ OK ] PdbAtomEntryTest.CanCreateEntryWithOccupAndBfac (0 ms) 46: [ RUN ] PdbAtomEntryTest.CanCreateFullEntry 46: [ OK ] PdbAtomEntryTest.CanCreateFullEntry (0 ms) 46: [----------] 3 tests from PdbAtomEntryTest (0 ms total) 46: 46: [----------] 3 tests from ExclusionBlockTest 46: [ RUN ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks 46: [ OK ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks (0 ms) 46: [ RUN ] ExclusionBlockTest.ConvertExclusionBlockToBlocka 46: [ OK ] ExclusionBlockTest.ConvertExclusionBlockToBlocka (0 ms) 46: [ RUN ] ExclusionBlockTest.MergeExclusions 46: [ OK ] ExclusionBlockTest.MergeExclusions (0 ms) 46: [----------] 3 tests from ExclusionBlockTest (0 ms total) 46: 46: [----------] 6 tests from InteractionListTest 46: [ RUN ] InteractionListTest.EmptyWorks 46: [ OK ] InteractionListTest.EmptyWorks (0 ms) 46: [ RUN ] InteractionListTest.CanAddInteractionArray 46: [ OK ] InteractionListTest.CanAddInteractionArray (0 ms) 46: [ RUN ] InteractionListTest.CanAddInteractionArrayMultipleAtoms 46: [ OK ] InteractionListTest.CanAddInteractionArrayMultipleAtoms (0 ms) 46: [ RUN ] InteractionListTest.CanAddInteractionPointer 46: [ OK ] InteractionListTest.CanAddInteractionPointer (0 ms) 46: [ RUN ] InteractionListTest.CanAddListToOtherList 46: [ OK ] InteractionListTest.CanAddListToOtherList (0 ms) 46: [ RUN ] InteractionListTest.ClearingWorks 46: [ OK ] InteractionListTest.ClearingWorks (0 ms) 46: [----------] 6 tests from InteractionListTest (0 ms total) 46: 46: [----------] 3 tests from IndexTest 46: [ RUN ] IndexTest.AnalyseWorksDefaultGroups 46: 46: WARNING: Masses and atomic (Van der Waals) radii will be guessed 46: based on residue and atom names, since they could not be 46: definitively assigned from the information in your input 46: files. These guessed numbers might deviate from the mass 46: and radius of the atom type. Please check the output 46: files if necessary. Note, that this functionality may 46: be removed in a future GROMACS version. Please, consider 46: using another file format for your input. 46: 46: [ OK ] IndexTest.AnalyseWorksDefaultGroups (6 ms) 46: [ RUN ] IndexTest.WriteIndexWorks 46: 46: WARNING: Masses and atomic (Van der Waals) radii will be guessed 46: based on residue and atom names, since they could not be 46: definitively assigned from the information in your input 46: files. These guessed numbers might deviate from the mass 46: and radius of the atom type. Please check the output 46: files if necessary. Note, that this functionality may 46: be removed in a future GROMACS version. Please, consider 46: using another file format for your input. 46: 46: [ OK ] IndexTest.WriteIndexWorks (5 ms) 46: [ RUN ] IndexTest.WriteAndReadIndexWorks 46: 46: WARNING: Masses and atomic (Van der Waals) radii will be guessed 46: based on residue and atom names, since they could not be 46: definitively assigned from the information in your input 46: files. These guessed numbers might deviate from the mass 46: and radius of the atom type. Please check the output 46: files if necessary. Note, that this functionality may 46: be removed in a future GROMACS version. Please, consider 46: using another file format for your input. 46: 46: [ OK ] IndexTest.WriteAndReadIndexWorks (4 ms) 46: [----------] 3 tests from IndexTest (17 ms total) 46: 46: [----------] 4 tests from MtopTest 46: [ RUN ] MtopTest.RangeBasedLoop 46: [ OK ] MtopTest.RangeBasedLoop (0 ms) 46: [ RUN ] MtopTest.Operators 46: [ OK ] MtopTest.Operators (0 ms) 46: [ RUN ] MtopTest.CanFindResidueStartAndEndAtoms 46: [ OK ] MtopTest.CanFindResidueStartAndEndAtoms (0 ms) 46: [ RUN ] MtopTest.CanSortPerturbedInteractionsCorrectly 46: [ OK ] MtopTest.CanSortPerturbedInteractionsCorrectly (0 ms) 46: [----------] 4 tests from MtopTest (0 ms total) 46: 46: [----------] 2 tests from IListRangeTest 46: [ RUN ] IListRangeTest.RangeBasedLoopWorks 46: [ OK ] IListRangeTest.RangeBasedLoopWorks (0 ms) 46: [ RUN ] IListRangeTest.RangeBasedLoopWithIntermolecularInteraction 46: [ OK ] IListRangeTest.RangeBasedLoopWithIntermolecularInteraction (0 ms) 46: [----------] 2 tests from IListRangeTest (0 ms total) 46: 46: [----------] 13 tests from StringTableTest 46: [ RUN ] StringTableTest.AddSingleEntry 46: [ OK ] StringTableTest.AddSingleEntry (0 ms) 46: [ RUN ] StringTableTest.CanAccessWithAt 46: [ OK ] StringTableTest.CanAccessWithAt (0 ms) 46: [ RUN ] StringTableTest.CanAccessWithBracket 46: [ OK ] StringTableTest.CanAccessWithBracket (0 ms) 46: [ RUN ] StringTableTest.ThrowsOutOfRange 46: [ OK ] StringTableTest.ThrowsOutOfRange (0 ms) 46: [ RUN ] StringTableTest.StringCompareIsCorrect 46: [ OK ] StringTableTest.StringCompareIsCorrect (0 ms) 46: [ RUN ] StringTableTest.AddTwoDistinctEntries 46: [ OK ] StringTableTest.AddTwoDistinctEntries (0 ms) 46: [ RUN ] StringTableTest.TryToAddDuplicates 46: [ OK ] StringTableTest.TryToAddDuplicates (0 ms) 46: [ RUN ] StringTableTest.AddLargeNumberOfEntries 46: [ OK ] StringTableTest.AddLargeNumberOfEntries (0 ms) 46: [ RUN ] StringTableTest.NoDuplicatesInLargeTable 46: [ OK ] StringTableTest.NoDuplicatesInLargeTable (0 ms) 46: [ RUN ] StringTableTest.CanWriteToBuffer 46: [ OK ] StringTableTest.CanWriteToBuffer (0 ms) 46: [ RUN ] StringTableTest.Roundtrip 46: [ OK ] StringTableTest.Roundtrip (0 ms) 46: [ RUN ] StringTableTest.RoundtripWithCorrectStringIndices 46: [ OK ] StringTableTest.RoundtripWithCorrectStringIndices (0 ms) 46: [ RUN ] StringTableTest.CanCopyToLegacyTable 46: [ OK ] StringTableTest.CanCopyToLegacyTable (0 ms) 46: [----------] 13 tests from StringTableTest (2 ms total) 46: 46: [----------] 6 tests from LegacySymtabTest 46: [ RUN ] LegacySymtabTest.EmptyOnOpen 46: [ OK ] LegacySymtabTest.EmptyOnOpen (0 ms) 46: [ RUN ] LegacySymtabTest.AddSingleEntry 46: [ OK ] LegacySymtabTest.AddSingleEntry (0 ms) 46: [ RUN ] LegacySymtabTest.AddTwoDistinctEntries 46: [ OK ] LegacySymtabTest.AddTwoDistinctEntries (0 ms) 46: [ RUN ] LegacySymtabTest.TryToAddDuplicates 46: [ OK ] LegacySymtabTest.TryToAddDuplicates (0 ms) 46: [ RUN ] LegacySymtabTest.AddLargeNumberOfEntries 46: [ OK ] LegacySymtabTest.AddLargeNumberOfEntries (0 ms) 46: [ RUN ] LegacySymtabTest.NoDuplicatesInLargeTable 46: [ OK ] LegacySymtabTest.NoDuplicatesInLargeTable (0 ms) 46: [----------] 6 tests from LegacySymtabTest (0 ms total) 46: 46: [----------] 5 tests from TopSortTest 46: [ RUN ] TopSortTest.WorksOnEmptyIdef 46: [ OK ] TopSortTest.WorksOnEmptyIdef (0 ms) 46: [ RUN ] TopSortTest.WorksOnIdefWithNoPerturbedInteraction 46: [ OK ] TopSortTest.WorksOnIdefWithNoPerturbedInteraction (0 ms) 46: [ RUN ] TopSortTest.WorksOnIdefWithPerturbedInteractions 46: [ OK ] TopSortTest.WorksOnIdefWithPerturbedInteractions (0 ms) 46: [ RUN ] TopSortTest.SortsIdefWithPerturbedInteractions 46: [ OK ] TopSortTest.SortsIdefWithPerturbedInteractions (0 ms) 46: [ RUN ] TopSortTest.SortsMoreComplexIdefWithPerturbedInteractions 46: [ OK ] TopSortTest.SortsMoreComplexIdefWithPerturbedInteractions (0 ms) 46: [----------] 5 tests from TopSortTest (0 ms total) 46: 46: [----------] 108 tests from BuildsValidDataStructure/SimulationParticleTest 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/0 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/0 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/1 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/1 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/2 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/2 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/3 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/3 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/4 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/4 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/5 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/5 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/6 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/6 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/7 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/7 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/8 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/8 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/9 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/9 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/10 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/10 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/11 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/11 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/12 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/12 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/13 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/13 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/14 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/14 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/15 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/15 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/16 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/16 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/17 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/17 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/18 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/18 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/19 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/19 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/20 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/20 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/21 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/21 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/22 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/22 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/23 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/23 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/24 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/24 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/25 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/25 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/26 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/26 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/27 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/27 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/28 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/28 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/29 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/29 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/30 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/30 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/31 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/31 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/32 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/32 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/33 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/33 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/34 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/34 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/35 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/35 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/36 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/36 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/37 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/37 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/38 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/38 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/39 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/39 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/40 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/40 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/41 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/41 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/42 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/42 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/43 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/43 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/44 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/44 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/45 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/45 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/46 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/46 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/47 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/47 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/48 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/48 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/49 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/49 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/50 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/50 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/51 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/51 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/52 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/52 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/53 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/53 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/0 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/0 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/1 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/1 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/2 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/2 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/3 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/3 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/4 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/4 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/5 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/5 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/6 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/6 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/7 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/7 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/8 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/8 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/9 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/9 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/10 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/10 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/11 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/11 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/12 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/12 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/13 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/13 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/14 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/14 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/15 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/15 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/16 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/16 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/17 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/17 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/18 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/18 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/19 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/19 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/20 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/20 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/21 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/21 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/22 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/22 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/23 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/23 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/24 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/24 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/25 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/25 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/26 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/26 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/27 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/27 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/28 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/28 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/29 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/29 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/30 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/30 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/31 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/31 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/32 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/32 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/33 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/33 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/34 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/34 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/35 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/35 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/36 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/36 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/37 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/37 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/38 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/38 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/39 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/39 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/40 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/40 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/41 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/41 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/42 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/42 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/43 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/43 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/44 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/44 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/45 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/45 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/46 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/46 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/47 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/47 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/48 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/48 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/49 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/49 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/50 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/50 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/51 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/51 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/52 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/52 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/53 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/53 (0 ms) 46: [----------] 108 tests from BuildsValidDataStructure/SimulationParticleTest (13 ms total) 46: 46: [----------] Global test environment tear-down 46: [==========] 153 tests from 10 test suites ran. (34 ms total) 46: [ PASSED ] 153 tests. 46: 46: YOU HAVE 1 DISABLED TEST 46: 46/90 Test #46: TopologyTest .............................. Passed 0.07 sec test 47 Start 47: PullTest 47: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/pull-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/PullTest.xml" 47: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/pulling/tests 47: Test timeout computed to be: 30 47: [==========] Running 10 tests from 1 test suite. 47: [----------] Global test environment set-up. 47: [----------] 10 tests from PullTest 47: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox 47: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (0 ms) 47: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox 47: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms) 47: [ RUN ] PullTest.MaxPullDistanceXyzTricBox 47: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms) 47: [ RUN ] PullTest.MaxPullDistanceXyzLongBox 47: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms) 47: [ RUN ] PullTest.MaxPullDistanceXySkewedBox 47: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms) 47: [ RUN ] PullTest.TransformationCoordSimple 47: [ OK ] PullTest.TransformationCoordSimple (0 ms) 47: [ RUN ] PullTest.TransformationCoordAdvanced 47: [ OK ] PullTest.TransformationCoordAdvanced (0 ms) 47: [ RUN ] PullTest.TransformationCoordTime 47: [ OK ] PullTest.TransformationCoordTime (0 ms) 47: [ RUN ] PullTest.TransformationCoordTimeNotAllowed 47: [ OK ] PullTest.TransformationCoordTimeNotAllowed (0 ms) 47: [ RUN ] PullTest.TransformationCoordDummyExpression 47: [ OK ] PullTest.TransformationCoordDummyExpression (0 ms) 47: [----------] 10 tests from PullTest (0 ms total) 47: 47: [----------] Global test environment tear-down 47: [==========] 10 tests from 1 test suite ran. (0 ms total) 47: [ PASSED ] 10 tests. 47/90 Test #47: PullTest .................................. Passed 0.03 sec test 48 Start 48: SimdUnitTests 48: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/simd-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/SimdUnitTests.xml" 48: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/simd/tests 48: Test timeout computed to be: 30 48: [==========] Running 288 tests from 22 test suites. 48: [----------] Global test environment set-up. 48: [----------] 9 tests from SimdBootstrapTest 48: [ RUN ] SimdBootstrapTest.loadStore 48: [ OK ] SimdBootstrapTest.loadStore (0 ms) 48: [ RUN ] SimdBootstrapTest.loadU 48: [ OK ] SimdBootstrapTest.loadU (0 ms) 48: [ RUN ] SimdBootstrapTest.storeU 48: [ OK ] SimdBootstrapTest.storeU (0 ms) 48: [ RUN ] SimdBootstrapTest.loadStoreI 48: [ OK ] SimdBootstrapTest.loadStoreI (0 ms) 48: [ RUN ] SimdBootstrapTest.loadUI 48: [ OK ] SimdBootstrapTest.loadUI (0 ms) 48: [ RUN ] SimdBootstrapTest.storeUI 48: [ OK ] SimdBootstrapTest.storeUI (0 ms) 48: [ RUN ] SimdBootstrapTest.simd4LoadStore 48: [ OK ] SimdBootstrapTest.simd4LoadStore (0 ms) 48: [ RUN ] SimdBootstrapTest.simd4LoadU 48: [ OK ] SimdBootstrapTest.simd4LoadU (0 ms) 48: [ RUN ] SimdBootstrapTest.simd4StoreU 48: [ OK ] SimdBootstrapTest.simd4StoreU (0 ms) 48: [----------] 9 tests from SimdBootstrapTest (0 ms total) 48: 48: [----------] 41 tests from SimdScalarTest 48: [ RUN ] SimdScalarTest.load 48: [ OK ] SimdScalarTest.load (0 ms) 48: [ RUN ] SimdScalarTest.loadU 48: [ OK ] SimdScalarTest.loadU (0 ms) 48: [ RUN ] SimdScalarTest.store 48: [ OK ] SimdScalarTest.store (0 ms) 48: [ RUN ] SimdScalarTest.storeU 48: [ OK ] SimdScalarTest.storeU (0 ms) 48: [ RUN ] SimdScalarTest.setZero 48: [ OK ] SimdScalarTest.setZero (0 ms) 48: [ RUN ] SimdScalarTest.andNot 48: [ OK ] SimdScalarTest.andNot (0 ms) 48: [ RUN ] SimdScalarTest.fma 48: [ OK ] SimdScalarTest.fma (0 ms) 48: [ RUN ] SimdScalarTest.fms 48: [ OK ] SimdScalarTest.fms (0 ms) 48: [ RUN ] SimdScalarTest.fnma 48: [ OK ] SimdScalarTest.fnma (0 ms) 48: [ RUN ] SimdScalarTest.fnms 48: [ OK ] SimdScalarTest.fnms (0 ms) 48: [ RUN ] SimdScalarTest.maskAdd 48: [ OK ] SimdScalarTest.maskAdd (0 ms) 48: [ RUN ] SimdScalarTest.maskzMul 48: [ OK ] SimdScalarTest.maskzMul (0 ms) 48: [ RUN ] SimdScalarTest.maskzFma 48: [ OK ] SimdScalarTest.maskzFma (0 ms) 48: [ RUN ] SimdScalarTest.abs 48: [ OK ] SimdScalarTest.abs (0 ms) 48: [ RUN ] SimdScalarTest.max 48: [ OK ] SimdScalarTest.max (0 ms) 48: [ RUN ] SimdScalarTest.min 48: [ OK ] SimdScalarTest.min (0 ms) 48: [ RUN ] SimdScalarTest.round 48: [ OK ] SimdScalarTest.round (0 ms) 48: [ RUN ] SimdScalarTest.trunc 48: [ OK ] SimdScalarTest.trunc (0 ms) 48: [ RUN ] SimdScalarTest.reduce 48: [ OK ] SimdScalarTest.reduce (0 ms) 48: [ RUN ] SimdScalarTest.testBits 48: [ OK ] SimdScalarTest.testBits (0 ms) 48: [ RUN ] SimdScalarTest.anyTrue 48: [ OK ] SimdScalarTest.anyTrue (0 ms) 48: [ RUN ] SimdScalarTest.selectByMask 48: [ OK ] SimdScalarTest.selectByMask (0 ms) 48: [ RUN ] SimdScalarTest.selectByNotMask 48: [ OK ] SimdScalarTest.selectByNotMask (0 ms) 48: [ RUN ] SimdScalarTest.blend 48: [ OK ] SimdScalarTest.blend (0 ms) 48: [ RUN ] SimdScalarTest.cvtR2I 48: [ OK ] SimdScalarTest.cvtR2I (0 ms) 48: [ RUN ] SimdScalarTest.cvttR2I 48: [ OK ] SimdScalarTest.cvttR2I (0 ms) 48: [ RUN ] SimdScalarTest.cvtI2R 48: [ OK ] SimdScalarTest.cvtI2R (0 ms) 48: [ RUN ] SimdScalarTest.cvtF2D 48: [ OK ] SimdScalarTest.cvtF2D (0 ms) 48: [ RUN ] SimdScalarTest.cvtD2D 48: [ OK ] SimdScalarTest.cvtD2D (0 ms) 48: [ RUN ] SimdScalarTest.loadI 48: [ OK ] SimdScalarTest.loadI (0 ms) 48: [ RUN ] SimdScalarTest.loadUI 48: [ OK ] SimdScalarTest.loadUI (0 ms) 48: [ RUN ] SimdScalarTest.storeI 48: [ OK ] SimdScalarTest.storeI (0 ms) 48: [ RUN ] SimdScalarTest.storeUI 48: [ OK ] SimdScalarTest.storeUI (0 ms) 48: [ RUN ] SimdScalarTest.andNotI 48: [ OK ] SimdScalarTest.andNotI (0 ms) 48: [ RUN ] SimdScalarTest.testBitsI 48: [ OK ] SimdScalarTest.testBitsI (0 ms) 48: [ RUN ] SimdScalarTest.selectByMaskI 48: [ OK ] SimdScalarTest.selectByMaskI (0 ms) 48: [ RUN ] SimdScalarTest.selectByNotMaskI 48: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms) 48: [ RUN ] SimdScalarTest.blendI 48: [ OK ] SimdScalarTest.blendI (0 ms) 48: [ RUN ] SimdScalarTest.cvtB2IB 48: [ OK ] SimdScalarTest.cvtB2IB (0 ms) 48: [ RUN ] SimdScalarTest.cvtIB2B 48: [ OK ] SimdScalarTest.cvtIB2B (0 ms) 48: [ RUN ] SimdScalarTest.expandScalarsToTriplets 48: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms) 48: [----------] 41 tests from SimdScalarTest (0 ms total) 48: 48: [----------] 8 tests from SimdScalarUtilTest 48: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose 48: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms) 48: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose 48: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms) 48: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU 48: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms) 48: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU 48: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms) 48: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU 48: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms) 48: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose 48: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms) 48: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose 48: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms) 48: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum 48: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms) 48: [----------] 8 tests from SimdScalarUtilTest (0 ms total) 48: 48: [----------] 37 tests from SimdScalarMathTest 48: [ RUN ] SimdScalarMathTest.copysign 48: [ OK ] SimdScalarMathTest.copysign (0 ms) 48: [ RUN ] SimdScalarMathTest.invsqrtPair 48: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms) 48: [ RUN ] SimdScalarMathTest.inv 48: [ OK ] SimdScalarMathTest.inv (0 ms) 48: [ RUN ] SimdScalarMathTest.maskzInvsqrt 48: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms) 48: [ RUN ] SimdScalarMathTest.log 48: [ OK ] SimdScalarMathTest.log (0 ms) 48: [ RUN ] SimdScalarMathTest.exp2 48: [ OK ] SimdScalarMathTest.exp2 (0 ms) 48: [ RUN ] SimdScalarMathTest.exp 48: [ OK ] SimdScalarMathTest.exp (0 ms) 48: [ RUN ] SimdScalarMathTest.erf 48: [ OK ] SimdScalarMathTest.erf (0 ms) 48: [ RUN ] SimdScalarMathTest.erfc 48: [ OK ] SimdScalarMathTest.erfc (0 ms) 48: [ RUN ] SimdScalarMathTest.sincos 48: [ OK ] SimdScalarMathTest.sincos (0 ms) 48: [ RUN ] SimdScalarMathTest.sin 48: [ OK ] SimdScalarMathTest.sin (0 ms) 48: [ RUN ] SimdScalarMathTest.cos 48: [ OK ] SimdScalarMathTest.cos (0 ms) 48: [ RUN ] SimdScalarMathTest.tan 48: [ OK ] SimdScalarMathTest.tan (0 ms) 48: [ RUN ] SimdScalarMathTest.asin 48: [ OK ] SimdScalarMathTest.asin (0 ms) 48: [ RUN ] SimdScalarMathTest.acos 48: [ OK ] SimdScalarMathTest.acos (0 ms) 48: [ RUN ] SimdScalarMathTest.atan 48: [ OK ] SimdScalarMathTest.atan (0 ms) 48: [ RUN ] SimdScalarMathTest.atan2 48: [ OK ] SimdScalarMathTest.atan2 (0 ms) 48: [ RUN ] SimdScalarMathTest.pmeForceCorrection 48: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms) 48: [ RUN ] SimdScalarMathTest.pmePotentialCorrection 48: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms) 48: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy 48: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.invSingleAccuracy 48: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy 48: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.logSingleAccuracy 48: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy 48: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.expSingleAccuracy 48: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.erfSingleAccuracy 48: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy 48: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy 48: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.sinSingleAccuracy 48: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.cosSingleAccuracy 48: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.tanSingleAccuracy 48: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.asinSingleAccuracy 48: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.acosSingleAccuracy 48: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.atanSingleAccuracy 48: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy 48: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy 48: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy 48: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 48: [----------] 37 tests from SimdScalarMathTest (0 ms total) 48: 48: [----------] 1 test from SimdTest 48: [ RUN ] SimdTest.GmxAligned 48: [ OK ] SimdTest.GmxAligned (0 ms) 48: [----------] 1 test from SimdTest (0 ms total) 48: 48: [----------] 42 tests from SimdFloatingpointTest 48: [ RUN ] SimdFloatingpointTest.setZero 48: [ OK ] SimdFloatingpointTest.setZero (0 ms) 48: [ RUN ] SimdFloatingpointTest.set 48: [ OK ] SimdFloatingpointTest.set (0 ms) 48: [ RUN ] SimdFloatingpointTest.add 48: [ OK ] SimdFloatingpointTest.add (0 ms) 48: [ RUN ] SimdFloatingpointTest.maskAdd 48: [ OK ] SimdFloatingpointTest.maskAdd (0 ms) 48: [ RUN ] SimdFloatingpointTest.sub 48: [ OK ] SimdFloatingpointTest.sub (0 ms) 48: [ RUN ] SimdFloatingpointTest.mul 48: [ OK ] SimdFloatingpointTest.mul (0 ms) 48: [ RUN ] SimdFloatingpointTest.maskzMul 48: [ OK ] SimdFloatingpointTest.maskzMul (0 ms) 48: [ RUN ] SimdFloatingpointTest.fma 48: [ OK ] SimdFloatingpointTest.fma (0 ms) 48: [ RUN ] SimdFloatingpointTest.maskzFma 48: [ OK ] SimdFloatingpointTest.maskzFma (0 ms) 48: [ RUN ] SimdFloatingpointTest.fms 48: [ OK ] SimdFloatingpointTest.fms (0 ms) 48: [ RUN ] SimdFloatingpointTest.fnma 48: [ OK ] SimdFloatingpointTest.fnma (0 ms) 48: [ RUN ] SimdFloatingpointTest.fnms 48: [ OK ] SimdFloatingpointTest.fnms (0 ms) 48: [ RUN ] SimdFloatingpointTest.abs 48: [ OK ] SimdFloatingpointTest.abs (0 ms) 48: [ RUN ] SimdFloatingpointTest.neg 48: [ OK ] SimdFloatingpointTest.neg (0 ms) 48: [ RUN ] SimdFloatingpointTest.and 48: [ OK ] SimdFloatingpointTest.and (0 ms) 48: [ RUN ] SimdFloatingpointTest.or 48: [ OK ] SimdFloatingpointTest.or (0 ms) 48: [ RUN ] SimdFloatingpointTest.xor 48: [ OK ] SimdFloatingpointTest.xor (0 ms) 48: [ RUN ] SimdFloatingpointTest.andNot 48: [ OK ] SimdFloatingpointTest.andNot (0 ms) 48: [ RUN ] SimdFloatingpointTest.max 48: [ OK ] SimdFloatingpointTest.max (0 ms) 48: [ RUN ] SimdFloatingpointTest.min 48: [ OK ] SimdFloatingpointTest.min (0 ms) 48: [ RUN ] SimdFloatingpointTest.round 48: [ OK ] SimdFloatingpointTest.round (0 ms) 48: [ RUN ] SimdFloatingpointTest.roundMode 48: [ OK ] SimdFloatingpointTest.roundMode (0 ms) 48: [ RUN ] SimdFloatingpointTest.trunc 48: [ OK ] SimdFloatingpointTest.trunc (0 ms) 48: [ RUN ] SimdFloatingpointTest.frexp 48: [ OK ] SimdFloatingpointTest.frexp (0 ms) 48: [ RUN ] SimdFloatingpointTest.ldexp 48: [ OK ] SimdFloatingpointTest.ldexp (0 ms) 48: [ RUN ] SimdFloatingpointTest.rsqrt 48: [ OK ] SimdFloatingpointTest.rsqrt (0 ms) 48: [ RUN ] SimdFloatingpointTest.maskzRsqrt 48: [ OK ] SimdFloatingpointTest.maskzRsqrt (0 ms) 48: [ RUN ] SimdFloatingpointTest.rcp 48: [ OK ] SimdFloatingpointTest.rcp (0 ms) 48: [ RUN ] SimdFloatingpointTest.maskzRcp 48: [ OK ] SimdFloatingpointTest.maskzRcp (0 ms) 48: [ RUN ] SimdFloatingpointTest.cmpEqAndSelectByMask 48: [ OK ] SimdFloatingpointTest.cmpEqAndSelectByMask (0 ms) 48: [ RUN ] SimdFloatingpointTest.selectByNotMask 48: [ OK ] SimdFloatingpointTest.selectByNotMask (0 ms) 48: [ RUN ] SimdFloatingpointTest.cmpNe 48: [ OK ] SimdFloatingpointTest.cmpNe (0 ms) 48: [ RUN ] SimdFloatingpointTest.cmpLe 48: [ OK ] SimdFloatingpointTest.cmpLe (0 ms) 48: [ RUN ] SimdFloatingpointTest.cmpLt 48: [ OK ] SimdFloatingpointTest.cmpLt (0 ms) 48: [ RUN ] SimdFloatingpointTest.testBits 48: [ OK ] SimdFloatingpointTest.testBits (0 ms) 48: [ RUN ] SimdFloatingpointTest.andB 48: [ OK ] SimdFloatingpointTest.andB (0 ms) 48: [ RUN ] SimdFloatingpointTest.orB 48: [ OK ] SimdFloatingpointTest.orB (0 ms) 48: [ RUN ] SimdFloatingpointTest.anyTrueB 48: [ OK ] SimdFloatingpointTest.anyTrueB (0 ms) 48: [ RUN ] SimdFloatingpointTest.blend 48: [ OK ] SimdFloatingpointTest.blend (0 ms) 48: [ RUN ] SimdFloatingpointTest.reduce 48: [ OK ] SimdFloatingpointTest.reduce (0 ms) 48: [ RUN ] SimdFloatingpointTest.cvtFloat2Double 48: [ OK ] SimdFloatingpointTest.cvtFloat2Double (0 ms) 48: [ RUN ] SimdFloatingpointTest.cvtDouble2Float 48: [ OK ] SimdFloatingpointTest.cvtDouble2Float (0 ms) 48: [----------] 42 tests from SimdFloatingpointTest (0 ms total) 48: 48: [----------] 16 tests from SimdFloatingpointUtilTest 48: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose4 48: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose4 (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose2 48: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose2 (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 48: [ OK ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.transposeScatterStoreU3 48: [ OK ] SimdFloatingpointUtilTest.transposeScatterStoreU3 (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3 48: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3 (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping 48: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3 48: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3 (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping 48: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.expandScalarsToTriplets 48: [ OK ] SimdFloatingpointUtilTest.expandScalarsToTriplets (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 48: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 48: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 48: [ OK ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.reduceIncr4Sum 48: [ OK ] SimdFloatingpointUtilTest.reduceIncr4Sum (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.loadUNDuplicate4 48: [ OK ] SimdFloatingpointUtilTest.loadUNDuplicate4 (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.load4DuplicateN 48: [ OK ] SimdFloatingpointUtilTest.load4DuplicateN (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.loadU4NOffset 48: [ OK ] SimdFloatingpointUtilTest.loadU4NOffset (0 ms) 48: [----------] 16 tests from SimdFloatingpointUtilTest (0 ms total) 48: 48: [----------] 23 tests from SimdIntegerTest 48: [ RUN ] SimdIntegerTest.setZero 48: [ OK ] SimdIntegerTest.setZero (0 ms) 48: [ RUN ] SimdIntegerTest.set 48: [ OK ] SimdIntegerTest.set (0 ms) 48: [ RUN ] SimdIntegerTest.add 48: [ OK ] SimdIntegerTest.add (0 ms) 48: [ RUN ] SimdIntegerTest.sub 48: [ OK ] SimdIntegerTest.sub (0 ms) 48: [ RUN ] SimdIntegerTest.mul 48: [ OK ] SimdIntegerTest.mul (0 ms) 48: [ RUN ] SimdIntegerTest.and 48: [ OK ] SimdIntegerTest.and (0 ms) 48: [ RUN ] SimdIntegerTest.andNot 48: [ OK ] SimdIntegerTest.andNot (0 ms) 48: [ RUN ] SimdIntegerTest.or 48: [ OK ] SimdIntegerTest.or (0 ms) 48: [ RUN ] SimdIntegerTest.xor 48: [ OK ] SimdIntegerTest.xor (0 ms) 48: [ RUN ] SimdIntegerTest.extract 48: [ OK ] SimdIntegerTest.extract (0 ms) 48: [ RUN ] SimdIntegerTest.cvtR2I 48: [ OK ] SimdIntegerTest.cvtR2I (0 ms) 48: [ RUN ] SimdIntegerTest.cvttR2I 48: [ OK ] SimdIntegerTest.cvttR2I (0 ms) 48: [ RUN ] SimdIntegerTest.cvtI2R 48: [ OK ] SimdIntegerTest.cvtI2R (0 ms) 48: [ RUN ] SimdIntegerTest.cmpEqAndSelectMask 48: [ OK ] SimdIntegerTest.cmpEqAndSelectMask (0 ms) 48: [ RUN ] SimdIntegerTest.cmpEqAndSelectNotMask 48: [ OK ] SimdIntegerTest.cmpEqAndSelectNotMask (0 ms) 48: [ RUN ] SimdIntegerTest.cmpLt 48: [ OK ] SimdIntegerTest.cmpLt (0 ms) 48: [ RUN ] SimdIntegerTest.testBits 48: [ OK ] SimdIntegerTest.testBits (0 ms) 48: [ RUN ] SimdIntegerTest.andB 48: [ OK ] SimdIntegerTest.andB (0 ms) 48: [ RUN ] SimdIntegerTest.orB 48: [ OK ] SimdIntegerTest.orB (0 ms) 48: [ RUN ] SimdIntegerTest.anyTrue 48: [ OK ] SimdIntegerTest.anyTrue (0 ms) 48: [ RUN ] SimdIntegerTest.blend 48: [ OK ] SimdIntegerTest.blend (0 ms) 48: [ RUN ] SimdIntegerTest.cvtB2IB 48: [ OK ] SimdIntegerTest.cvtB2IB (0 ms) 48: [ RUN ] SimdIntegerTest.cvtIB2B 48: [ OK ] SimdIntegerTest.cvtIB2B (0 ms) 48: [----------] 23 tests from SimdIntegerTest (0 ms total) 48: 48: [----------] 56 tests from SimdMathTest 48: [ RUN ] SimdMathTest.generateTestPointsFloat 48: [ OK ] SimdMathTest.generateTestPointsFloat (0 ms) 48: [ RUN ] SimdMathTest.copysign 48: [ OK ] SimdMathTest.copysign (0 ms) 48: [ RUN ] SimdMathTest.invsqrt 48: [ OK ] SimdMathTest.invsqrt (0 ms) 48: [ RUN ] SimdMathTest.maskzInvsqrt 48: [ OK ] SimdMathTest.maskzInvsqrt (0 ms) 48: [ RUN ] SimdMathTest.invsqrtPair 48: [ OK ] SimdMathTest.invsqrtPair (0 ms) 48: [ RUN ] SimdMathTest.sqrt 48: [ OK ] SimdMathTest.sqrt (0 ms) 48: [ RUN ] SimdMathTest.sqrtUnsafe 48: [ OK ] SimdMathTest.sqrtUnsafe (0 ms) 48: [ RUN ] SimdMathTest.inv 48: [ OK ] SimdMathTest.inv (10 ms) 48: [ RUN ] SimdMathTest.maskzInv 48: [ OK ] SimdMathTest.maskzInv (0 ms) 48: [ RUN ] SimdMathTest.cbrt 48: [ OK ] SimdMathTest.cbrt (0 ms) 48: [ RUN ] SimdMathTest.invcbrt 48: [ OK ] SimdMathTest.invcbrt (1 ms) 48: [ RUN ] SimdMathTest.log2 48: [ OK ] SimdMathTest.log2 (0 ms) 48: [ RUN ] SimdMathTest.log 48: [ OK ] SimdMathTest.log (0 ms) 48: [ RUN ] SimdMathTest.exp2 48: [ OK ] SimdMathTest.exp2 (1 ms) 48: [ RUN ] SimdMathTest.exp2Unsafe 48: [ OK ] SimdMathTest.exp2Unsafe (0 ms) 48: [ RUN ] SimdMathTest.exp 48: [ OK ] SimdMathTest.exp (6 ms) 48: [ RUN ] SimdMathTest.expUnsafe 48: [ OK ] SimdMathTest.expUnsafe (0 ms) 48: [ RUN ] SimdMathTest.pow 48: [ OK ] SimdMathTest.pow (0 ms) 48: [ RUN ] SimdMathTest.powUnsafe 48: [ OK ] SimdMathTest.powUnsafe (0 ms) 48: [ RUN ] SimdMathTest.erf 48: [ OK ] SimdMathTest.erf (1 ms) 48: [ RUN ] SimdMathTest.erfc 48: [ OK ] SimdMathTest.erfc (5 ms) 48: [ RUN ] SimdMathTest.sin 48: [ OK ] SimdMathTest.sin (1 ms) 48: [ RUN ] SimdMathTest.cos 48: [ OK ] SimdMathTest.cos (1 ms) 48: [ RUN ] SimdMathTest.tan 48: [ OK ] SimdMathTest.tan (1 ms) 48: [ RUN ] SimdMathTest.asin 48: [ OK ] SimdMathTest.asin (0 ms) 48: [ RUN ] SimdMathTest.acos 48: [ OK ] SimdMathTest.acos (0 ms) 48: [ RUN ] SimdMathTest.atan 48: [ OK ] SimdMathTest.atan (0 ms) 48: [ RUN ] SimdMathTest.atan2 48: [ OK ] SimdMathTest.atan2 (0 ms) 48: [ RUN ] SimdMathTest.pmeForceCorrection 48: [ OK ] SimdMathTest.pmeForceCorrection (8 ms) 48: [ RUN ] SimdMathTest.pmePotentialCorrection 48: [ OK ] SimdMathTest.pmePotentialCorrection (0 ms) 48: [ RUN ] SimdMathTest.invsqrtSingleAccuracy 48: [ OK ] SimdMathTest.invsqrtSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.invsqrtPairSingleAccuracy 48: [ OK ] SimdMathTest.invsqrtPairSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.sqrtSingleAccuracy 48: [ OK ] SimdMathTest.sqrtSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.sqrtSingleAccuracyUnsafe 48: [ OK ] SimdMathTest.sqrtSingleAccuracyUnsafe (0 ms) 48: [ RUN ] SimdMathTest.invSingleAccuracy 48: [ OK ] SimdMathTest.invSingleAccuracy (2 ms) 48: [ RUN ] SimdMathTest.cbrtSingleAccuracy 48: [ OK ] SimdMathTest.cbrtSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.invcbrtSingleAccuracy 48: [ OK ] SimdMathTest.invcbrtSingleAccuracy (1 ms) 48: [ RUN ] SimdMathTest.log2SingleAccuracy 48: [ OK ] SimdMathTest.log2SingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.logSingleAccuracy 48: [ OK ] SimdMathTest.logSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.exp2SingleAccuracy 48: [ OK ] SimdMathTest.exp2SingleAccuracy (5 ms) 48: [ RUN ] SimdMathTest.exp2SingleAccuracyUnsafe 48: [ OK ] SimdMathTest.exp2SingleAccuracyUnsafe (0 ms) 48: [ RUN ] SimdMathTest.expSingleAccuracy 48: [ OK ] SimdMathTest.expSingleAccuracy (6 ms) 48: [ RUN ] SimdMathTest.expSingleAccuracyUnsafe 48: [ OK ] SimdMathTest.expSingleAccuracyUnsafe (0 ms) 48: [ RUN ] SimdMathTest.powSingleAccuracy 48: [ OK ] SimdMathTest.powSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.powSingleAccuracyUnsafe 48: [ OK ] SimdMathTest.powSingleAccuracyUnsafe (0 ms) 48: [ RUN ] SimdMathTest.erfSingleAccuracy 48: [ OK ] SimdMathTest.erfSingleAccuracy (1 ms) 48: [ RUN ] SimdMathTest.erfcSingleAccuracy 48: [ OK ] SimdMathTest.erfcSingleAccuracy (2 ms) 48: [ RUN ] SimdMathTest.sinSingleAccuracy 48: [ OK ] SimdMathTest.sinSingleAccuracy (1 ms) 48: [ RUN ] SimdMathTest.cosSingleAccuracy 48: [ OK ] SimdMathTest.cosSingleAccuracy (1 ms) 48: [ RUN ] SimdMathTest.tanSingleAccuracy 48: [ OK ] SimdMathTest.tanSingleAccuracy (9 ms) 48: [ RUN ] SimdMathTest.asinSingleAccuracy 48: [ OK ] SimdMathTest.asinSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.acosSingleAccuracy 48: [ OK ] SimdMathTest.acosSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.atanSingleAccuracy 48: [ OK ] SimdMathTest.atanSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.atan2SingleAccuracy 48: [ OK ] SimdMathTest.atan2SingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.pmeForceCorrectionSingleAccuracy 48: [ OK ] SimdMathTest.pmeForceCorrectionSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.pmePotentialCorrectionSingleAccuracy 48: [ OK ] SimdMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 48: [----------] 56 tests from SimdMathTest (88 ms total) 48: 48: [----------] 1 test from EmptyArrayRefTest 48: [ RUN ] EmptyArrayRefTest.IsEmpty 48: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 48: [----------] 1 test from EmptyArrayRefTest (0 ms total) 48: 48: [----------] 3 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 48: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 48: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 48: [ RUN ] ArrayRefTest/0.ConstructFromArrayRefWorks 48: [ OK ] ArrayRefTest/0.ConstructFromArrayRefWorks (0 ms) 48: [ RUN ] ArrayRefTest/0.ConstructFromArrayWorks 48: [ OK ] ArrayRefTest/0.ConstructFromArrayWorks (0 ms) 48: [----------] 3 tests from ArrayRefTest/0 (0 ms total) 48: 48: [----------] 3 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 48: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 48: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 48: [ RUN ] ArrayRefTest/1.ConstructFromArrayRefWorks 48: [ OK ] ArrayRefTest/1.ConstructFromArrayRefWorks (0 ms) 48: [ RUN ] ArrayRefTest/1.ConstructFromArrayWorks 48: [ OK ] ArrayRefTest/1.ConstructFromArrayWorks (0 ms) 48: [----------] 3 tests from ArrayRefTest/1 (0 ms total) 48: 48: [----------] 3 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 48: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 48: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 48: [ RUN ] ArrayRefTest/2.ConstructFromArrayRefWorks 48: [ OK ] ArrayRefTest/2.ConstructFromArrayRefWorks (0 ms) 48: [ RUN ] ArrayRefTest/2.ConstructFromArrayWorks 48: [ OK ] ArrayRefTest/2.ConstructFromArrayWorks (0 ms) 48: [----------] 3 tests from ArrayRefTest/2 (0 ms total) 48: 48: [----------] 3 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 48: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 48: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 48: [ RUN ] ArrayRefTest/3.ConstructFromArrayRefWorks 48: [ OK ] ArrayRefTest/3.ConstructFromArrayRefWorks (0 ms) 48: [ RUN ] ArrayRefTest/3.ConstructFromArrayWorks 48: [ OK ] ArrayRefTest/3.ConstructFromArrayWorks (0 ms) 48: [----------] 3 tests from ArrayRefTest/3 (0 ms total) 48: 48: [----------] 1 test from ArrayRefReadWriteTest/0, where TypeParam = gmx::ArrayRef 48: [ RUN ] ArrayRefReadWriteTest/0.Assignment 48: [ OK ] ArrayRefReadWriteTest/0.Assignment (0 ms) 48: [----------] 1 test from ArrayRefReadWriteTest/0 (0 ms total) 48: 48: [----------] 1 test from ArrayRefReadWriteTest/1, where TypeParam = gmx::ArrayRef 48: [ RUN ] ArrayRefReadWriteTest/1.Assignment 48: [ OK ] ArrayRefReadWriteTest/1.Assignment (0 ms) 48: [----------] 1 test from ArrayRefReadWriteTest/1 (0 ms total) 48: 48: [----------] 1 test from ArrayRefArithmeticTest/0, where TypeParam = gmx::ArrayRef 48: [ RUN ] ArrayRefArithmeticTest/0.Basic 48: [ OK ] ArrayRefArithmeticTest/0.Basic (0 ms) 48: [----------] 1 test from ArrayRefArithmeticTest/0 (0 ms total) 48: 48: [----------] 1 test from ArrayRefArithmeticTest/1, where TypeParam = gmx::ArrayRef 48: [ RUN ] ArrayRefArithmeticTest/1.Basic 48: [ OK ] ArrayRefArithmeticTest/1.Basic (0 ms) 48: [----------] 1 test from ArrayRefArithmeticTest/1 (0 ms total) 48: 48: [----------] 3 tests from SimdVectorOperationsTest 48: [ RUN ] SimdVectorOperationsTest.iprod 48: [ OK ] SimdVectorOperationsTest.iprod (0 ms) 48: [ RUN ] SimdVectorOperationsTest.norm2 48: [ OK ] SimdVectorOperationsTest.norm2 (0 ms) 48: [ RUN ] SimdVectorOperationsTest.cprod 48: [ OK ] SimdVectorOperationsTest.cprod (0 ms) 48: [----------] 3 tests from SimdVectorOperationsTest (0 ms total) 48: 48: [----------] 32 tests from Simd4FloatingpointTest 48: [ RUN ] Simd4FloatingpointTest.setZero 48: [ OK ] Simd4FloatingpointTest.setZero (0 ms) 48: [ RUN ] Simd4FloatingpointTest.set 48: [ OK ] Simd4FloatingpointTest.set (0 ms) 48: [ RUN ] Simd4FloatingpointTest.add 48: [ OK ] Simd4FloatingpointTest.add (0 ms) 48: [ RUN ] Simd4FloatingpointTest.sub 48: [ OK ] Simd4FloatingpointTest.sub (0 ms) 48: [ RUN ] Simd4FloatingpointTest.mul 48: [ OK ] Simd4FloatingpointTest.mul (0 ms) 48: [ RUN ] Simd4FloatingpointTest.fma 48: [ OK ] Simd4FloatingpointTest.fma (0 ms) 48: [ RUN ] Simd4FloatingpointTest.fms 48: [ OK ] Simd4FloatingpointTest.fms (0 ms) 48: [ RUN ] Simd4FloatingpointTest.fnma 48: [ OK ] Simd4FloatingpointTest.fnma (0 ms) 48: [ RUN ] Simd4FloatingpointTest.fnms 48: [ OK ] Simd4FloatingpointTest.fnms (0 ms) 48: [ RUN ] Simd4FloatingpointTest.abs 48: [ OK ] Simd4FloatingpointTest.abs (0 ms) 48: [ RUN ] Simd4FloatingpointTest.neg 48: [ OK ] Simd4FloatingpointTest.neg (0 ms) 48: [ RUN ] Simd4FloatingpointTest.and 48: [ OK ] Simd4FloatingpointTest.and (0 ms) 48: [ RUN ] Simd4FloatingpointTest.or 48: [ OK ] Simd4FloatingpointTest.or (0 ms) 48: [ RUN ] Simd4FloatingpointTest.xor 48: [ OK ] Simd4FloatingpointTest.xor (0 ms) 48: [ RUN ] Simd4FloatingpointTest.andNot 48: [ OK ] Simd4FloatingpointTest.andNot (0 ms) 48: [ RUN ] Simd4FloatingpointTest.max 48: [ OK ] Simd4FloatingpointTest.max (0 ms) 48: [ RUN ] Simd4FloatingpointTest.min 48: [ OK ] Simd4FloatingpointTest.min (0 ms) 48: [ RUN ] Simd4FloatingpointTest.round 48: [ OK ] Simd4FloatingpointTest.round (0 ms) 48: [ RUN ] Simd4FloatingpointTest.trunc 48: [ OK ] Simd4FloatingpointTest.trunc (0 ms) 48: [ RUN ] Simd4FloatingpointTest.gmxSimd4RsqrtR 48: [ OK ] Simd4FloatingpointTest.gmxSimd4RsqrtR (0 ms) 48: [ RUN ] Simd4FloatingpointTest.cmpEqAndSelectByMask 48: [ OK ] Simd4FloatingpointTest.cmpEqAndSelectByMask (0 ms) 48: [ RUN ] Simd4FloatingpointTest.selectByNotMask 48: [ OK ] Simd4FloatingpointTest.selectByNotMask (0 ms) 48: [ RUN ] Simd4FloatingpointTest.cmpNe 48: [ OK ] Simd4FloatingpointTest.cmpNe (0 ms) 48: [ RUN ] Simd4FloatingpointTest.cmpLe 48: [ OK ] Simd4FloatingpointTest.cmpLe (0 ms) 48: [ RUN ] Simd4FloatingpointTest.cmpLt 48: [ OK ] Simd4FloatingpointTest.cmpLt (0 ms) 48: [ RUN ] Simd4FloatingpointTest.andB 48: [ OK ] Simd4FloatingpointTest.andB (0 ms) 48: [ RUN ] Simd4FloatingpointTest.orB 48: [ OK ] Simd4FloatingpointTest.orB (0 ms) 48: [ RUN ] Simd4FloatingpointTest.anyTrue 48: [ OK ] Simd4FloatingpointTest.anyTrue (0 ms) 48: [ RUN ] Simd4FloatingpointTest.blend 48: [ OK ] Simd4FloatingpointTest.blend (0 ms) 48: [ RUN ] Simd4FloatingpointTest.reduce 48: [ OK ] Simd4FloatingpointTest.reduce (0 ms) 48: [ RUN ] Simd4FloatingpointTest.dotProduct 48: [ OK ] Simd4FloatingpointTest.dotProduct (0 ms) 48: [ RUN ] Simd4FloatingpointTest.transpose 48: [ OK ] Simd4FloatingpointTest.transpose (0 ms) 48: [----------] 32 tests from Simd4FloatingpointTest (0 ms total) 48: 48: [----------] 2 tests from Simd4MathTest 48: [ RUN ] Simd4MathTest.invsqrt 48: [ OK ] Simd4MathTest.invsqrt (0 ms) 48: [ RUN ] Simd4MathTest.invsqrtSingleAccuracy 48: [ OK ] Simd4MathTest.invsqrtSingleAccuracy (0 ms) 48: [----------] 2 tests from Simd4MathTest (0 ms total) 48: 48: [----------] 1 test from Simd4VectorOperationsTest 48: [ RUN ] Simd4VectorOperationsTest.norm2 48: [ OK ] Simd4VectorOperationsTest.norm2 (0 ms) 48: [----------] 1 test from Simd4VectorOperationsTest (0 ms total) 48: 48: [----------] Global test environment tear-down 48: [==========] 288 tests from 22 test suites ran. (90 ms total) 48: [ PASSED ] 288 tests. 48/90 Test #48: SimdUnitTests ............................. Passed 0.16 sec test 49 Start 49: CompatibilityHelpersTests 49: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/compat-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/CompatibilityHelpersTests.xml" 49: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/compat/tests 49: Test timeout computed to be: 30 49: [==========] Running 9 tests from 6 test suites. 49: [----------] Global test environment set-up. 49: [----------] 4 tests from TemplateMPTest 49: [ RUN ] TemplateMPTest.MpWithIndexInt 49: [ OK ] TemplateMPTest.MpWithIndexInt (0 ms) 49: [ RUN ] TemplateMPTest.MpWithIndexIntBad 49: [ OK ] TemplateMPTest.MpWithIndexIntBad (0 ms) 49: [ RUN ] TemplateMPTest.MpWithIndexBool 49: [ OK ] TemplateMPTest.MpWithIndexBool (0 ms) 49: [ RUN ] TemplateMPTest.MpWithIndexEnum 49: [ OK ] TemplateMPTest.MpWithIndexEnum (0 ms) 49: [----------] 4 tests from TemplateMPTest (0 ms total) 49: 49: [----------] 1 test from NotNullConstruction 49: [ RUN ] NotNullConstruction.Works 49: [ OK ] NotNullConstruction.Works (0 ms) 49: [----------] 1 test from NotNullConstruction (0 ms total) 49: 49: [----------] 1 test from NotNullCasting 49: [ RUN ] NotNullCasting.Works 49: [ OK ] NotNullCasting.Works (0 ms) 49: [----------] 1 test from NotNullCasting (0 ms total) 49: 49: [----------] 1 test from NotNullAssignment 49: [ RUN ] NotNullAssignment.Works 49: [ OK ] NotNullAssignment.Works (0 ms) 49: [----------] 1 test from NotNullAssignment (0 ms total) 49: 49: [----------] 1 test from MakeNotNull 49: [ RUN ] MakeNotNull.Works 49: [ OK ] MakeNotNull.Works (0 ms) 49: [----------] 1 test from MakeNotNull (0 ms total) 49: 49: [----------] 1 test from NotNull 49: [ RUN ] NotNull.WorksInContainers 49: [ OK ] NotNull.WorksInContainers (0 ms) 49: [----------] 1 test from NotNull (0 ms total) 49: 49: [----------] Global test environment tear-down 49: [==========] 9 tests from 6 test suites ran. (0 ms total) 49: [ PASSED ] 9 tests. 49/90 Test #49: CompatibilityHelpersTests ................. Passed 0.04 sec test 50 Start 50: GmxAnaTest 50: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/gmxana-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/GmxAnaTest.xml" 50: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxana/tests 50: Test timeout computed to be: 600 50: [==========] Running 31 tests from 4 test suites. 50: [----------] Global test environment set-up. 50: [----------] 7 tests from Entropy 50: [ RUN ] Entropy.Schlitter_300_NoLinear 50: [ OK ] Entropy.Schlitter_300_NoLinear (0 ms) 50: [ RUN ] Entropy.Schlitter_300_Linear 50: [ OK ] Entropy.Schlitter_300_Linear (0 ms) 50: [ RUN ] Entropy.QuasiHarmonic_300_NoLinear 50: [ OK ] Entropy.QuasiHarmonic_300_NoLinear (0 ms) 50: [ RUN ] Entropy.QuasiHarmonic_200_NoLinear 50: [ OK ] Entropy.QuasiHarmonic_200_NoLinear (0 ms) 50: [ RUN ] Entropy.QuasiHarmonic_200_Linear 50: [ OK ] Entropy.QuasiHarmonic_200_Linear (0 ms) 50: [ RUN ] Entropy.EntropyCompare_200_Linear 50: [ OK ] Entropy.EntropyCompare_200_Linear (0 ms) 50: [ RUN ] Entropy.EntropyCompare_300_Linear 50: [ OK ] Entropy.EntropyCompare_300_Linear (0 ms) 50: [----------] 7 tests from Entropy (0 ms total) 50: 50: [----------] 2 tests from GmxChiTest 50: [ RUN ] GmxChiTest.gmxchiWorksWithAll 50: Analyzing from residue 1 to residue 11 50: 10 residues with dihedrals found 50: 46 dihedrals found 50: Reading frames from gro file 'First 10 residues from 1AKI t= 0.00000 step= 0', 156 atoms. 50: Reading frame 0 time 0.000 Reading frame 1 time 0.020 Reading frame 2 time 0.040 Last frame 2 time 0.040 50: j after resetting (nr. active dihedrals) = 46 50: Printing phiLYS1.xvg Printing phiVAL2.xvg Printing phiPHE3.xvg Printing phiGLY4.xvg Printing phiARG5.xvg Printing phiCYS6.xvg Printing phiGLU7.xvg Printing phiLEU8.xvg Printing phiALA9.xvg Printing phiALA10.xvg Printing psiLYS1.xvg Printing psiVAL2.xvg Printing psiPHE3.xvg Printing psiGLY4.xvg Printing psiARG5.xvg Printing psiCYS6.xvg Printing psiGLU7.xvg Printing psiLEU8.xvg Printing psiALA9.xvg Printing psiALA10.xvg Printing omegaVAL2.xvg Printing omegaPHE3.xvg Printing omegaGLY4.xvg Printing omegaARG5.xvg Printing omegaCYS6.xvg Printing omegaGLU7.xvg Printing omegaLEU8.xvg Printing omegaALA9.xvg Printing omegaALA10.xvg Printing chi1LYS1.xvg Printing chi1VAL2.xvg Printing chi1PHE3.xvg Printing chi1ARG5.xvg Printing chi1CYS6.xvg Printing chi1GLU7.xvg Printing chi1LEU8.xvg Printing chi2LYS1.xvg Printing chi2PHE3.xvg Printing chi2ARG5.xvg Printing chi2GLU7.xvg Printing chi2LEU8.xvg Printing chi3LYS1.xvg Printing chi3ARG5.xvg Printing chi3GLU7.xvg Printing chi4LYS1.xvg Printing chi4ARG5.xvg 50: Now calculating transitions... 50: Total number of transitions: 0 50: Now printing out transitions and OPs... 50: Now printing out rotamer occupancies... 50: Now calculating Chi product trajectories... 50: Printing chiproductLYS1.xvg and histo-chiprodLYS1.xvg Printing chiproductVAL2.xvg and histo-chiprodVAL2.xvg Printing chiproductPHE3.xvg and histo-chiprodPHE3.xvg Printing chiproductARG5.xvg and histo-chiprodARG5.xvg Printing chiproductCYS6.xvg and histo-chiprodCYS6.xvg Printing chiproductGLU7.xvg and histo-chiprodGLU7.xvg Printing chiproductLEU8.xvg and histo-chiprodLEU8.xvg 50: [ OK ] GmxChiTest.gmxchiWorksWithAll (1314 ms) 50: [ RUN ] GmxChiTest.gmxchiWorksWithr0AndrN 50: Analyzing from residue 2 to residue 6 50: 5 residues with dihedrals found 50: 23 dihedrals found 50: Reading frames from gro file 'First 10 residues from 1AKI t= 0.00000 step= 0', 156 atoms. 50: Reading frame 0 time 0.000 Reading frame 1 time 0.020 Reading frame 2 time 0.040 Last frame 2 time 0.040 50: j after resetting (nr. active dihedrals) = 23 50: Printing phiVAL2.xvg Printing phiPHE3.xvg Printing phiGLY4.xvg Printing phiARG5.xvg Printing phiCYS6.xvg Printing psiVAL2.xvg Printing psiPHE3.xvg Printing psiGLY4.xvg Printing psiARG5.xvg Printing psiCYS6.xvg Printing omegaVAL2.xvg Printing omegaPHE3.xvg Printing omegaGLY4.xvg Printing omegaARG5.xvg Printing omegaCYS6.xvg Printing chi1VAL2.xvg Printing chi1PHE3.xvg Printing chi1ARG5.xvg Printing chi1CYS6.xvg Printing chi2PHE3.xvg Printing chi2ARG5.xvg Printing chi3ARG5.xvg Printing chi4ARG5.xvg 50: Now calculating transitions... 50: Total number of transitions: 0 50: Now printing out transitions and OPs... 50: Now printing out rotamer occupancies... 50: Now calculating Chi product trajectories... 50: Printing chiproductVAL2.xvg and histo-chiprodVAL2.xvg Printing chiproductPHE3.xvg and histo-chiprodPHE3.xvg Printing chiproductARG5.xvg and histo-chiprodARG5.xvg Printing chiproductCYS6.xvg and histo-chiprodCYS6.xvg 50: [ OK ] GmxChiTest.gmxchiWorksWithr0AndrN (611 ms) 50: [----------] 2 tests from GmxChiTest (2159 ms total) 50: 50: [----------] 10 tests from MindistTest 50: [ RUN ] MindistTest.mindistWorksWithSingleAtoms 50: Group 0 ( atom1) has 1 elements 50: Group 1 ( atom2) has 1 elements 50: Group 2 ( atom3) has 1 elements 50: Group 3 ( atoms12) has 2 elements 50: Group 4 ( atoms23) has 2 elements 50: Group 5 ( atoms123) has 3 elements 50: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 50: Reading frame 0 time 0.000 Last frame 0 time 0.000 50: Selected 0: 'atom1' 50: Selected 1: 'atom2' 50: [ OK ] MindistTest.mindistWorksWithSingleAtoms (30 ms) 50: [ RUN ] MindistTest.mindistWorksWithMultipleAtoms 50: Group 0 ( atom1) has 1 elements 50: Group 1 ( atom2) has 1 elements 50: Group 2 ( atom3) has 1 elements 50: Group 3 ( atoms12) has 2 elements 50: Group 4 ( atoms23) has 2 elements 50: Group 5 ( atoms123) has 3 elements 50: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 50: Reading frame 0 time 0.000 Last frame 0 time 0.000 50: Selected 2: 'atom3' 50: Selected 3: 'atoms12' 50: [ OK ] MindistTest.mindistWorksWithMultipleAtoms (9 ms) 50: [ RUN ] MindistTest.mindistDoesNotPickUpContacts 50: Group 0 ( atom1) has 1 elements 50: Group 1 ( atom2) has 1 elements 50: Group 2 ( atom3) has 1 elements 50: Group 3 ( atoms12) has 2 elements 50: Group 4 ( atoms23) has 2 elements 50: Group 5 ( atoms123) has 3 elements 50: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 50: Reading frame 0 time 0.000 Last frame 0 time 0.000 50: Selected 0: 'atom1' 50: Selected 1: 'atom2' 50: [ OK ] MindistTest.mindistDoesNotPickUpContacts (0 ms) 50: [ RUN ] MindistTest.mindistPicksUpContacts 50: Group 0 ( atom1) has 1 elements 50: Group 1 ( atom2) has 1 elements 50: Group 2 ( atom3) has 1 elements 50: Group 3 ( atoms12) has 2 elements 50: Group 4 ( atoms23) has 2 elements 50: Group 5 ( atoms123) has 3 elements 50: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 50: Reading frame 0 time 0.000 Last frame 0 time 0.000 50: Selected 0: 'atom1' 50: Selected 1: 'atom2' 50: [ OK ] MindistTest.mindistPicksUpContacts (1 ms) 50: [ RUN ] MindistTest.ngWorks 50: Group 0 ( atom1) has 1 elements 50: Group 1 ( atom2) has 1 elements 50: Group 2 ( atom3) has 1 elements 50: Group 3 ( atoms12) has 2 elements 50: Group 4 ( atoms23) has 2 elements 50: Group 5 ( atoms123) has 3 elements 50: Select a group: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 50: Reading frame 0 time 0.000 Last frame 0 time 0.000 50: Selected 0: 'atom1' 50: Selected 1: 'atom2' 50: Selected 2: 'atom3' 50: [ OK ] MindistTest.ngWorks (3 ms) 50: [ RUN ] MindistTest.groupWorks 50: Group 0 ( atom1) has 1 elements 50: Group 1 ( atom2) has 1 elements 50: Group 2 ( atom3) has 1 elements 50: Group 3 ( atoms12) has 2 elements 50: Group 4 ( atoms23) has 2 elements 50: Group 5 ( atoms123) has 3 elements 50: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 50: Reading frame 0 time 0.000 Last frame 0 time 0.000 50: Selected 3: 'atoms12' 50: Selected 2: 'atom3' 50: [ OK ] MindistTest.groupWorks (0 ms) 50: [ RUN ] MindistTest.maxDistWorks 50: Group 0 ( atom1) has 1 elements 50: Group 1 ( atom2) has 1 elements 50: Group 2 ( atom3) has 1 elements 50: Group 3 ( atoms12) has 2 elements 50: Group 4 ( atoms23) has 2 elements 50: Group 5 ( atoms123) has 3 elements 50: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 50: Reading frame 0 time 0.000 Last frame 0 time 0.000 50: Selected 2: 'atom3' 50: Selected 3: 'atoms12' 50: [ OK ] MindistTest.maxDistWorks (9 ms) 50: [ RUN ] MindistTest.noPbcWorks 50: Group 0 ( atom1) has 1 elements 50: Group 1 ( atom2) has 1 elements 50: Group 2 ( atom3) has 1 elements 50: Group 3 ( atoms12) has 2 elements 50: Group 4 ( atoms23) has 2 elements 50: Group 5 ( atoms123) has 3 elements 50: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 50: Reading frame 0 time 0.000 Last frame 0 time 0.000 50: Selected 0: 'atom1' 50: Selected 1: 'atom2' 50: [ OK ] MindistTest.noPbcWorks (1 ms) 50: [ RUN ] MindistTest.resPerTimeWorks 50: Group 0 ( atom1) has 1 elements 50: Group 1 ( atom2) has 1 elements 50: Group 2 ( atom3) has 1 elements 50: Group 3 ( atoms12) has 2 elements 50: Group 4 ( atoms23) has 2 elements 50: Group 5 ( atoms123) has 3 elements 50: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 50: Reading frame 0 time 0.000 Last frame 0 time 0.000 50: Selected 3: 'atoms12' 50: Selected 2: 'atom3' 50: [ OK ] MindistTest.resPerTimeWorks (1 ms) 50: [ RUN ] MindistTest.matrixWorks 50: Group 0 ( atom1) has 1 elements 50: Group 1 ( atom2) has 1 elements 50: Group 2 ( atom3) has 1 elements 50: Group 3 ( atoms12) has 2 elements 50: Group 4 ( atoms23) has 2 elements 50: Group 5 ( atoms123) has 3 elements 50: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 50: Reading frame 0 time 0.000 Last frame 0 time 0.000 50: Selected 5: 'atoms123' 50: Special case: making distance matrix between all atoms in group atoms123 50: [ OK ] MindistTest.matrixWorks (1 ms) 50: [----------] 10 tests from MindistTest (59 ms total) 50: 50: [----------] 12 tests from NoFatalErrorWhenWritingFrom/GmxTraj 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: trr version: GMX_trn_file (single precision) 50: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 (1 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 (1 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 50: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 (1 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 50: Reading frame 1 time 1.000 Last frame 1 time 1.000 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 (3 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 (1 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 (3 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/0 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frame 0 time 0.000 50: WARNING: If there are molecules in the input trajectory file 50: that are broken across periodic boundaries, they 50: cannot be made whole (or treated as whole) without 50: you providing a run input file. 50: 50: Reading frame 1 time 1.000 Last frame 1 time 1.000 50: 50: WARNING: Masses and atomic (Van der Waals) radii will be guessed 50: based on residue and atom names, since they could not be 50: definitively assigned from the information in your input 50: files. These guessed numbers might deviate from the mass 50: and radius of the atom type. Please check the output 50: files if necessary. Note, that this functionality may 50: be removed in a future GROMACS version. Please, consider 50: using another file format for your input. 50: 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/0 (7 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/1 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frame 0 time 0.000 50: WARNING: If there are molecules in the input trajectory file 50: that are broken across periodic boundaries, they 50: cannot be made whole (or treated as whole) without 50: you providing a run input file. 50: 50: Reading frame 1 time 1.000 Last frame 1 time 1.000 50: 50: WARNING: Masses and atomic (Van der Waals) radii will be guessed 50: based on residue and atom names, since they could not be 50: definitively assigned from the information in your input 50: files. These guessed numbers might deviate from the mass 50: and radius of the atom type. Please check the output 50: files if necessary. Note, that this functionality may 50: be removed in a future GROMACS version. Please, consider 50: using another file format for your input. 50: 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/1 (7 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/2 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 50: Reading frame 0 time 0.000 50: WARNING: If there are molecules in the input trajectory file 50: that are broken across periodic boundaries, they 50: cannot be made whole (or treated as whole) without 50: you providing a run input file. 50: 50: Reading frame 1 time 1.000 Last frame 1 time 1.000 50: 50: WARNING: Masses and atomic (Van der Waals) radii will be guessed 50: based on residue and atom names, since they could not be 50: definitively assigned from the information in your input 50: files. These guessed numbers might deviate from the mass 50: and radius of the atom type. Please check the output 50: files if necessary. Note, that this functionality may 50: be removed in a future GROMACS version. Please, consider 50: using another file format for your input. 50: 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/2 (11 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/3 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 50: WARNING: If there are molecules in the input trajectory file 50: that are broken across periodic boundaries, they 50: cannot be made whole (or treated as whole) without 50: you providing a run input file. 50: 50: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 50: Reading frame 1 time 1.000 Last frame 1 time 1.000 50: 50: WARNING: Masses and atomic (Van der Waals) radii will be guessed 50: based on residue and atom names, since they could not be 50: definitively assigned from the information in your input 50: files. These guessed numbers might deviate from the mass 50: and radius of the atom type. Please check the output 50: files if necessary. Note, that this functionality may 50: be removed in a future GROMACS version. Please, consider 50: using another file format for your input. 50: 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/3 (2 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/4 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frame 0 time 0.000 50: WARNING: If there are molecules in the input trajectory file 50: that are broken across periodic boundaries, they 50: cannot be made whole (or treated as whole) without 50: you providing a run input file. 50: 50: Reading frame 1 time 1.000 Last frame 1 time 1.000 50: 50: WARNING: Masses and atomic (Van der Waals) radii will be guessed 50: based on residue and atom names, since they could not be 50: definitively assigned from the information in your input 50: files. These guessed numbers might deviate from the mass 50: and radius of the atom type. Please check the output 50: files if necessary. Note, that this functionality may 50: be removed in a future GROMACS version. Please, consider 50: using another file format for your input. 50: 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/4 (20 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/5 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frame 0 time 0.000 50: WARNING: If there are molecules in the input trajectory file 50: that are broken across periodic boundaries, they 50: cannot be made whole (or treated as whole) without 50: you providing a run input file. 50: 50: Reading frame 1 time 1.000 Last frame 1 time 1.000 50: 50: WARNING: Masses and atomic (Van der Waals) radii will be guessed 50: based on residue and atom names, since they could not be 50: definitively assigned from the information in your input 50: files. These guessed numbers might deviate from the mass 50: and radius of the atom type. Please check the output 50: files if necessary. Note, that this functionality may 50: be removed in a future GROMACS version. Please, consider 50: using another file format for your input. 50: 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/5 (4 ms) 50: [----------] 12 tests from NoFatalErrorWhenWritingFrom/GmxTraj (68 ms total) 50: 50: [----------] Global test environment tear-down 50: [==========] 31 tests from 4 test suites ran. (2288 ms total) 50: [ PASSED ] 31 tests. 50/90 Test #50: GmxAnaTest ................................ Passed 2.36 sec test 51 Start 51: GmxPreprocessTests 51: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/gmxpreprocess-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/GmxPreprocessTests.xml" 51: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests 51: Test timeout computed to be: 1920 51: [==========] Running 257 tests from 16 test suites. 51: [----------] Global test environment set-up. 51: [----------] 1 test from ConvertInteractionsTest 51: [ RUN ] ConvertInteractionsTest.DoingNothingWorks 51: [ OK ] ConvertInteractionsTest.DoingNothingWorks (0 ms) 51: [----------] 1 test from ConvertInteractionsTest (0 ms total) 51: 51: [----------] 4 tests from GenconfTest 51: [ RUN ] GenconfTest.nbox_Works 51: [ OK ] GenconfTest.nbox_Works (1 ms) 51: [ RUN ] GenconfTest.nbox_norenumber_Works 51: [ OK ] GenconfTest.nbox_norenumber_Works (1 ms) 51: [ RUN ] GenconfTest.nbox_dist_Works 51: [ OK ] GenconfTest.nbox_dist_Works (0 ms) 51: [ RUN ] GenconfTest.nbox_rot_Works 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: [ OK ] GenconfTest.nbox_rot_Works (0 ms) 51: [----------] 4 tests from GenconfTest (4 ms total) 51: 51: [----------] 2 tests from GenionTest 51: [ RUN ] GenionTest.HighConcentrationIonPlacement 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 51: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet 51: buffer. The cluster pair list does have a buffering effect, but choosing 51: a larger rlist might be necessary for good energy conservation. 51: 51: 51: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 51: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 51: < 0 51: 51: 51: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: Generating 1-4 interactions: fudge = 0.5 51: Number of degrees of freedom in T-Coupling group rest is 1308.00 51: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 51: 51: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 51: You are using a plain Coulomb cut-off, which might produce artifacts. 51: You might want to consider using PME electrostatics. 51: 51: 51: 51: There were 4 NOTEs 51: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 51: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 51: Group 0 ( System) has 653 elements 51: Group 1 ( Water) has 648 elements 51: Group 2 ( SOL) has 648 elements 51: Group 3 ( non-Water) has 5 elements 51: Group 4 ( Other) has 5 elements 51: Group 5 ( METH) has 5 elements 51: Select a group: Number of (3-atomic) solvent molecules: 216 51: Using random seed 1997. 51: Replacing solvent molecule 56 (atom 168) with NA 51: Replacing solvent molecule 120 (atom 360) with NA 51: Replacing solvent molecule 182 (atom 546) with NA 51: Replacing solvent molecule 71 (atom 213) with NA 51: Replacing solvent molecule 189 (atom 567) with CL 51: Replacing solvent molecule 54 (atom 162) with CL 51: Replacing solvent molecule 155 (atom 465) with CL 51: Replacing solvent molecule 99 (atom 297) with CL 51: 51: Setting the LD random seed to -4538369 51: 51: Generated 331705 of the 331705 non-bonded parameter combinations 51: 51: Generated 331705 of the 331705 1-4 parameter combinations 51: 51: Excluding 2 bonded neighbours molecule type 'SOL' 51: 51: Excluding 3 bonded neighbours molecule type 'methane' 51: 51: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc216_with_methane.gro' 51: Analysing residue names: 51: There are: 216 Water residues 51: There are: 1 Other residues 51: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 51: 51: This run will generate roughly 0 Mb of data 51: Will try to add 4 NA ions and 4 CL ions. 51: Select a continuous group of solvent molecules 51: Selected 1: 'Water' 51: [ OK ] GenionTest.HighConcentrationIonPlacement (669 ms) 51: [ RUN ] GenionTest.NoIonPlacement 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 51: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet 51: buffer. The cluster pair list does have a buffering effect, but choosing 51: a larger rlist might be necessary for good energy conservation. 51: 51: 51: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 51: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 51: < 0 51: 51: 51: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: Generating 1-4 interactions: fudge = 0.5 51: Number of degrees of freedom in T-Coupling group rest is 1308.00 51: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 51: 51: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 51: You are using a plain Coulomb cut-off, which might produce artifacts. 51: You might want to consider using PME electrostatics. 51: 51: 51: 51: There were 4 NOTEs 51: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 51: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 51: No ions to add, will just copy input configuration. 51: Setting the LD random seed to -33571329 51: 51: Generated 331705 of the 331705 non-bonded parameter combinations 51: 51: Generated 331705 of the 331705 1-4 parameter combinations 51: 51: Excluding 2 bonded neighbours molecule type 'SOL' 51: 51: Excluding 3 bonded neighbours molecule type 'methane' 51: 51: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc216_with_methane.gro' 51: Analysing residue names: 51: There are: 216 Water residues 51: There are: 1 Other residues 51: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 51: 51: This run will generate roughly 0 Mb of data 51: [ OK ] GenionTest.NoIonPlacement (959 ms) 51: [----------] 2 tests from GenionTest (1628 ms total) 51: 51: [----------] 1 test from GenRestrTest 51: [ RUN ] GenRestrTest.SimpleRestraintsGenerated 51: 51: Reading structure file 51: Group 0 ( System) has 156 elements 51: Group 1 ( Protein) has 156 elements 51: Group 2 ( Protein-H) has 75 elements 51: Group 3 ( C-alpha) has 10 elements 51: Group 4 ( Backbone) has 30 elements 51: Group 5 ( MainChain) has 40 elements 51: Group 6 ( MainChain+Cb) has 49 elements 51: Group 7 ( MainChain+H) has 52 elements 51: Group 8 ( SideChain) has 104 elements 51: Group 9 ( SideChain-H) has 35 elements 51: Select a group: Select group to position restrain 51: Selected 3: 'C-alpha' 51: [ OK ] GenRestrTest.SimpleRestraintsGenerated (2 ms) 51: [----------] 1 test from GenRestrTest (2 ms total) 51: 51: [----------] 9 tests from PreprocessingAtomTypesTest 51: [ RUN ] PreprocessingAtomTypesTest.EmptyOnCreate 51: [ OK ] PreprocessingAtomTypesTest.EmptyOnCreate (0 ms) 51: [ RUN ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid 51: [ OK ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid (0 ms) 51: [ RUN ] PreprocessingAtomTypesTest.AddTypeWorks 51: [ OK ] PreprocessingAtomTypesTest.AddTypeWorks (0 ms) 51: [ RUN ] PreprocessingAtomTypesTest.AddMultipleTypesWorks 51: [ OK ] PreprocessingAtomTypesTest.AddMultipleTypesWorks (0 ms) 51: [ RUN ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry 51: [ OK ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry (0 ms) 51: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFound 51: [ OK ] PreprocessingAtomTypesTest.CorrectNameFound (0 ms) 51: [ RUN ] PreprocessingAtomTypesTest.WrongNameNotFound 51: [ OK ] PreprocessingAtomTypesTest.WrongNameNotFound (0 ms) 51: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber 51: [ OK ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber (0 ms) 51: [ RUN ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber 51: [ OK ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber (0 ms) 51: [----------] 9 tests from PreprocessingAtomTypesTest (0 ms total) 51: 51: [----------] 10 tests from PreprocessingBondAtomTypeTest 51: [ RUN ] PreprocessingBondAtomTypeTest.EmptyOnCreate 51: [ OK ] PreprocessingBondAtomTypeTest.EmptyOnCreate (0 ms) 51: [ RUN ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid 51: [ OK ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid (0 ms) 51: [ RUN ] PreprocessingBondAtomTypeTest.AddTypeWorks 51: [ OK ] PreprocessingBondAtomTypeTest.AddTypeWorks (0 ms) 51: [ RUN ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks 51: [ OK ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks (0 ms) 51: [ RUN ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry 51: [ OK ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry (0 ms) 51: [ RUN ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType 51: [ OK ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType (0 ms) 51: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFound 51: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFound (0 ms) 51: [ RUN ] PreprocessingBondAtomTypeTest.WrongNameNotFound 51: [ OK ] PreprocessingBondAtomTypeTest.WrongNameNotFound (0 ms) 51: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber 51: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber (0 ms) 51: [ RUN ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber 51: [ OK ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber (0 ms) 51: [----------] 10 tests from PreprocessingBondAtomTypeTest (0 ms total) 51: 51: [----------] 3 tests from GromppDirectiveTest 51: [ RUN ] GromppDirectiveTest.edgeCaseAtomTypeNames 51: Ignoring obsolete mdp entry 'title' 51: Generating 1-4 interactions: fudge = 0.5 51: 51: NOTE 1 [file directives.top, line 59]: 51: In moleculetype 'A' 2 atoms are not bound by a potential or constraint to 51: any other atom in the same moleculetype. Although technically this might 51: not cause issues in a simulation, this often means that the user forgot 51: to add a bond/potential/constraint or put multiple molecules in the same 51: moleculetype definition by mistake. Run with -v to get information for 51: each atom. 51: 51: Number of degrees of freedom in T-Coupling group rest is 9.00 51: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 51: 51: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_edgeCaseAtomTypeNames_directives.mdp]: 51: NVE simulation: will use the initial temperature of 300.000 K for 51: determining the Verlet buffer size 51: 51: 51: There were 2 NOTEs 51: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_edgeCaseAtomTypeNames_directives.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 51: Setting the LD random seed to 234749113 51: 51: Generated 10 of the 10 non-bonded parameter combinations 51: 51: Generated 10 of the 10 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to -8396801 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: Analysing residue names: 51: There are: 1 Other residues 51: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 51: 51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 51: 51: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 51: 51: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 51: 51: Note that mdrun will redetermine rlist based on the actual pair-list setup 51: 51: This run will generate roughly 0 Mb of data 51: [ OK ] GromppDirectiveTest.edgeCaseAtomTypeNames (93 ms) 51: [ RUN ] GromppDirectiveTest.NoteOnDihedralNotSumToZero 51: Ignoring obsolete mdp entry 'title' 51: Generating 1-4 interactions: fudge = 0.5 51: 51: NOTE 1 [file directives.top, line 59]: 51: 1 dihedrals with function type 3 (Ryckaert-Bellemans or Fourier) have 51: coefficients that do not sum to zero. This does not affect the simulation 51: and can be ignored, unless you are comparing potential energy values with 51: other force field ports and/or MD software. 51: First such dihedral in molecule A, involving atoms 0 2 1 3 51: 51: 51: NOTE 2 [file directives.top, line 59]: 51: In moleculetype 'A' 2 atoms are not bound by a potential or constraint to 51: any other atom in the same moleculetype. Although technically this might 51: not cause issues in a simulation, this often means that the user forgot 51: to add a bond/potential/constraint or put multiple molecules in the same 51: moleculetype definition by mistake. Run with -v to get information for 51: each atom. 51: 51: Number of degrees of freedom in T-Coupling group rest is 9.00 51: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 51: 51: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_NoteOnDihedralNotSumToZero_directives.mdp]: 51: NVE simulation: will use the initial temperature of 300.000 K for 51: determining the Verlet buffer size 51: 51: 51: There were 3 NOTEs 51: Setting the LD random seed to 1205714427 51: 51: Generated 10 of the 10 non-bonded parameter combinations 51: 51: Generated 10 of the 10 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to 1979648873 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: Analysing residue names: 51: There are: 1 Other residues 51: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 51: 51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 51: 51: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 51: 51: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 51: 51: Note that mdrun will redetermine rlist based on the actual pair-list setup 51: 51: This run will generate roughly 0 Mb of data 51: [ OK ] GromppDirectiveTest.NoteOnDihedralNotSumToZero (7 ms) 51: [ RUN ] GromppDirectiveTest.WarnOnDihedralSumDifferentForFreeEnergy 51: Setting the LD random seed to -570435874 51: 51: Generated 10 of the 10 non-bonded parameter combinations 51: 51: Generated 10 of the 10 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to -1174470729 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: Analysing residue names: 51: There are: 1 Other residues 51: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 51: 51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 51: 51: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 51: 51: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 51: 51: Note that mdrun will redetermine rlist based on the actual pair-list setup 51: 51: This run will generate roughly 0 Mb of data 51: [ OK ] GromppDirectiveTest.WarnOnDihedralSumDifferentForFreeEnergy (189 ms) 51: [----------] 3 tests from GromppDirectiveTest (291 ms total) 51: 51: [----------] 6 tests from InsertMoleculesTest 51: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration 51: Reading solute configuration 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. (1964) 51: DOI: 10.1021/j100785a001 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Using random seed 1997 51: Try 1 success (now 8 atoms)! 51: 51: Added 1 molecules (out of 1 requested) 51: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoExistingConfiguration_out.gro 51: 51: Output configuration contains 8 atoms in 4 residues 51: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration (3 ms) 51: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. (1964) 51: DOI: 10.1021/j100785a001 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Using random seed 1997 51: Try 1 success (now 2 atoms)! 51: Try 2 success (now 4 atoms)! 51: Try 3 success (now 6 atoms)! 51: Try 4 success (now 8 atoms)! 51: Try 5 success (now 10 atoms)! 51: 51: Added 5 molecules (out of 5 requested) 51: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBox_out.gro 51: 51: Output configuration contains 10 atoms in 10 residues 51: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox (1 ms) 51: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBoxConcentration 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. (1964) 51: DOI: 10.1021/j100785a001 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Using random seed 1997 51: Try 1 success (now 2 atoms)! 51: Try 2 success (now 4 atoms)! 51: Try 3 success (now 6 atoms)! 51: Try 4 success (now 8 atoms)! 51: Try 5 success (now 10 atoms)! 51: 51: Added 5 molecules (out of 5 requested) 51: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBoxConcentration_out.gro 51: 51: Output configuration contains 10 atoms in 10 residues 51: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBoxConcentration (1 ms) 51: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox 51: Reading solute configuration 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. (1964) 51: DOI: 10.1021/j100785a001 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Using random seed 1997 51: Try 1 success (now 8 atoms)! 51: Try 2 success (now 10 atoms)! 51: 51: Added 2 molecules (out of 2 requested) 51: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEnlargedBox_out.gro 51: 51: Output configuration contains 10 atoms in 4 residues 51: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox (14 ms) 51: [ RUN ] InsertMoleculesTest.InsertsMoleculesWithReplacement 51: Reading solute configuration 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. (1964) 51: DOI: 10.1021/j100785a001 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Using random seed 1997 51: Try 1 success (now 650 atoms)! 51: Try 2 success (now 652 atoms)! 51: Try 3 success (now 654 atoms)! 51: Try 4 success (now 656 atoms)! 51: 51: Added 4 molecules (out of 4 requested) 51: Replaced 8 residues (24 atoms) 51: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesWithReplacement_out.gro 51: 51: Output configuration contains 632 atoms in 212 residues 51: [ OK ] InsertMoleculesTest.InsertsMoleculesWithReplacement (5 ms) 51: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. (1964) 51: DOI: 10.1021/j100785a001 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Using random seed 1997 51: Read 4 positions from file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_5.dat 51: 51: Try 1 success (now 2 atoms)! 51: Try 2 success (now 4 atoms)! 51: Try 3 Try 4 Try 5 Try 6 Try 7 Try 8 Try 9 Try 10 Try 11 Try 12 skipped position (0.990, 2.010, 3.000) 51: Try 13 success (now 6 atoms)! 51: 51: Added 3 molecules (out of 4 requested) 51: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_out.gro 51: 51: Output configuration contains 6 atoms in 3 residues 51: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions (6 ms) 51: [----------] 6 tests from InsertMoleculesTest (33 ms total) 51: 51: [----------] 3 tests from MassRepartitioning 51: [ RUN ] MassRepartitioning.ValidCaseWorks 51: The smallest mass in the system is 2, setting the minimum mass to 6 51: [ OK ] MassRepartitioning.ValidCaseWorks (0 ms) 51: [ RUN ] MassRepartitioning.UnboundGivesWarning 51: 51: WARNING 1 [file unknown]: 51: The are 1 atoms that have a mass below the mass repartitioning limit but 51: are not bound. These masses cannot be repartitioned. 51: 51: The smallest mass in the system is 2, setting the minimum mass to 6 51: [ OK ] MassRepartitioning.UnboundGivesWarning (0 ms) 51: [ RUN ] MassRepartitioning.LightPartnerGivesError 51: 51: ERROR 1 [file unknown]: 51: Light atoms are bound to at least one atom that has a too low mass for 51: repartitioning 51: 51: The smallest mass in the system is 2, setting the minimum mass to 6 51: [ OK ] MassRepartitioning.LightPartnerGivesError (0 ms) 51: [----------] 3 tests from MassRepartitioning (0 ms total) 51: 51: [----------] 35 tests from GetIrTest 51: [ RUN ] GetIrTest.HandlesDifferentKindsOfMdpLines 51: Ignoring obsolete mdp entry 'title' 51: Replacing old mdp entry 'xtc_grps' by 'compressed-x-grps' 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.HandlesDifferentKindsOfMdpLines (18 ms) 51: [ RUN ] GetIrTest.RejectsNonCommentLineWithNoEquals 51: [ OK ] GetIrTest.RejectsNonCommentLineWithNoEquals (14 ms) 51: [ RUN ] GetIrTest.AcceptsKeyWithoutValue 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsKeyWithoutValue_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.AcceptsKeyWithoutValue (4 ms) 51: [ RUN ] GetIrTest.RejectsValueWithoutKey 51: [ OK ] GetIrTest.RejectsValueWithoutKey (24 ms) 51: [ RUN ] GetIrTest.RejectsEmptyKeyAndEmptyValue 51: [ OK ] GetIrTest.RejectsEmptyKeyAndEmptyValue (19 ms) 51: [ RUN ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsDefineParametersWithValuesIncludingAssignment_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment (4 ms) 51: [ RUN ] GetIrTest.AcceptsEmptyLines 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsEmptyLines_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.AcceptsEmptyLines (12 ms) 51: [ RUN ] GetIrTest.MtsCheckNstcalcenergy 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstcalcenergy_input.mdp]: 51: With MTS, nstcalcenergy = 5 should be a multiple of mts-factor = 2 51: 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstcalcenergy_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.MtsCheckNstcalcenergy (2 ms) 51: [ RUN ] GetIrTest.MtsCheckNstenergy 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 51: With MTS, nstenergy = 5 should be a multiple of mts-factor = 2 51: 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 51: Setting nstcalcenergy (100) equal to nstenergy (5) 51: 51: 51: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.MtsCheckNstenergy (6 ms) 51: [ RUN ] GetIrTest.MtsCheckNstpcouple 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp, line 7]: 51: Pressure coupling incorrect number of values (I need exactly 1) 51: 51: 51: ERROR 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp, line 7]: 51: Pressure coupling incorrect number of values (I need exactly 1) 51: 51: 51: ERROR 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 51: With multiple time stepping, nstpcouple should be a multiple of 51: mts-factor 51: 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: 51: ERROR 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 51: The Berendsen barostat does not generate any strictly correct ensemble, 51: and should not be used for new production simulations (in our opinion). 51: We recommend using the C-rescale barostat instead. 51: 51: 51: ERROR 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 51: compressibility must be > 0 when using pressure coupling Berendsen 51: 51: 51: [ OK ] GetIrTest.MtsCheckNstpcouple (3 ms) 51: [ RUN ] GetIrTest.MtsCheckNstdhdl 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 51: With MTS, nstdhdl = 5 should be a multiple of mts-factor = 2 51: 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 51: Setting nstcalcenergy (100) equal to nstdhdl (5) 51: 51: 51: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: 51: ERROR 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 51: Lambda state must be set, either with init-lambda-state or with 51: init-lambda 51: 51: [ OK ] GetIrTest.MtsCheckNstdhdl (10 ms) 51: [ RUN ] GetIrTest.MtsCheckSDNotSupported 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckSDNotSupported_input.mdp]: 51: Multiple time stepping is only supported with integrator md 51: 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckSDNotSupported_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.MtsCheckSDNotSupported (4 ms) 51: [ RUN ] GetIrTest.AcceptsElectricField 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricField_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.AcceptsElectricField (8 ms) 51: [ RUN ] GetIrTest.AcceptsElectricFieldPulsed 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldPulsed_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.AcceptsElectricFieldPulsed (4 ms) 51: [ RUN ] GetIrTest.AcceptsElectricFieldOscillating 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldOscillating_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.AcceptsElectricFieldOscillating (7 ms) 51: [ RUN ] GetIrTest.RejectsDuplicateOldAndNewKeys 51: [ OK ] GetIrTest.RejectsDuplicateOldAndNewKeys (21 ms) 51: [ RUN ] GetIrTest.AcceptsImplicitSolventNo 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsImplicitSolventNo_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.AcceptsImplicitSolventNo (4 ms) 51: [ RUN ] GetIrTest.RejectsImplicitSolventYes 51: [ OK ] GetIrTest.RejectsImplicitSolventYes (37 ms) 51: [ RUN ] GetIrTest.AcceptsMimic 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsMimic_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.AcceptsMimic (11 ms) 51: [ RUN ] GetIrTest.AcceptsTransformationCoord 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsTransformationCoord_input.mdp, line 11]: 51: pull-coord2 has a non-zero force constant and is also referenced in 51: pull-coord1-expression. Make sure that this is intended. In most use 51: cases, the pull coordinates referenced by a transformation coordinate 51: should have their force constant set to zero. 51: 51: 51: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsTransformationCoord_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.AcceptsTransformationCoord (3 ms) 51: [ RUN ] GetIrTest.InvalidTransformationCoordWithConstraint 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordWithConstraint_input.mdp, line 7]: 51: pull-coord1 cannot have type 'constraint' and geometry 'transformation' 51: 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordWithConstraint_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.InvalidTransformationCoordWithConstraint (13 ms) 51: [ RUN ] GetIrTest.InvalidPullCoordWithConstraintInTransformationExpression 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidPullCoordWithConstraintInTransformationExpression_input.mdp, line 10]: 51: pull-coord2 can not use pull-coord1 in the transformation since this is a 51: constraint 51: 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidPullCoordWithConstraintInTransformationExpression_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.InvalidPullCoordWithConstraintInTransformationExpression (13 ms) 51: [ RUN ] GetIrTest.InvalidTransformationCoordDxValue 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordDxValue_input.mdp, line 7]: 51: pull-coord1-dx cannot be set to zero for pull coordinate of geometry 51: 'transformation' 51: 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordDxValue_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.InvalidTransformationCoordDxValue (3 ms) 51: [ RUN ] GetIrTest.MissingTransformationCoordExpression 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MissingTransformationCoordExpression_input.mdp, line 5]: 51: pull-coord1-expression not set for pull coordinate of geometry 51: 'transformation' 51: 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MissingTransformationCoordExpression_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.MissingTransformationCoordExpression (5 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep 51: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep (2 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep_negativeDelta 51: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep_negativeDelta (3 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep 51: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep (10 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep_negativeDelta 51: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep_negativeDelta (18 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_SC_And_OneStepTooMuch_input.mdp]: 51: With init-lambda = 0 and delta_lambda = 1e-05 and no explicit input, 51: coul-lambdas and vdw-lambdas will be greater than 1 after step 100000 of 51: in total 100001 steps. This is not compatible with using soft-core 51: potentials. 51: 51: 51: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch (2 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta_input.mdp]: 51: With init-lambda = 1 and delta_lambda = -1e-05, the lambda components 51: won't change anymore after step 100000 until the end of the simulation 51: after 100001 steps. 51: 51: 51: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta (2 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta_input.mdp]: 51: With init-lambda = 1 and delta_lambda = -1e-05, the lambda components 51: won't change anymore after step 100000 until the end of the simulation 51: after 100001 steps. 51: 51: 51: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta (6 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_input.mdp]: 51: With init-lambda-state = 0 and delta_lambda = 1e-05, the lambda 51: components won't change anymore after step 100000 until the end of the 51: simulation after 100001 steps. 51: 51: 51: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch (2 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta_input.mdp]: 51: With init-lambda-state = 2 and delta_lambda = -1e-05, the lambda 51: components won't change anymore after step 100000 until the end of the 51: simulation after 100001 steps. 51: 51: 51: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta (2 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep 51: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep (2 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep_negativeDelta 51: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep_negativeDelta (1 ms) 51: [----------] 35 tests from GetIrTest (317 ms total) 51: 51: [----------] 6 tests from SolvateTest 51: [ RUN ] SolvateTest.cs_box_Works 51: Reading solvent configuration 51: 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. (1964) 51: DOI: 10.1021/j100785a001 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Generating solvent configuration 51: Will generate new solvent configuration of 1x1x1 boxes 51: Solvent box contains 270 atoms in 90 residues 51: Removed 129 solvent atoms due to solvent-solvent overlap 51: Sorting configuration 51: Found 1 molecule type: 51: SOL ( 3 atoms): 47 residues 51: Generated solvent containing 141 atoms in 47 residues 51: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_box_Works_out.gro 51: 51: Output configuration contains 141 atoms in 47 residues 51: Volume : 1.331 (nm^3) 51: Density : 1056.36 (g/l) 51: Number of solvent molecules: 47 51: 51: [ OK ] SolvateTest.cs_box_Works (5 ms) 51: [ RUN ] SolvateTest.cs_cp_Works 51: Reading solute configuration 51: Reading solvent configuration 51: 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. (1964) 51: DOI: 10.1021/j100785a001 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Generating solvent configuration 51: Will generate new solvent configuration of 2x2x2 boxes 51: Solvent box contains 3660 atoms in 1220 residues 51: Removed 987 solvent atoms due to solvent-solvent overlap 51: Removed 15 solvent atoms due to solute-solvent overlap 51: Sorting configuration 51: Found 1 molecule type: 51: SOL ( 3 atoms): 886 residues 51: Generated solvent containing 2658 atoms in 886 residues 51: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_Works_out.gro 51: 51: Output configuration contains 2664 atoms in 888 residues 51: Volume : 27.2709 (nm^3) 51: Density : 974.777 (g/l) 51: Number of solvent molecules: 886 51: 51: [ OK ] SolvateTest.cs_cp_Works (27 ms) 51: [ RUN ] SolvateTest.cs_cp_p_Works 51: Reading solute configuration 51: Reading solvent configuration 51: 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. (1964) 51: DOI: 10.1021/j100785a001 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Generating solvent configuration 51: Will generate new solvent configuration of 2x2x2 boxes 51: Solvent box contains 3660 atoms in 1220 residues 51: Removed 987 solvent atoms due to solvent-solvent overlap 51: Removed 15 solvent atoms due to solute-solvent overlap 51: Sorting configuration 51: Found 1 molecule type: 51: SOL ( 3 atoms): 886 residues 51: Generated solvent containing 2658 atoms in 886 residues 51: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_out.gro 51: 51: Output configuration contains 2664 atoms in 888 residues 51: Volume : 27.2709 (nm^3) 51: Density : 974.777 (g/l) 51: Number of solvent molecules: 886 51: 51: Processing topology 51: Adding line for 886 solvent molecules with resname (SOL) to topology file (/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_spc-and-methanol.top) 51: [ OK ] SolvateTest.cs_cp_p_Works (28 ms) 51: [ RUN ] SolvateTest.shell_Works 51: Reading solute configuration 51: Reading solvent configuration 51: 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. (1964) 51: DOI: 10.1021/j100785a001 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Generating solvent configuration 51: Will generate new solvent configuration of 2x2x2 boxes 51: Solvent box contains 3660 atoms in 1220 residues 51: Removed 987 solvent atoms due to solvent-solvent overlap 51: Removed 1902 solvent atoms more than 1.000000 nm from solute. 51: Removed 15 solvent atoms due to solute-solvent overlap 51: Sorting configuration 51: Found 1 molecule type: 51: SOL ( 3 atoms): 252 residues 51: Generated solvent containing 756 atoms in 252 residues 51: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_shell_Works_out.gro 51: 51: Output configuration contains 762 atoms in 254 residues 51: Volume : 27.2709 (nm^3) 51: Density : 279.3 (g/l) 51: Number of solvent molecules: 252 51: 51: [ OK ] SolvateTest.shell_Works (17 ms) 51: [ RUN ] SolvateTest.update_Topology_Works 51: Reading solute configuration 51: Reading solvent configuration 51: 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. (1964) 51: DOI: 10.1021/j100785a001 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Generating solvent configuration 51: Will generate new solvent configuration of 3x3x3 boxes 51: Solvent box contains 14952 atoms in 4984 residues 51: Removed 2787 solvent atoms due to solvent-solvent overlap 51: Removed 30 solvent atoms due to solute-solvent overlap 51: Sorting configuration 51: Found 2 different molecule types: 51: HOH ( 3 atoms): 1876 residues 51: SOL ( 3 atoms): 2169 residues 51: Generated solvent containing 0 atoms in 0 residues 51: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_out.gro 51: 51: Output configuration contains 12141 atoms in 4047 residues 51: Volume : 125 (nm^3) 51: Density : 968.963 (g/l) 51: Number of solvent molecules: 4045 51: 51: Processing topology 51: Adding line for 1876 solvent molecules with resname (HOH) to topology file (/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 51: Adding line for 2169 solvent molecules with resname (SOL) to topology file (/build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 51: [ OK ] SolvateTest.update_Topology_Works (102 ms) 51: [ RUN ] SolvateTest.cs_pdb_big_box_Works 51: Reading solvent configuration 51: 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. (1964) 51: DOI: 10.1021/j100785a001 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Generating solvent configuration 51: Will generate new solvent configuration of 2x2x2 boxes 51: Solvent box contains 1218 atoms in 406 residues 51: Removed 555 solvent atoms due to solvent-solvent overlap 51: Sorting configuration 51: Found 1 molecule type: 51: SOL ( 3 atoms): 221 residues 51: Generated solvent containing 663 atoms in 221 residues 51: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_pdb_big_box_Works_out.gro 51: 51: Output configuration contains 663 atoms in 221 residues 51: Volume : 8 (nm^3) 51: Density : 826.409 (g/l) 51: Number of solvent molecules: 221 51: 51: [ OK ] SolvateTest.cs_pdb_big_box_Works (17 ms) 51: [----------] 6 tests from SolvateTest (199 ms total) 51: 51: [----------] 1 test from TopDirTests 51: [ RUN ] TopDirTests.NamesArrayHasCorrectSize 51: [ OK ] TopDirTests.NamesArrayHasCorrectSize (0 ms) 51: [----------] 1 test from TopDirTests (0 ms total) 51: 51: [----------] 95 tests from InteractionFunctionKind/ConvertInteractionsTest 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Bond 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Bond (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Morse 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Morse (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Cubic_Bonds 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Cubic_Bonds (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Connect_Bonds 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Connect_Bonds (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Harmonic_Pot_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Harmonic_Pot_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/FENE_Bonds 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/FENE_Bonds (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds_NC 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds_NC (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restraint_Pot_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restraint_Pot_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Angle 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Angle (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Angles 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Angles (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Lin__Angle 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Lin__Angle (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond_Cross 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond_Cross (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/BA_Cross 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/BA_Cross (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/U_B 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/U_B (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quartic_Angles 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quartic_Angles (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Angles 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Angles (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Proper_Dih_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Proper_Dih_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ryckaert_Bell_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ryckaert_Bell_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Dih_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Dih_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/CBT_Dih_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/CBT_Dih_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Fourier_Dih_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Fourier_Dih_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Improper_Dih_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Improper_Dih_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Per__Imp__Dih_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Per__Imp__Dih_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Dih_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Dih_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/CMAP_Dih_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/CMAP_Dih_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_2_Pol_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_2_Pol_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_3_Pol_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_3_Pol_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_4_Pol_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_4_Pol_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_Polariz_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_Polariz_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Nonpolar_Sol_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Nonpolar_Sol_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_14 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_14 (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb_14 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb_14 (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_14_q 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_14_q (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_Pairs_NB 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_Pairs_NB (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ__SR_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ__SR_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Buck_ham__SR_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Buck_ham__SR_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/B_ham 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/B_ham (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Disper__corr_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Disper__corr_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb__SR_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb__SR_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/RF_excl_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/RF_excl_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul__recip_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul__recip_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_recip_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_recip_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/DPD 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/DPD (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Polarization 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Polarization (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Water_Pol_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Water_Pol_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Thole_Pol_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Thole_Pol_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Anharm__Pol_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Anharm__Pol_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Position_Rest_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Position_Rest_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Flat_b__P_R_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Flat_b__P_R_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dis__Rest_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dis__Rest_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/D_R_Viol___nm_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/D_R_Viol___nm_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Orient__Rest_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Orient__Rest_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ori__R__RMSD 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ori__R__RMSD (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest__Z 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest__Z (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest__Vi_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest__Vi_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constraint 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constraint (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constr__No_Co_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constr__No_Co_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Settle 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Settle (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_1 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_1 (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_2 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_2 (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_2fd 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_2fd (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_3 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_3 (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_3fd 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_3fd (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3fad 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3fad (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3out 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3out (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_4fd 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_4fd (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_4fdn 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_4fdn (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_N 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_N (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/COM_Pull_En_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/COM_Pull_En_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dens__fitting 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dens__fitting (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quantum_En_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quantum_En_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/NN_Potential 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/NN_Potential (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Potential 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Potential (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Kinetic_En_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Kinetic_En_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Total_Energy 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Total_Energy (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Conserved_En_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Conserved_En_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Temperature 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Temperature (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__Temp_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__Temp_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pres__DC 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pres__DC (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pressure 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pressure (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dH_dl_constr_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dH_dl_constr_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVremain_dl 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVremain_dl (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dEkin_dl 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dEkin_dl (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVcoul_dl 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVcoul_dl (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVvdw_dl 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVvdw_dl (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVbonded_dl 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVbonded_dl (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVrestraint_dl 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVrestraint_dl (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVtemp_dl 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVtemp_dl (0 ms) 51: [----------] 95 tests from InteractionFunctionKind/ConvertInteractionsTest (2 ms total) 51: 51: [----------] 45 tests from SinglePeptideFragments/EditconfTest 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/0 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/0 (11 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/1 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/1 (13 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/2 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/2 (9 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/3 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/3 (2 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/4 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/4 (13 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/5 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/5 (13 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/6 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/6 (13 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/7 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/7 (3 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/8 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/8 (5 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/0 51: 51: Select a group for output: 51: Group 0 ( two_residues) has 23 elements 51: There is one group in the index 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/0 (9 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/1 51: 51: Select a group for output: 51: Group 0 ( two_residues) has 23 elements 51: There is one group in the index 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/1 (4 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/2 51: 51: Select a group for output: 51: Group 0 ( two_residues) has 23 elements 51: There is one group in the index 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/2 (4 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/3 51: 51: Select a group for output: 51: Group 0 ( two_residues) has 23 elements 51: There is one group in the index 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/3 (1 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/4 51: 51: Select a group for output: 51: Group 0 ( two_residues) has 23 elements 51: There is one group in the index 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/4 (2 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/5 51: 51: Select a group for output: 51: Group 0 ( two_residues) has 23 elements 51: There is one group in the index 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/5 (2 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/6 51: 51: Select a group for output: 51: Group 0 ( two_residues) has 23 elements 51: There is one group in the index 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/6 (2 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/7 51: 51: Select a group for output: 51: Group 0 ( two_residues) has 23 elements 51: There is one group in the index 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/7 (2 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/8 51: 51: Select a group for output: 51: Group 0 ( two_residues) has 23 elements 51: There is one group in the index 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/8 (2 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/0 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : 0.212 1.187 3.527 (nm) 51: new center : 4.028 2.819 3.723 (nm) 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/0 (5 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/1 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : 0.212 1.187 3.527 (nm) 51: new center : 4.028 2.819 3.723 (nm) 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/1 (4 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/2 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : 0.212 1.187 3.527 (nm) 51: new center : 4.028 2.819 3.723 (nm) 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/2 (12 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/3 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : 0.212 1.187 3.527 (nm) 51: new center : 4.028 2.819 3.723 (nm) 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/3 (3 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/4 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : 0.212 1.187 3.527 (nm) 51: new center : 4.028 2.819 3.723 (nm) 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/4 (2 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/5 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : 0.212 1.187 3.527 (nm) 51: new center : 4.028 2.819 3.723 (nm) 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/5 (2 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/6 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : 0.212 1.187 3.527 (nm) 51: new center : 4.028 2.819 3.723 (nm) 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/6 (3 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/7 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : 0.212 1.187 3.527 (nm) 51: new center : 4.028 2.819 3.723 (nm) 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/7 (7 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/8 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : 0.212 1.187 3.527 (nm) 51: new center : 4.028 2.819 3.723 (nm) 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/8 (4 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/0 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : -0.814 1.104 2.657 (nm) 51: new center : 3.002 2.736 2.852 (nm) 51: new box vectors : 6.004 5.472 5.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 187.42 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/0 (6 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/1 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : -0.814 1.104 2.657 (nm) 51: new center : 3.002 2.736 2.852 (nm) 51: new box vectors : 6.004 5.472 5.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 187.42 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/1 (5 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/2 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : -0.814 1.104 2.657 (nm) 51: new center : 3.002 2.736 2.852 (nm) 51: new box vectors : 6.004 5.472 5.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 187.42 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/2 (5 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/3 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : -0.814 1.104 2.657 (nm) 51: new center : 3.002 2.736 2.852 (nm) 51: new box vectors : 6.004 5.472 5.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 187.40 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/3 (3 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/4 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : -0.814 1.104 2.657 (nm) 51: new center : 3.002 2.736 2.852 (nm) 51: new box vectors : 6.004 5.472 5.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 187.40 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/4 (2 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/5 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : -0.814 1.104 2.657 (nm) 51: new center : 3.002 2.736 2.852 (nm) 51: new box vectors : 6.004 5.472 5.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 187.40 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/5 (2 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/6 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : -0.814 1.104 2.657 (nm) 51: new center : 3.002 2.736 2.852 (nm) 51: new box vectors : 6.004 5.472 5.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 187.40 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/6 (5 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/7 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : -0.814 1.104 2.657 (nm) 51: new center : 3.002 2.736 2.852 (nm) 51: new box vectors : 6.004 5.472 5.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 187.40 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/7 (5 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/8 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : -0.814 1.104 2.657 (nm) 51: new center : 3.002 2.736 2.852 (nm) 51: new box vectors : 6.004 5.472 5.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 187.40 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/8 (4 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/0 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: new center : 3.816 1.632 0.195 (nm) 51: new box vectors : 5.004 4.472 4.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 105.28 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/0 (5 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/1 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: new center : 3.816 1.632 0.195 (nm) 51: new box vectors : 5.004 4.472 4.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 105.28 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/1 (7 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/2 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: new center : 3.816 1.632 0.195 (nm) 51: new box vectors : 5.004 4.472 4.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 105.28 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/2 (5 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/3 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: new center : 3.816 1.632 0.195 (nm) 51: new box vectors : 5.004 4.472 4.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 105.27 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/3 (3 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/4 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: new center : 3.816 1.632 0.195 (nm) 51: new box vectors : 5.004 4.472 4.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 105.27 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/4 (2 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/5 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: new center : 3.816 1.632 0.195 (nm) 51: new box vectors : 5.004 4.472 4.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 105.27 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/5 (2 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/6 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: new center : 3.816 1.632 0.195 (nm) 51: new box vectors : 5.004 4.472 4.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 105.27 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/6 (3 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/7 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: new center : 3.816 1.632 0.195 (nm) 51: new box vectors : 5.004 4.472 4.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 105.27 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/7 (3 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/8 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: new center : 3.816 1.632 0.195 (nm) 51: new box vectors : 5.004 4.472 4.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 105.27 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/8 (4 ms) 51: [----------] 45 tests from SinglePeptideFragments/EditconfTest (249 ms total) 51: 51: [----------] 16 tests from CorrectVelocity/MaxwellTest 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/0 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/0 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/1 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/1 (1 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/2 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/2 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/3 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/3 (1 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/4 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/4 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/5 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/5 (1 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/6 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/6 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/7 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/7 (1 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/8 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/8 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/9 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/9 (1 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/10 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/10 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/11 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/11 (1 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/12 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/12 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/13 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/13 (2 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/14 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/14 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/15 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/15 (1 ms) 51: [----------] 16 tests from CorrectVelocity/MaxwellTest (20 ms total) 51: 51: [----------] 20 tests from CMAPDefinesAndErrors/GromppDirectiveTest 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/0 51: Setting the LD random seed to -839910785 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/0 (13 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/1 51: Setting the LD random seed to 2117454175 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/1 (17 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/2 51: Ignoring obsolete mdp entry 'title' 51: Generating 1-4 interactions: fudge = 0.5 51: 51: NOTE 1 [file directives-cmap.top, line 105]: 51: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 51: any other atom in the same moleculetype. Although technically this might 51: not cause issues in a simulation, this often means that the user forgot 51: to add a bond/potential/constraint or put multiple molecules in the same 51: moleculetype definition by mistake. Run with -v to get information for 51: each atom. 51: 51: Number of degrees of freedom in T-Coupling group rest is 12.00 51: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 51: 51: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_2_directives-cmap.mdp]: 51: NVE simulation: will use the initial temperature of 300.000 K for 51: determining the Verlet buffer size 51: 51: 51: There were 2 NOTEs 51: Setting the LD random seed to 797426687 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to -67186721 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: Analysing residue names: 51: There are: 1 Other residues 51: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 51: 51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 51: 51: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 51: 51: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 51: 51: Note that mdrun will redetermine rlist based on the actual pair-list setup 51: 51: This run will generate roughly 0 Mb of data 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/2 (7 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/3 51: Setting the LD random seed to -1213241890 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/3 (18 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/4 51: Setting the LD random seed to -1143144917 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to 1842347855 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/4 (25 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/5 51: Setting the LD random seed to -1696596177 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/5 (27 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/6 51: Setting the LD random seed to 998143727 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to -1111762133 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/6 (25 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/7 51: Setting the LD random seed to 1870232059 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to -570687537 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/7 (29 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/8 51: Setting the LD random seed to -339747139 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to -3312129 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/8 (24 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/9 51: Setting the LD random seed to -616841225 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to -1908966942 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/9 (40 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/10 51: Setting the LD random seed to 1972763621 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to -67108869 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/10 (15 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/11 51: Setting the LD random seed to -10129443 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to -304088731 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/11 (12 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/12 51: Setting the LD random seed to -1109771265 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to -1895956737 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/12 (18 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/13 51: Ignoring obsolete mdp entry 'title' 51: Generating 1-4 interactions: fudge = 0.5 51: 51: NOTE 1 [file directives-cmap.top, line 105]: 51: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 51: any other atom in the same moleculetype. Although technically this might 51: not cause issues in a simulation, this often means that the user forgot 51: to add a bond/potential/constraint or put multiple molecules in the same 51: moleculetype definition by mistake. Run with -v to get information for 51: each atom. 51: 51: Number of degrees of freedom in T-Coupling group rest is 12.00 51: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 51: 51: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_13_directives-cmap.mdp]: 51: NVE simulation: will use the initial temperature of 300.000 K for 51: determining the Verlet buffer size 51: 51: 51: There were 2 NOTEs 51: Setting the LD random seed to -1360653313 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to -70287501 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: Analysing residue names: 51: There are: 1 Other residues 51: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 51: 51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 51: 51: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 51: 51: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 51: 51: Note that mdrun will redetermine rlist based on the actual pair-list setup 51: 51: This run will generate roughly 0 Mb of data 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/13 (9 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/14 51: Ignoring obsolete mdp entry 'title' 51: Generating 1-4 interactions: fudge = 0.5 51: 51: NOTE 1 [file directives-cmap.top, line 105]: 51: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 51: any other atom in the same moleculetype. Although technically this might 51: not cause issues in a simulation, this often means that the user forgot 51: to add a bond/potential/constraint or put multiple molecules in the same 51: moleculetype definition by mistake. Run with -v to get information for 51: each atom. 51: 51: Number of degrees of freedom in T-Coupling group rest is 12.00 51: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 51: 51: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_14_directives-cmap.mdp]: 51: NVE simulation: will use the initial temperature of 300.000 K for 51: determining the Verlet buffer size 51: 51: 51: There were 2 NOTEs 51: Setting the LD random seed to -133267 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to -155190538 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: Analysing residue names: 51: There are: 1 Other residues 51: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 51: 51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 51: 51: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 51: 51: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 51: 51: Note that mdrun will redetermine rlist based on the actual pair-list setup 51: 51: This run will generate roughly 0 Mb of data 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/14 (7 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/15 51: Setting the LD random seed to 1324052478 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/15 (14 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/16 51: Setting the LD random seed to 1006501621 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to -100669459 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: Analysing residue names: 51: There are: 1 Other residues 51: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 51: 51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 51: 51: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 51: 51: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 51: 51: Note that mdrun will redetermine rlist based on the actual pair-list setup 51: 51: This run will generate roughly 0 Mb of data 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/16 (22 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/17 51: Setting the LD random seed to -1938030853 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/17 (13 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/18 51: Ignoring obsolete mdp entry 'title' 51: Generating 1-4 interactions: fudge = 0.5 51: 51: NOTE 1 [file directives-cmap.top, line 105]: 51: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 51: any other atom in the same moleculetype. Although technically this might 51: not cause issues in a simulation, this often means that the user forgot 51: to add a bond/potential/constraint or put multiple molecules in the same 51: moleculetype definition by mistake. Run with -v to get information for 51: each atom. 51: 51: Number of degrees of freedom in T-Coupling group rest is 12.00 51: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 51: 51: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_18_directives-cmap.mdp]: 51: NVE simulation: will use the initial temperature of 300.000 K for 51: determining the Verlet buffer size 51: 51: 51: There were 2 NOTEs 51: Setting the LD random seed to -1846083778 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to -610354694 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: Analysing residue names: 51: There are: 1 Other residues 51: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 51: 51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 51: 51: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 51: 51: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 51: 51: Note that mdrun will redetermine rlist based on the actual pair-list setup 51: 51: This run will generate roughly 0 Mb of data 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/18 (6 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/19 51: Setting the LD random seed to -269182157 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/19 (25 ms) 51: [----------] 20 tests from CMAPDefinesAndErrors/GromppDirectiveTest (376 ms total) 51: 51: [----------] Global test environment tear-down 51: [==========] 257 tests from 16 test suites ran. (3125 ms total) 51: [ PASSED ] 217 tests. 51: [ SKIPPED ] 40 tests, listed below: 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_2_Pol_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_3_Pol_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_4_Pol_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_Polariz_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Nonpolar_Sol_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb_14 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ__SR_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Buck_ham__SR_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/B_ham 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Disper__corr_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb__SR_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/RF_excl_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul__recip_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_recip_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/DPD 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/D_R_Viol___nm_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ori__R__RMSD 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest__Vi_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/COM_Pull_En_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dens__fitting 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quantum_En_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/NN_Potential 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Potential 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Kinetic_En_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Total_Energy 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Conserved_En_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Temperature 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__Temp_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pres__DC 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pressure 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dH_dl_constr_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVremain_dl 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dEkin_dl 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVcoul_dl 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVvdw_dl 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVbonded_dl 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVrestraint_dl 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVtemp_dl 51/90 Test #51: GmxPreprocessTests ........................ Passed 3.17 sec test 52 Start 52: Pdb2gmx1Test 52: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/pdb2gmx1-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/Pdb2gmx1Test.xml" 52: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests 52: Test timeout computed to be: 1920 52: [==========] Running 30 tests from 1 test suite. 52: [----------] Global test environment set-up. 52: [----------] 30 tests from Oplsaa/Pdb2gmxTest 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Before cleaning: 653 pairs 52: Before cleaning: 663 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 128 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (128 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 252 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 254, now 254 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 663 dihedrals, 51 impropers, 457 angles 52: 650 pairs, 254 bonds and 0 virtual sites 52: 52: Total mass 1846.112 a.m.u. 52: 52: Total charge -0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 52: 52: The Oplsaa force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (43 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 30 donors and 22 acceptors were found. 52: There are 36 hydrogen bonds 52: Will use HISE for residue 29 52: Will use HISE for residue 32 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS27 HIS29 52: SG90 NE2111 52: HIS29 NE2111 0.987 52: HIS32 NE2135 1.590 1.155 52: Before cleaning: 748 pairs 52: Before cleaning: 778 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 52: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 149 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (149 atoms, 16 residues) 52: 52: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue PHE33 as a ending terminus. 52: Start terminus THR-18: NH3+ 52: End terminus PHE-33: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 281 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 290, now 290 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 778 dihedrals, 72 impropers, 516 angles 52: 736 pairs, 290 bonds and 0 virtual sites 52: 52: Total mass 2088.357 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 52: 52: The Oplsaa force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (42 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 22 acceptors were found. 52: There are 26 hydrogen bonds 52: Will use HISE for residue 45 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS45 52: NE295 52: MET46 SD102 1.078 52: Before cleaning: 676 pairs 52: Before cleaning: 696 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 52: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 132 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (132 atoms, 16 residues) 52: 52: Identified residue ALA34 as a starting terminus. 52: 52: Identified residue ALA49 as a ending terminus. 52: Start terminus ALA-34: NH3+ 52: End terminus ALA-49: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 255 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 261, now 261 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 696 dihedrals, 56 impropers, 472 angles 52: 667 pairs, 261 bonds and 0 virtual sites 52: 52: Total mass 1861.128 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 52: 52: The Oplsaa force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (38 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 21 acceptors were found. 52: There are 30 hydrogen bonds 52: Will use HISE for residue 60 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS60 52: NE285 52: CYS62 SG98 0.803 52: Before cleaning: 603 pairs 52: Before cleaning: 618 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 52: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 117 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (117 atoms, 16 residues) 52: 52: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue LYS50 as a starting terminus. 52: 52: Identified residue PRO65 as a ending terminus. 52: Start terminus LYS-50: NH3+ 52: End terminus PRO-65: PRO-COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 228 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 232, now 232 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 618 dihedrals, 48 impropers, 419 angles 52: 597 pairs, 232 bonds and 0 virtual sites 52: 52: Total mass 1662.883 a.m.u. 52: 52: Total charge -0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 52: 52: The Oplsaa force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (42 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 89 donors and 98 acceptors were found. 52: There are 129 hydrogen bonds 52: Will use HISE for residue 31 52: Will use HISE for residue 51 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS25 HIS31 HIS51 52: SG14 NE264 NE2226 52: HIS31 NE264 1.921 52: HIS51 NE2226 1.498 2.650 52: CYS80 SG477 0.207 1.984 1.570 52: Linking CYS-25 SG-14 and CYS-80 SG-477... 52: Before cleaning: 2499 pairs 52: Before cleaning: 2524 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 52: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 58 488 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 'A' (488 atoms, 58 residues) 52: 52: Identified residue ASN24 as a starting terminus. 52: 52: Identified residue ARG81 as a ending terminus. 52: Start terminus ASN-24: NH3+ 52: End terminus ARG-81: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 58 residues with 936 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 951, now 951 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 2524 dihedrals, 208 impropers, 1704 angles 52: 2469 pairs, 951 bonds and 0 virtual sites 52: 52: Total mass 6908.578 a.m.u. 52: 52: Total charge -6.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 52: 52: The Oplsaa force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (123 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Marked 124 virtual sites 52: Added 16 dummy masses 52: Added 26 new constraints 52: Before cleaning: 653 pairs 52: Before cleaning: 663 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 128 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (128 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 252 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 254, now 254 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 663 dihedrals, 51 impropers, 457 angles 52: 650 pairs, 254 bonds and 130 virtual sites 52: 52: Total mass 1846.112 a.m.u. 52: 52: Total charge -0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 52: 52: The Oplsaa force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (47 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 30 donors and 22 acceptors were found. 52: There are 36 hydrogen bonds 52: Will use HISE for residue 29 52: Will use HISE for residue 32 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS27 HIS29 52: SG90 NE2111 52: HIS29 NE2111 0.987 52: HIS32 NE2135 1.590 1.155 52: Marked 132 virtual sites 52: Added 10 dummy masses 52: Added 19 new constraints 52: Before cleaning: 748 pairs 52: Before cleaning: 778 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 52: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 149 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (149 atoms, 16 residues) 52: 52: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue PHE33 as a ending terminus. 52: Start terminus THR-18: NH3+ 52: End terminus PHE-33: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 281 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 290, now 290 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 778 dihedrals, 72 impropers, 516 angles 52: 736 pairs, 290 bonds and 133 virtual sites 52: 52: Total mass 2088.357 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 52: 52: The Oplsaa force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (43 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 22 acceptors were found. 52: There are 26 hydrogen bonds 52: Will use HISE for residue 45 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS45 52: NE295 52: MET46 SD102 1.078 52: Marked 123 virtual sites 52: Added 22 dummy masses 52: Added 35 new constraints 52: Before cleaning: 676 pairs 52: Before cleaning: 696 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 52: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 132 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (132 atoms, 16 residues) 52: 52: Identified residue ALA34 as a starting terminus. 52: 52: Identified residue ALA49 as a ending terminus. 52: Start terminus ALA-34: NH3+ 52: End terminus ALA-49: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 255 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 261, now 261 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 696 dihedrals, 56 impropers, 472 angles 52: 667 pairs, 261 bonds and 132 virtual sites 52: 52: Total mass 1861.128 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 52: 52: The Oplsaa force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (39 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 21 acceptors were found. 52: There are 30 hydrogen bonds 52: Will use HISE for residue 60 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS60 52: NE285 52: CYS62 SG98 0.803 52: Marked 111 virtual sites 52: Added 18 dummy masses 52: Added 31 new constraints 52: Before cleaning: 603 pairs 52: Before cleaning: 618 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 52: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 117 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (117 atoms, 16 residues) 52: 52: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue LYS50 as a starting terminus. 52: 52: Identified residue PRO65 as a ending terminus. 52: Start terminus LYS-50: NH3+ 52: End terminus PRO-65: PRO-COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 228 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 232, now 232 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 618 dihedrals, 48 impropers, 419 angles 52: 597 pairs, 232 bonds and 116 virtual sites 52: 52: Total mass 1662.883 a.m.u. 52: 52: Total charge -0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 52: 52: The Oplsaa force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (40 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 89 donors and 98 acceptors were found. 52: There are 129 hydrogen bonds 52: Will use HISE for residue 31 52: Will use HISE for residue 51 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS25 HIS31 HIS51 52: SG14 NE264 NE2226 52: HIS31 NE264 1.921 52: HIS51 NE2226 1.498 2.650 52: CYS80 SG477 0.207 1.984 1.570 52: Linking CYS-25 SG-14 and CYS-80 SG-477... 52: Marked 447 virtual sites 52: Added 58 dummy masses 52: Added 101 new constraints 52: Before cleaning: 2499 pairs 52: Before cleaning: 2524 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 52: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 58 488 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 'A' (488 atoms, 58 residues) 52: 52: Identified residue ASN24 as a starting terminus. 52: 52: Identified residue ARG81 as a ending terminus. 52: Start terminus ASN-24: NH3+ 52: End terminus ARG-81: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 58 residues with 936 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 951, now 951 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 2524 dihedrals, 208 impropers, 1704 angles 52: 2469 pairs, 951 bonds and 462 virtual sites 52: 52: Total mass 6908.578 a.m.u. 52: 52: Total charge -6.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 52: 52: The Oplsaa force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (113 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Before cleaning: 653 pairs 52: Before cleaning: 663 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 128 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (128 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 252 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 254, now 254 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 663 dihedrals, 51 impropers, 457 angles 52: 650 pairs, 254 bonds and 0 virtual sites 52: 52: Total mass 1846.112 a.m.u. 52: 52: Total charge -0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 52: 52: The Oplsaa force field and the tip4p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (35 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 30 donors and 22 acceptors were found. 52: There are 36 hydrogen bonds 52: Will use HISE for residue 29 52: Will use HISE for residue 32 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS27 HIS29 52: SG90 NE2111 52: HIS29 NE2111 0.987 52: HIS32 NE2135 1.590 1.155 52: Before cleaning: 748 pairs 52: Before cleaning: 778 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 52: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 149 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (149 atoms, 16 residues) 52: 52: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue PHE33 as a ending terminus. 52: Start terminus THR-18: NH3+ 52: End terminus PHE-33: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 281 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 290, now 290 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 778 dihedrals, 72 impropers, 516 angles 52: 736 pairs, 290 bonds and 0 virtual sites 52: 52: Total mass 2088.357 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 52: 52: The Oplsaa force field and the tip4p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (41 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 22 acceptors were found. 52: There are 26 hydrogen bonds 52: Will use HISE for residue 45 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS45 52: NE295 52: MET46 SD102 1.078 52: Before cleaning: 676 pairs 52: Before cleaning: 696 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 52: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 132 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (132 atoms, 16 residues) 52: 52: Identified residue ALA34 as a starting terminus. 52: 52: Identified residue ALA49 as a ending terminus. 52: Start terminus ALA-34: NH3+ 52: End terminus ALA-49: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 255 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 261, now 261 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 696 dihedrals, 56 impropers, 472 angles 52: 667 pairs, 261 bonds and 0 virtual sites 52: 52: Total mass 1861.128 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 52: 52: The Oplsaa force field and the tip4p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (36 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 21 acceptors were found. 52: There are 30 hydrogen bonds 52: Will use HISE for residue 60 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS60 52: NE285 52: CYS62 SG98 0.803 52: Before cleaning: 603 pairs 52: Before cleaning: 618 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 52: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 117 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (117 atoms, 16 residues) 52: 52: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue LYS50 as a starting terminus. 52: 52: Identified residue PRO65 as a ending terminus. 52: Start terminus LYS-50: NH3+ 52: End terminus PRO-65: PRO-COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 228 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 232, now 232 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 618 dihedrals, 48 impropers, 419 angles 52: 597 pairs, 232 bonds and 0 virtual sites 52: 52: Total mass 1662.883 a.m.u. 52: 52: Total charge -0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 52: 52: The Oplsaa force field and the tip4p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (34 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 89 donors and 98 acceptors were found. 52: There are 129 hydrogen bonds 52: Will use HISE for residue 31 52: Will use HISE for residue 51 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS25 HIS31 HIS51 52: SG14 NE264 NE2226 52: HIS31 NE264 1.921 52: HIS51 NE2226 1.498 2.650 52: CYS80 SG477 0.207 1.984 1.570 52: Linking CYS-25 SG-14 and CYS-80 SG-477... 52: Before cleaning: 2499 pairs 52: Before cleaning: 2524 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 52: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 58 488 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 'A' (488 atoms, 58 residues) 52: 52: Identified residue ASN24 as a starting terminus. 52: 52: Identified residue ARG81 as a ending terminus. 52: Start terminus ASN-24: NH3+ 52: End terminus ARG-81: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 58 residues with 936 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 951, now 951 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 2524 dihedrals, 208 impropers, 1704 angles 52: 2469 pairs, 951 bonds and 0 virtual sites 52: 52: Total mass 6908.578 a.m.u. 52: 52: Total charge -6.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 52: 52: The Oplsaa force field and the tip4p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (106 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Marked 124 virtual sites 52: Added 16 dummy masses 52: Added 26 new constraints 52: Before cleaning: 653 pairs 52: Before cleaning: 663 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 128 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (128 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 252 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 254, now 254 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 663 dihedrals, 51 impropers, 457 angles 52: 650 pairs, 254 bonds and 130 virtual sites 52: 52: Total mass 1846.112 a.m.u. 52: 52: Total charge -0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 52: 52: The Oplsaa force field and the tip4p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (38 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 30 donors and 22 acceptors were found. 52: There are 36 hydrogen bonds 52: Will use HISE for residue 29 52: Will use HISE for residue 32 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS27 HIS29 52: SG90 NE2111 52: HIS29 NE2111 0.987 52: HIS32 NE2135 1.590 1.155 52: Marked 132 virtual sites 52: Added 10 dummy masses 52: Added 19 new constraints 52: Before cleaning: 748 pairs 52: Before cleaning: 778 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 52: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 149 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (149 atoms, 16 residues) 52: 52: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue PHE33 as a ending terminus. 52: Start terminus THR-18: NH3+ 52: End terminus PHE-33: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 281 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 290, now 290 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 778 dihedrals, 72 impropers, 516 angles 52: 736 pairs, 290 bonds and 133 virtual sites 52: 52: Total mass 2088.357 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 52: 52: The Oplsaa force field and the tip4p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (41 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 22 acceptors were found. 52: There are 26 hydrogen bonds 52: Will use HISE for residue 45 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS45 52: NE295 52: MET46 SD102 1.078 52: Marked 123 virtual sites 52: Added 22 dummy masses 52: Added 35 new constraints 52: Before cleaning: 676 pairs 52: Before cleaning: 696 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 52: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 132 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (132 atoms, 16 residues) 52: 52: Identified residue ALA34 as a starting terminus. 52: 52: Identified residue ALA49 as a ending terminus. 52: Start terminus ALA-34: NH3+ 52: End terminus ALA-49: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 255 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 261, now 261 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 696 dihedrals, 56 impropers, 472 angles 52: 667 pairs, 261 bonds and 132 virtual sites 52: 52: Total mass 1861.128 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 52: 52: The Oplsaa force field and the tip4p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (40 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 21 acceptors were found. 52: There are 30 hydrogen bonds 52: Will use HISE for residue 60 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS60 52: NE285 52: CYS62 SG98 0.803 52: Marked 111 virtual sites 52: Added 18 dummy masses 52: Added 31 new constraints 52: Before cleaning: 603 pairs 52: Before cleaning: 618 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 52: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 117 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (117 atoms, 16 residues) 52: 52: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue LYS50 as a starting terminus. 52: 52: Identified residue PRO65 as a ending terminus. 52: Start terminus LYS-50: NH3+ 52: End terminus PRO-65: PRO-COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 228 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 232, now 232 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 618 dihedrals, 48 impropers, 419 angles 52: 597 pairs, 232 bonds and 116 virtual sites 52: 52: Total mass 1662.883 a.m.u. 52: 52: Total charge -0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 52: 52: The Oplsaa force field and the tip4p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (38 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 89 donors and 98 acceptors were found. 52: There are 129 hydrogen bonds 52: Will use HISE for residue 31 52: Will use HISE for residue 51 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS25 HIS31 HIS51 52: SG14 NE264 NE2226 52: HIS31 NE264 1.921 52: HIS51 NE2226 1.498 2.650 52: CYS80 SG477 0.207 1.984 1.570 52: Linking CYS-25 SG-14 and CYS-80 SG-477... 52: Marked 447 virtual sites 52: Added 58 dummy masses 52: Added 101 new constraints 52: Before cleaning: 2499 pairs 52: Before cleaning: 2524 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 52: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 58 488 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 'A' (488 atoms, 58 residues) 52: 52: Identified residue ASN24 as a starting terminus. 52: 52: Identified residue ARG81 as a ending terminus. 52: Start terminus ASN-24: NH3+ 52: End terminus ARG-81: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 58 residues with 936 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 951, now 951 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 2524 dihedrals, 208 impropers, 1704 angles 52: 2469 pairs, 951 bonds and 462 virtual sites 52: 52: Total mass 6908.578 a.m.u. 52: 52: Total charge -6.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 52: 52: The Oplsaa force field and the tip4p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (116 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Before cleaning: 653 pairs 52: Before cleaning: 663 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 128 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (128 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 252 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 254, now 254 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 663 dihedrals, 51 impropers, 457 angles 52: 650 pairs, 254 bonds and 0 virtual sites 52: 52: Total mass 1846.112 a.m.u. 52: 52: Total charge -0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 52: 52: The Oplsaa force field and the tip5p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (38 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 30 donors and 22 acceptors were found. 52: There are 36 hydrogen bonds 52: Will use HISE for residue 29 52: Will use HISE for residue 32 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS27 HIS29 52: SG90 NE2111 52: HIS29 NE2111 0.987 52: HIS32 NE2135 1.590 1.155 52: Before cleaning: 748 pairs 52: Before cleaning: 778 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 52: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 149 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (149 atoms, 16 residues) 52: 52: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue PHE33 as a ending terminus. 52: Start terminus THR-18: NH3+ 52: End terminus PHE-33: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 281 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 290, now 290 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 778 dihedrals, 72 impropers, 516 angles 52: 736 pairs, 290 bonds and 0 virtual sites 52: 52: Total mass 2088.357 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 52: 52: The Oplsaa force field and the tip5p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (44 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 22 acceptors were found. 52: There are 26 hydrogen bonds 52: Will use HISE for residue 45 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS45 52: NE295 52: MET46 SD102 1.078 52: Before cleaning: 676 pairs 52: Before cleaning: 696 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 52: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 132 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (132 atoms, 16 residues) 52: 52: Identified residue ALA34 as a starting terminus. 52: 52: Identified residue ALA49 as a ending terminus. 52: Start terminus ALA-34: NH3+ 52: End terminus ALA-49: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 255 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 261, now 261 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 696 dihedrals, 56 impropers, 472 angles 52: 667 pairs, 261 bonds and 0 virtual sites 52: 52: Total mass 1861.128 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 52: 52: The Oplsaa force field and the tip5p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (37 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 21 acceptors were found. 52: There are 30 hydrogen bonds 52: Will use HISE for residue 60 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS60 52: NE285 52: CYS62 SG98 0.803 52: Before cleaning: 603 pairs 52: Before cleaning: 618 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 52: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 117 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (117 atoms, 16 residues) 52: 52: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue LYS50 as a starting terminus. 52: 52: Identified residue PRO65 as a ending terminus. 52: Start terminus LYS-50: NH3+ 52: End terminus PRO-65: PRO-COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 228 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 232, now 232 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 618 dihedrals, 48 impropers, 419 angles 52: 597 pairs, 232 bonds and 0 virtual sites 52: 52: Total mass 1662.883 a.m.u. 52: 52: Total charge -0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 52: 52: The Oplsaa force field and the tip5p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (44 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 89 donors and 98 acceptors were found. 52: There are 129 hydrogen bonds 52: Will use HISE for residue 31 52: Will use HISE for residue 51 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS25 HIS31 HIS51 52: SG14 NE264 NE2226 52: HIS31 NE264 1.921 52: HIS51 NE2226 1.498 2.650 52: CYS80 SG477 0.207 1.984 1.570 52: Linking CYS-25 SG-14 and CYS-80 SG-477... 52: Before cleaning: 2499 pairs 52: Before cleaning: 2524 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 52: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 58 488 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 'A' (488 atoms, 58 residues) 52: 52: Identified residue ASN24 as a starting terminus. 52: 52: Identified residue ARG81 as a ending terminus. 52: Start terminus ASN-24: NH3+ 52: End terminus ARG-81: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 58 residues with 936 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 951, now 951 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 2524 dihedrals, 208 impropers, 1704 angles 52: 2469 pairs, 951 bonds and 0 virtual sites 52: 52: Total mass 6908.578 a.m.u. 52: 52: Total charge -6.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 52: 52: The Oplsaa force field and the tip5p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (106 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Marked 124 virtual sites 52: Added 16 dummy masses 52: Added 26 new constraints 52: Before cleaning: 653 pairs 52: Before cleaning: 663 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 128 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (128 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 252 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 254, now 254 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 663 dihedrals, 51 impropers, 457 angles 52: 650 pairs, 254 bonds and 130 virtual sites 52: 52: Total mass 1846.112 a.m.u. 52: 52: Total charge -0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 52: 52: The Oplsaa force field and the tip5p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (51 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 30 donors and 22 acceptors were found. 52: There are 36 hydrogen bonds 52: Will use HISE for residue 29 52: Will use HISE for residue 32 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS27 HIS29 52: SG90 NE2111 52: HIS29 NE2111 0.987 52: HIS32 NE2135 1.590 1.155 52: Marked 132 virtual sites 52: Added 10 dummy masses 52: Added 19 new constraints 52: Before cleaning: 748 pairs 52: Before cleaning: 778 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 52: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 149 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (149 atoms, 16 residues) 52: 52: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue PHE33 as a ending terminus. 52: Start terminus THR-18: NH3+ 52: End terminus PHE-33: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 281 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 290, now 290 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 778 dihedrals, 72 impropers, 516 angles 52: 736 pairs, 290 bonds and 133 virtual sites 52: 52: Total mass 2088.357 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 52: 52: The Oplsaa force field and the tip5p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (76 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 22 acceptors were found. 52: There are 26 hydrogen bonds 52: Will use HISE for residue 45 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS45 52: NE295 52: MET46 SD102 1.078 52: Marked 123 virtual sites 52: Added 22 dummy masses 52: Added 35 new constraints 52: Before cleaning: 676 pairs 52: Before cleaning: 696 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 52: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 132 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (132 atoms, 16 residues) 52: 52: Identified residue ALA34 as a starting terminus. 52: 52: Identified residue ALA49 as a ending terminus. 52: Start terminus ALA-34: NH3+ 52: End terminus ALA-49: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 255 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 261, now 261 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 696 dihedrals, 56 impropers, 472 angles 52: 667 pairs, 261 bonds and 132 virtual sites 52: 52: Total mass 1861.128 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 52: 52: The Oplsaa force field and the tip5p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (52 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 21 acceptors were found. 52: There are 30 hydrogen bonds 52: Will use HISE for residue 60 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS60 52: NE285 52: CYS62 SG98 0.803 52: Marked 111 virtual sites 52: Added 18 dummy masses 52: Added 31 new constraints 52: Before cleaning: 603 pairs 52: Before cleaning: 618 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 52: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 117 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (117 atoms, 16 residues) 52: 52: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue LYS50 as a starting terminus. 52: 52: Identified residue PRO65 as a ending terminus. 52: Start terminus LYS-50: NH3+ 52: End terminus PRO-65: PRO-COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 228 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 232, now 232 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 618 dihedrals, 48 impropers, 419 angles 52: 597 pairs, 232 bonds and 116 virtual sites 52: 52: Total mass 1662.883 a.m.u. 52: 52: Total charge -0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 52: 52: The Oplsaa force field and the tip5p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (51 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 89 donors and 98 acceptors were found. 52: There are 129 hydrogen bonds 52: Will use HISE for residue 31 52: Will use HISE for residue 51 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS25 HIS31 HIS51 52: SG14 NE264 NE2226 52: HIS31 NE264 1.921 52: HIS51 NE2226 1.498 2.650 52: CYS80 SG477 0.207 1.984 1.570 52: Linking CYS-25 SG-14 and CYS-80 SG-477... 52: Marked 447 virtual sites 52: Added 58 dummy masses 52: Added 101 new constraints 52: Before cleaning: 2499 pairs 52: Before cleaning: 2524 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 52: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 58 488 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 'A' (488 atoms, 58 residues) 52: 52: Identified residue ASN24 as a starting terminus. 52: 52: Identified residue ARG81 as a ending terminus. 52: Start terminus ASN-24: NH3+ 52: End terminus ARG-81: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 58 residues with 936 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 951, now 951 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 2524 dihedrals, 208 impropers, 1704 angles 52: 2469 pairs, 951 bonds and 462 virtual sites 52: 52: Total mass 6908.578 a.m.u. 52: 52: Total charge -6.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 52: 52: The Oplsaa force field and the tip5p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (130 ms) 52: [----------] 30 tests from Oplsaa/Pdb2gmxTest (1743 ms total) 52: 52: [----------] Global test environment tear-down 52: [==========] 30 tests from 1 test suite ran. (1743 ms total) 52: [ PASSED ] 30 tests. 52/90 Test #52: Pdb2gmx1Test .............................. Passed 1.77 sec test 53 Start 53: Pdb2gmx2Test 53: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/pdb2gmx2-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/Pdb2gmx2Test.xml" 53: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests 53: Test timeout computed to be: 1920 53: [==========] Running 40 tests from 2 test suites. 53: [----------] Global test environment set-up. 53: [----------] 20 tests from G43a1/Pdb2gmxTest 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 25 donors and 23 acceptors were found. 53: There are 41 hydrogen bonds 53: Will use HISE for residue 8 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS3 HIS8 53: SG9 NE251 53: HIS8 NE251 1.055 53: MET12 SD83 0.763 0.990 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 267 pairs 53: Before cleaning: 305 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 53: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 128 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (128 atoms, 16 residues) 53: 53: Identified residue ALA2 as a starting terminus. 53: 53: Identified residue SER17 as a ending terminus. 53: Start terminus ALA-2: NH3+ 53: End terminus SER-17: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 165 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 172, now 167 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 90 dihedrals, 77 impropers, 241 angles 53: 267 pairs, 167 bonds and 0 virtual sites 53: 53: Total mass 1846.116 a.m.u. 53: 53: Total charge 0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 53: 53: The Gromos43a1 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (61 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 30 donors and 22 acceptors were found. 53: There are 36 hydrogen bonds 53: Will use HISE for residue 29 53: Will use HISE for residue 32 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS27 HIS29 53: SG90 NE2111 53: HIS29 NE2111 0.987 53: HIS32 NE2135 1.590 1.155 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 273 pairs 53: Before cleaning: 429 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 53: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 149 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (149 atoms, 16 residues) 53: 53: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue THR18 as a starting terminus. 53: 53: Identified residue PHE33 as a ending terminus. 53: Start terminus THR-18: NH3+ 53: End terminus PHE-33: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 202 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 216, now 211 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 93 dihedrals, 134 impropers, 316 angles 53: 273 pairs, 211 bonds and 0 virtual sites 53: 53: Total mass 2088.361 a.m.u. 53: 53: Total charge 1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 53: 53: The Gromos43a1 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (52 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 22 acceptors were found. 53: There are 26 hydrogen bonds 53: Will use HISE for residue 45 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS45 53: NE295 53: MET46 SD102 1.078 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 242 pairs 53: Before cleaning: 349 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 53: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 132 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (132 atoms, 16 residues) 53: 53: Identified residue ALA34 as a starting terminus. 53: 53: Identified residue ALA49 as a ending terminus. 53: Start terminus ALA-34: NH3+ 53: End terminus ALA-49: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 168 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 179, now 174 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 81 dihedrals, 102 impropers, 260 angles 53: 242 pairs, 174 bonds and 0 virtual sites 53: 53: Total mass 1861.132 a.m.u. 53: 53: Total charge -1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 53: 53: The Gromos43a1 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (50 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 21 acceptors were found. 53: There are 30 hydrogen bonds 53: Will use HISE for residue 60 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS60 53: NE285 53: CYS62 SG98 0.803 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 232 pairs 53: Before cleaning: 299 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 53: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 117 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (117 atoms, 16 residues) 53: 53: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue LYS50 as a starting terminus. 53: 53: Identified residue PRO65 as a ending terminus. 53: Start terminus LYS-50: NH3+ 53: End terminus PRO-65: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 150 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 159, now 154 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 78 dihedrals, 80 impropers, 227 angles 53: 232 pairs, 154 bonds and 0 virtual sites 53: 53: Total mass 1662.887 a.m.u. 53: 53: Total charge 0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 53: 53: The Gromos43a1 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (59 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 89 donors and 98 acceptors were found. 53: There are 129 hydrogen bonds 53: Will use HISE for residue 31 53: Will use HISE for residue 51 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS25 HIS31 HIS51 53: SG14 NE264 NE2226 53: HIS31 NE264 1.921 53: HIS51 NE2226 1.498 2.650 53: CYS80 SG477 0.207 1.984 1.570 53: Linking CYS-25 SG-14 and CYS-80 SG-477... 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 972 pairs 53: Before cleaning: 1256 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 53: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 53: 53: chain #res #atoms 53: 53: 1 'A' 58 488 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 'A' (488 atoms, 58 residues) 53: 53: Identified residue ASN24 as a starting terminus. 53: 53: Identified residue ARG81 as a ending terminus. 53: Start terminus ASN-24: NH3+ 53: End terminus ARG-81: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 58 residues with 635 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 655, now 650 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 321 dihedrals, 350 impropers, 955 angles 53: 972 pairs, 650 bonds and 0 virtual sites 53: 53: Total mass 6908.582 a.m.u. 53: 53: Total charge -6.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 53: 53: The Gromos43a1 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (279 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 25 donors and 23 acceptors were found. 53: There are 41 hydrogen bonds 53: Will use HISE for residue 8 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS3 HIS8 53: SG9 NE251 53: HIS8 NE251 1.055 53: MET12 SD83 0.763 0.990 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 37 virtual sites 53: Added 4 dummy masses 53: Added 8 new constraints 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 267 pairs 53: Before cleaning: 305 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 53: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 128 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (128 atoms, 16 residues) 53: 53: Identified residue ALA2 as a starting terminus. 53: 53: Identified residue SER17 as a ending terminus. 53: Start terminus ALA-2: NH3+ 53: End terminus SER-17: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 165 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 172, now 167 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 90 dihedrals, 77 impropers, 241 angles 53: 267 pairs, 167 bonds and 37 virtual sites 53: 53: Total mass 1846.116 a.m.u. 53: 53: Total charge 0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 53: 53: The Gromos43a1 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (163 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 30 donors and 22 acceptors were found. 53: There are 36 hydrogen bonds 53: Will use HISE for residue 29 53: Will use HISE for residue 32 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS27 HIS29 53: SG90 NE2111 53: HIS29 NE2111 0.987 53: HIS32 NE2135 1.590 1.155 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 53 virtual sites 53: Added 4 dummy masses 53: Added 10 new constraints 53: 53: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 273 pairs 53: Before cleaning: 429 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 53: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 149 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (149 atoms, 16 residues) 53: 53: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue THR18 as a starting terminus. 53: 53: Identified residue PHE33 as a ending terminus. 53: Start terminus THR-18: NH3+ 53: End terminus PHE-33: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 202 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 216, now 211 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 93 dihedrals, 134 impropers, 316 angles 53: 273 pairs, 211 bonds and 51 virtual sites 53: 53: Total mass 2088.361 a.m.u. 53: 53: Total charge 1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 53: 53: The Gromos43a1 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (112 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 22 acceptors were found. 53: There are 26 hydrogen bonds 53: Will use HISE for residue 45 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS45 53: NE295 53: MET46 SD102 1.078 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 36 virtual sites 53: Added 4 dummy masses 53: Added 8 new constraints 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 242 pairs 53: Before cleaning: 349 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 53: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 132 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (132 atoms, 16 residues) 53: 53: Identified residue ALA34 as a starting terminus. 53: 53: Identified residue ALA49 as a ending terminus. 53: Start terminus ALA-34: NH3+ 53: End terminus ALA-49: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 168 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 179, now 174 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 81 dihedrals, 102 impropers, 260 angles 53: 242 pairs, 174 bonds and 36 virtual sites 53: 53: Total mass 1861.132 a.m.u. 53: 53: Total charge -1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 53: 53: The Gromos43a1 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (130 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 21 acceptors were found. 53: There are 30 hydrogen bonds 53: Will use HISE for residue 60 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS60 53: NE285 53: CYS62 SG98 0.803 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 33 virtual sites 53: Added 4 dummy masses 53: Added 10 new constraints 53: 53: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 232 pairs 53: Before cleaning: 299 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 53: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 117 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (117 atoms, 16 residues) 53: 53: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue LYS50 as a starting terminus. 53: 53: Identified residue PRO65 as a ending terminus. 53: Start terminus LYS-50: NH3+ 53: End terminus PRO-65: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 150 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 159, now 154 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 78 dihedrals, 80 impropers, 227 angles 53: 232 pairs, 154 bonds and 31 virtual sites 53: 53: Total mass 1662.887 a.m.u. 53: 53: Total charge 0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 53: 53: The Gromos43a1 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (119 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 89 donors and 98 acceptors were found. 53: There are 129 hydrogen bonds 53: Will use HISE for residue 31 53: Will use HISE for residue 51 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS25 HIS31 HIS51 53: SG14 NE264 NE2226 53: HIS31 NE264 1.921 53: HIS51 NE2226 1.498 2.650 53: CYS80 SG477 0.207 1.984 1.570 53: Linking CYS-25 SG-14 and CYS-80 SG-477... 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 146 virtual sites 53: Added 10 dummy masses 53: Added 29 new constraints 53: 53: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 972 pairs 53: Before cleaning: 1256 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 53: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 53: 53: chain #res #atoms 53: 53: 1 'A' 58 488 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 'A' (488 atoms, 58 residues) 53: 53: Identified residue ASN24 as a starting terminus. 53: 53: Identified residue ARG81 as a ending terminus. 53: Start terminus ASN-24: NH3+ 53: End terminus ARG-81: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 58 residues with 635 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 655, now 650 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 321 dihedrals, 350 impropers, 955 angles 53: 972 pairs, 650 bonds and 137 virtual sites 53: 53: Total mass 6908.582 a.m.u. 53: 53: Total charge -6.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 53: 53: The Gromos43a1 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (257 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 25 donors and 23 acceptors were found. 53: There are 41 hydrogen bonds 53: Will use HISE for residue 8 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS3 HIS8 53: SG9 NE251 53: HIS8 NE251 1.055 53: MET12 SD83 0.763 0.990 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 267 pairs 53: Before cleaning: 305 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 53: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 128 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (128 atoms, 16 residues) 53: 53: Identified residue ALA2 as a starting terminus. 53: 53: Identified residue SER17 as a ending terminus. 53: Start terminus ALA-2: NH3+ 53: End terminus SER-17: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 165 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 172, now 167 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 90 dihedrals, 77 impropers, 241 angles 53: 267 pairs, 167 bonds and 0 virtual sites 53: 53: Total mass 1846.116 a.m.u. 53: 53: Total charge 0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 53: 53: The Gromos43a1 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (139 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 30 donors and 22 acceptors were found. 53: There are 36 hydrogen bonds 53: Will use HISE for residue 29 53: Will use HISE for residue 32 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS27 HIS29 53: SG90 NE2111 53: HIS29 NE2111 0.987 53: HIS32 NE2135 1.590 1.155 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 273 pairs 53: Before cleaning: 429 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 53: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 149 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (149 atoms, 16 residues) 53: 53: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue THR18 as a starting terminus. 53: 53: Identified residue PHE33 as a ending terminus. 53: Start terminus THR-18: NH3+ 53: End terminus PHE-33: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 202 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 216, now 211 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 93 dihedrals, 134 impropers, 316 angles 53: 273 pairs, 211 bonds and 0 virtual sites 53: 53: Total mass 2088.361 a.m.u. 53: 53: Total charge 1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 53: 53: The Gromos43a1 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (160 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 22 acceptors were found. 53: There are 26 hydrogen bonds 53: Will use HISE for residue 45 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS45 53: NE295 53: MET46 SD102 1.078 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 242 pairs 53: Before cleaning: 349 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 53: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 132 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (132 atoms, 16 residues) 53: 53: Identified residue ALA34 as a starting terminus. 53: 53: Identified residue ALA49 as a ending terminus. 53: Start terminus ALA-34: NH3+ 53: End terminus ALA-49: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 168 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 179, now 174 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 81 dihedrals, 102 impropers, 260 angles 53: 242 pairs, 174 bonds and 0 virtual sites 53: 53: Total mass 1861.132 a.m.u. 53: 53: Total charge -1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 53: 53: The Gromos43a1 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (230 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 21 acceptors were found. 53: There are 30 hydrogen bonds 53: Will use HISE for residue 60 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS60 53: NE285 53: CYS62 SG98 0.803 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 232 pairs 53: Before cleaning: 299 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 53: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 117 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (117 atoms, 16 residues) 53: 53: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue LYS50 as a starting terminus. 53: 53: Identified residue PRO65 as a ending terminus. 53: Start terminus LYS-50: NH3+ 53: End terminus PRO-65: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 150 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 159, now 154 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 78 dihedrals, 80 impropers, 227 angles 53: 232 pairs, 154 bonds and 0 virtual sites 53: 53: Total mass 1662.887 a.m.u. 53: 53: Total charge 0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 53: 53: The Gromos43a1 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (233 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 89 donors and 98 acceptors were found. 53: There are 129 hydrogen bonds 53: Will use HISE for residue 31 53: Will use HISE for residue 51 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS25 HIS31 HIS51 53: SG14 NE264 NE2226 53: HIS31 NE264 1.921 53: HIS51 NE2226 1.498 2.650 53: CYS80 SG477 0.207 1.984 1.570 53: Linking CYS-25 SG-14 and CYS-80 SG-477... 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 972 pairs 53: Before cleaning: 1256 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 53: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 53: 53: chain #res #atoms 53: 53: 1 'A' 58 488 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 'A' (488 atoms, 58 residues) 53: 53: Identified residue ASN24 as a starting terminus. 53: 53: Identified residue ARG81 as a ending terminus. 53: Start terminus ASN-24: NH3+ 53: End terminus ARG-81: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 58 residues with 635 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 655, now 650 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 321 dihedrals, 350 impropers, 955 angles 53: 972 pairs, 650 bonds and 0 virtual sites 53: 53: Total mass 6908.582 a.m.u. 53: 53: Total charge -6.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 53: 53: The Gromos43a1 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (227 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 25 donors and 23 acceptors were found. 53: There are 41 hydrogen bonds 53: Will use HISE for residue 8 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS3 HIS8 53: SG9 NE251 53: HIS8 NE251 1.055 53: MET12 SD83 0.763 0.990 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 37 virtual sites 53: Added 4 dummy masses 53: Added 8 new constraints 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 267 pairs 53: Before cleaning: 305 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 53: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 128 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (128 atoms, 16 residues) 53: 53: Identified residue ALA2 as a starting terminus. 53: 53: Identified residue SER17 as a ending terminus. 53: Start terminus ALA-2: NH3+ 53: End terminus SER-17: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 165 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 172, now 167 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 90 dihedrals, 77 impropers, 241 angles 53: 267 pairs, 167 bonds and 37 virtual sites 53: 53: Total mass 1846.116 a.m.u. 53: 53: Total charge 0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 53: 53: The Gromos43a1 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (99 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 30 donors and 22 acceptors were found. 53: There are 36 hydrogen bonds 53: Will use HISE for residue 29 53: Will use HISE for residue 32 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS27 HIS29 53: SG90 NE2111 53: HIS29 NE2111 0.987 53: HIS32 NE2135 1.590 1.155 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 53 virtual sites 53: Added 4 dummy masses 53: Added 10 new constraints 53: 53: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 273 pairs 53: Before cleaning: 429 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 53: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 149 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (149 atoms, 16 residues) 53: 53: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue THR18 as a starting terminus. 53: 53: Identified residue PHE33 as a ending terminus. 53: Start terminus THR-18: NH3+ 53: End terminus PHE-33: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 202 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 216, now 211 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 93 dihedrals, 134 impropers, 316 angles 53: 273 pairs, 211 bonds and 51 virtual sites 53: 53: Total mass 2088.361 a.m.u. 53: 53: Total charge 1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 53: 53: The Gromos43a1 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (97 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 22 acceptors were found. 53: There are 26 hydrogen bonds 53: Will use HISE for residue 45 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS45 53: NE295 53: MET46 SD102 1.078 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 36 virtual sites 53: Added 4 dummy masses 53: Added 8 new constraints 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 242 pairs 53: Before cleaning: 349 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 53: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 132 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (132 atoms, 16 residues) 53: 53: Identified residue ALA34 as a starting terminus. 53: 53: Identified residue ALA49 as a ending terminus. 53: Start terminus ALA-34: NH3+ 53: End terminus ALA-49: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 168 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 179, now 174 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 81 dihedrals, 102 impropers, 260 angles 53: 242 pairs, 174 bonds and 36 virtual sites 53: 53: Total mass 1861.132 a.m.u. 53: 53: Total charge -1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 53: 53: The Gromos43a1 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (96 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 21 acceptors were found. 53: There are 30 hydrogen bonds 53: Will use HISE for residue 60 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS60 53: NE285 53: CYS62 SG98 0.803 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 33 virtual sites 53: Added 4 dummy masses 53: Added 10 new constraints 53: 53: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 232 pairs 53: Before cleaning: 299 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 53: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 117 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (117 atoms, 16 residues) 53: 53: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue LYS50 as a starting terminus. 53: 53: Identified residue PRO65 as a ending terminus. 53: Start terminus LYS-50: NH3+ 53: End terminus PRO-65: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 150 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 159, now 154 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 78 dihedrals, 80 impropers, 227 angles 53: 232 pairs, 154 bonds and 31 virtual sites 53: 53: Total mass 1662.887 a.m.u. 53: 53: Total charge 0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 53: 53: The Gromos43a1 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (104 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 89 donors and 98 acceptors were found. 53: There are 129 hydrogen bonds 53: Will use HISE for residue 31 53: Will use HISE for residue 51 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS25 HIS31 HIS51 53: SG14 NE264 NE2226 53: HIS31 NE264 1.921 53: HIS51 NE2226 1.498 2.650 53: CYS80 SG477 0.207 1.984 1.570 53: Linking CYS-25 SG-14 and CYS-80 SG-477... 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 146 virtual sites 53: Added 10 dummy masses 53: Added 29 new constraints 53: 53: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 972 pairs 53: Before cleaning: 1256 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 53: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 53: 53: chain #res #atoms 53: 53: 1 'A' 58 488 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 'A' (488 atoms, 58 residues) 53: 53: Identified residue ASN24 as a starting terminus. 53: 53: Identified residue ARG81 as a ending terminus. 53: Start terminus ASN-24: NH3+ 53: End terminus ARG-81: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 58 residues with 635 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 655, now 650 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 321 dihedrals, 350 impropers, 955 angles 53: 972 pairs, 650 bonds and 137 virtual sites 53: 53: Total mass 6908.582 a.m.u. 53: 53: Total charge -6.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 53: 53: The Gromos43a1 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (167 ms) 53: [----------] 20 tests from G43a1/Pdb2gmxTest (2852 ms total) 53: 53: [----------] 20 tests from G53a6/Pdb2gmxTest 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 25 donors and 23 acceptors were found. 53: There are 41 hydrogen bonds 53: Will use HISE for residue 8 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS3 HIS8 53: SG9 NE251 53: HIS8 NE251 1.055 53: MET12 SD83 0.763 0.990 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 267 pairs 53: Before cleaning: 312 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 53: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 128 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (128 atoms, 16 residues) 53: 53: Identified residue ALA2 as a starting terminus. 53: 53: Identified residue SER17 as a ending terminus. 53: Start terminus ALA-2: NH3+ 53: End terminus SER-17: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 167 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 174, now 169 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 90 dihedrals, 79 impropers, 245 angles 53: 267 pairs, 169 bonds and 0 virtual sites 53: 53: Total mass 1846.116 a.m.u. 53: 53: Total charge -0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 53: 53: The Gromos53a6 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (68 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 30 donors and 22 acceptors were found. 53: There are 36 hydrogen bonds 53: Will use HISE for residue 29 53: Will use HISE for residue 32 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS27 HIS29 53: SG90 NE2111 53: HIS29 NE2111 0.987 53: HIS32 NE2135 1.590 1.155 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 273 pairs 53: Before cleaning: 443 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 53: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 149 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (149 atoms, 16 residues) 53: 53: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue THR18 as a starting terminus. 53: 53: Identified residue PHE33 as a ending terminus. 53: Start terminus THR-18: NH3+ 53: End terminus PHE-33: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 206 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 220, now 215 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 93 dihedrals, 138 impropers, 324 angles 53: 273 pairs, 215 bonds and 0 virtual sites 53: 53: Total mass 2088.361 a.m.u. 53: 53: Total charge 1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 53: 53: The Gromos53a6 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (69 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 22 acceptors were found. 53: There are 26 hydrogen bonds 53: Will use HISE for residue 45 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS45 53: NE295 53: MET46 SD102 1.078 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 242 pairs 53: Before cleaning: 356 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 53: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 132 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (132 atoms, 16 residues) 53: 53: Identified residue ALA34 as a starting terminus. 53: 53: Identified residue ALA49 as a ending terminus. 53: Start terminus ALA-34: NH3+ 53: End terminus ALA-49: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 170 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 181, now 176 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 81 dihedrals, 104 impropers, 264 angles 53: 242 pairs, 176 bonds and 0 virtual sites 53: 53: Total mass 1861.132 a.m.u. 53: 53: Total charge -1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 53: 53: The Gromos53a6 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (69 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 21 acceptors were found. 53: There are 30 hydrogen bonds 53: Will use HISE for residue 60 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS60 53: NE285 53: CYS62 SG98 0.803 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 232 pairs 53: Before cleaning: 306 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 53: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 117 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (117 atoms, 16 residues) 53: 53: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue LYS50 as a starting terminus. 53: 53: Identified residue PRO65 as a ending terminus. 53: Start terminus LYS-50: NH3+ 53: End terminus PRO-65: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 152 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 161, now 156 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 78 dihedrals, 82 impropers, 231 angles 53: 232 pairs, 156 bonds and 0 virtual sites 53: 53: Total mass 1662.887 a.m.u. 53: 53: Total charge -0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 53: 53: The Gromos53a6 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (68 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 89 donors and 98 acceptors were found. 53: There are 129 hydrogen bonds 53: Will use HISE for residue 31 53: Will use HISE for residue 51 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS25 HIS31 HIS51 53: SG14 NE264 NE2226 53: HIS31 NE264 1.921 53: HIS51 NE2226 1.498 2.650 53: CYS80 SG477 0.207 1.984 1.570 53: Linking CYS-25 SG-14 and CYS-80 SG-477... 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 972 pairs 53: Before cleaning: 1270 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 53: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 53: 53: chain #res #atoms 53: 53: 1 'A' 58 488 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 'A' (488 atoms, 58 residues) 53: 53: Identified residue ASN24 as a starting terminus. 53: 53: Identified residue ARG81 as a ending terminus. 53: Start terminus ASN-24: NH3+ 53: End terminus ARG-81: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 58 residues with 639 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 659, now 654 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 321 dihedrals, 354 impropers, 963 angles 53: 972 pairs, 654 bonds and 0 virtual sites 53: 53: Total mass 6908.582 a.m.u. 53: 53: Total charge -6.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 53: 53: The Gromos53a6 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (164 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 25 donors and 23 acceptors were found. 53: There are 41 hydrogen bonds 53: Will use HISE for residue 8 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS3 HIS8 53: SG9 NE251 53: HIS8 NE251 1.055 53: MET12 SD83 0.763 0.990 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 39 virtual sites 53: Added 4 dummy masses 53: Added 8 new constraints 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 267 pairs 53: Before cleaning: 312 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 53: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 128 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (128 atoms, 16 residues) 53: 53: Identified residue ALA2 as a starting terminus. 53: 53: Identified residue SER17 as a ending terminus. 53: Start terminus ALA-2: NH3+ 53: End terminus SER-17: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 167 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 174, now 169 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 90 dihedrals, 79 impropers, 245 angles 53: 267 pairs, 169 bonds and 39 virtual sites 53: 53: Total mass 1846.116 a.m.u. 53: 53: Total charge -0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 53: 53: The Gromos53a6 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (106 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 30 donors and 22 acceptors were found. 53: There are 36 hydrogen bonds 53: Will use HISE for residue 29 53: Will use HISE for residue 32 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS27 HIS29 53: SG90 NE2111 53: HIS29 NE2111 0.987 53: HIS32 NE2135 1.590 1.155 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 57 virtual sites 53: Added 4 dummy masses 53: Added 10 new constraints 53: 53: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 273 pairs 53: Before cleaning: 443 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 53: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 149 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (149 atoms, 16 residues) 53: 53: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue THR18 as a starting terminus. 53: 53: Identified residue PHE33 as a ending terminus. 53: Start terminus THR-18: NH3+ 53: End terminus PHE-33: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 206 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 220, now 215 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 93 dihedrals, 138 impropers, 324 angles 53: 273 pairs, 215 bonds and 55 virtual sites 53: 53: Total mass 2088.361 a.m.u. 53: 53: Total charge 1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 53: 53: The Gromos53a6 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (110 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 22 acceptors were found. 53: There are 26 hydrogen bonds 53: Will use HISE for residue 45 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS45 53: NE295 53: MET46 SD102 1.078 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 38 virtual sites 53: Added 4 dummy masses 53: Added 8 new constraints 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 242 pairs 53: Before cleaning: 356 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 53: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 132 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (132 atoms, 16 residues) 53: 53: Identified residue ALA34 as a starting terminus. 53: 53: Identified residue ALA49 as a ending terminus. 53: Start terminus ALA-34: NH3+ 53: End terminus ALA-49: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 170 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 181, now 176 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 81 dihedrals, 104 impropers, 264 angles 53: 242 pairs, 176 bonds and 38 virtual sites 53: 53: Total mass 1861.132 a.m.u. 53: 53: Total charge -1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 53: 53: The Gromos53a6 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (120 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 21 acceptors were found. 53: There are 30 hydrogen bonds 53: Will use HISE for residue 60 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS60 53: NE285 53: CYS62 SG98 0.803 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 35 virtual sites 53: Added 4 dummy masses 53: Added 10 new constraints 53: 53: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 232 pairs 53: Before cleaning: 306 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 53: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 117 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (117 atoms, 16 residues) 53: 53: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue LYS50 as a starting terminus. 53: 53: Identified residue PRO65 as a ending terminus. 53: Start terminus LYS-50: NH3+ 53: End terminus PRO-65: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 152 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 161, now 156 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 78 dihedrals, 82 impropers, 231 angles 53: 232 pairs, 156 bonds and 33 virtual sites 53: 53: Total mass 1662.887 a.m.u. 53: 53: Total charge -0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 53: 53: The Gromos53a6 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (98 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 89 donors and 98 acceptors were found. 53: There are 129 hydrogen bonds 53: Will use HISE for residue 31 53: Will use HISE for residue 51 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS25 HIS31 HIS51 53: SG14 NE264 NE2226 53: HIS31 NE264 1.921 53: HIS51 NE2226 1.498 2.650 53: CYS80 SG477 0.207 1.984 1.570 53: Linking CYS-25 SG-14 and CYS-80 SG-477... 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 150 virtual sites 53: Added 10 dummy masses 53: Added 29 new constraints 53: 53: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 972 pairs 53: Before cleaning: 1270 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 53: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 53: 53: chain #res #atoms 53: 53: 1 'A' 58 488 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 'A' (488 atoms, 58 residues) 53: 53: Identified residue ASN24 as a starting terminus. 53: 53: Identified residue ARG81 as a ending terminus. 53: Start terminus ASN-24: NH3+ 53: End terminus ARG-81: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 58 residues with 639 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 659, now 654 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 321 dihedrals, 354 impropers, 963 angles 53: 972 pairs, 654 bonds and 141 virtual sites 53: 53: Total mass 6908.582 a.m.u. 53: 53: Total charge -6.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 53: 53: The Gromos53a6 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (160 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 25 donors and 23 acceptors were found. 53: There are 41 hydrogen bonds 53: Will use HISE for residue 8 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS3 HIS8 53: SG9 NE251 53: HIS8 NE251 1.055 53: MET12 SD83 0.763 0.990 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 267 pairs 53: Before cleaning: 312 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 53: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 128 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (128 atoms, 16 residues) 53: 53: Identified residue ALA2 as a starting terminus. 53: 53: Identified residue SER17 as a ending terminus. 53: Start terminus ALA-2: NH3+ 53: End terminus SER-17: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 167 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 174, now 169 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 90 dihedrals, 79 impropers, 245 angles 53: 267 pairs, 169 bonds and 0 virtual sites 53: 53: Total mass 1846.116 a.m.u. 53: 53: Total charge -0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 53: 53: The Gromos53a6 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (54 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 30 donors and 22 acceptors were found. 53: There are 36 hydrogen bonds 53: Will use HISE for residue 29 53: Will use HISE for residue 32 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS27 HIS29 53: SG90 NE2111 53: HIS29 NE2111 0.987 53: HIS32 NE2135 1.590 1.155 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 273 pairs 53: Before cleaning: 443 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 53: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 149 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (149 atoms, 16 residues) 53: 53: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue THR18 as a starting terminus. 53: 53: Identified residue PHE33 as a ending terminus. 53: Start terminus THR-18: NH3+ 53: End terminus PHE-33: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 206 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 220, now 215 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 93 dihedrals, 138 impropers, 324 angles 53: 273 pairs, 215 bonds and 0 virtual sites 53: 53: Total mass 2088.361 a.m.u. 53: 53: Total charge 1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 53: 53: The Gromos53a6 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (55 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 22 acceptors were found. 53: There are 26 hydrogen bonds 53: Will use HISE for residue 45 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS45 53: NE295 53: MET46 SD102 1.078 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 242 pairs 53: Before cleaning: 356 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 53: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 132 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (132 atoms, 16 residues) 53: 53: Identified residue ALA34 as a starting terminus. 53: 53: Identified residue ALA49 as a ending terminus. 53: Start terminus ALA-34: NH3+ 53: End terminus ALA-49: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 170 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 181, now 176 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 81 dihedrals, 104 impropers, 264 angles 53: 242 pairs, 176 bonds and 0 virtual sites 53: 53: Total mass 1861.132 a.m.u. 53: 53: Total charge -1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 53: 53: The Gromos53a6 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (53 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 21 acceptors were found. 53: There are 30 hydrogen bonds 53: Will use HISE for residue 60 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS60 53: NE285 53: CYS62 SG98 0.803 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 232 pairs 53: Before cleaning: 306 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 53: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 117 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (117 atoms, 16 residues) 53: 53: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue LYS50 as a starting terminus. 53: 53: Identified residue PRO65 as a ending terminus. 53: Start terminus LYS-50: NH3+ 53: End terminus PRO-65: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 152 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 161, now 156 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 78 dihedrals, 82 impropers, 231 angles 53: 232 pairs, 156 bonds and 0 virtual sites 53: 53: Total mass 1662.887 a.m.u. 53: 53: Total charge -0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 53: 53: The Gromos53a6 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (52 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 89 donors and 98 acceptors were found. 53: There are 129 hydrogen bonds 53: Will use HISE for residue 31 53: Will use HISE for residue 51 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS25 HIS31 HIS51 53: SG14 NE264 NE2226 53: HIS31 NE264 1.921 53: HIS51 NE2226 1.498 2.650 53: CYS80 SG477 0.207 1.984 1.570 53: Linking CYS-25 SG-14 and CYS-80 SG-477... 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 972 pairs 53: Before cleaning: 1270 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 53: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 53: 53: chain #res #atoms 53: 53: 1 'A' 58 488 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 'A' (488 atoms, 58 residues) 53: 53: Identified residue ASN24 as a starting terminus. 53: 53: Identified residue ARG81 as a ending terminus. 53: Start terminus ASN-24: NH3+ 53: End terminus ARG-81: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 58 residues with 639 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 659, now 654 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 321 dihedrals, 354 impropers, 963 angles 53: 972 pairs, 654 bonds and 0 virtual sites 53: 53: Total mass 6908.582 a.m.u. 53: 53: Total charge -6.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 53: 53: The Gromos53a6 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (97 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 25 donors and 23 acceptors were found. 53: There are 41 hydrogen bonds 53: Will use HISE for residue 8 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS3 HIS8 53: SG9 NE251 53: HIS8 NE251 1.055 53: MET12 SD83 0.763 0.990 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 39 virtual sites 53: Added 4 dummy masses 53: Added 8 new constraints 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 267 pairs 53: Before cleaning: 312 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 53: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 128 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (128 atoms, 16 residues) 53: 53: Identified residue ALA2 as a starting terminus. 53: 53: Identified residue SER17 as a ending terminus. 53: Start terminus ALA-2: NH3+ 53: End terminus SER-17: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 167 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 174, now 169 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 90 dihedrals, 79 impropers, 245 angles 53: 267 pairs, 169 bonds and 39 virtual sites 53: 53: Total mass 1846.116 a.m.u. 53: 53: Total charge -0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 53: 53: The Gromos53a6 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (54 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 30 donors and 22 acceptors were found. 53: There are 36 hydrogen bonds 53: Will use HISE for residue 29 53: Will use HISE for residue 32 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS27 HIS29 53: SG90 NE2111 53: HIS29 NE2111 0.987 53: HIS32 NE2135 1.590 1.155 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 57 virtual sites 53: Added 4 dummy masses 53: Added 10 new constraints 53: 53: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 273 pairs 53: Before cleaning: 443 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 53: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 149 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (149 atoms, 16 residues) 53: 53: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue THR18 as a starting terminus. 53: 53: Identified residue PHE33 as a ending terminus. 53: Start terminus THR-18: NH3+ 53: End terminus PHE-33: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 206 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 220, now 215 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 93 dihedrals, 138 impropers, 324 angles 53: 273 pairs, 215 bonds and 55 virtual sites 53: 53: Total mass 2088.361 a.m.u. 53: 53: Total charge 1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 53: 53: The Gromos53a6 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (59 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 22 acceptors were found. 53: There are 26 hydrogen bonds 53: Will use HISE for residue 45 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS45 53: NE295 53: MET46 SD102 1.078 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 38 virtual sites 53: Added 4 dummy masses 53: Added 8 new constraints 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 242 pairs 53: Before cleaning: 356 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 53: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 132 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (132 atoms, 16 residues) 53: 53: Identified residue ALA34 as a starting terminus. 53: 53: Identified residue ALA49 as a ending terminus. 53: Start terminus ALA-34: NH3+ 53: End terminus ALA-49: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 170 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 181, now 176 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 81 dihedrals, 104 impropers, 264 angles 53: 242 pairs, 176 bonds and 38 virtual sites 53: 53: Total mass 1861.132 a.m.u. 53: 53: Total charge -1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 53: 53: The Gromos53a6 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (55 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 21 acceptors were found. 53: There are 30 hydrogen bonds 53: Will use HISE for residue 60 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS60 53: NE285 53: CYS62 SG98 0.803 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 35 virtual sites 53: Added 4 dummy masses 53: Added 10 new constraints 53: 53: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 232 pairs 53: Before cleaning: 306 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 53: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 117 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (117 atoms, 16 residues) 53: 53: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue LYS50 as a starting terminus. 53: 53: Identified residue PRO65 as a ending terminus. 53: Start terminus LYS-50: NH3+ 53: End terminus PRO-65: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 152 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 161, now 156 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 78 dihedrals, 82 impropers, 231 angles 53: 232 pairs, 156 bonds and 33 virtual sites 53: 53: Total mass 1662.887 a.m.u. 53: 53: Total charge -0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 53: 53: The Gromos53a6 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (51 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 89 donors and 98 acceptors were found. 53: There are 129 hydrogen bonds 53: Will use HISE for residue 31 53: Will use HISE for residue 51 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS25 HIS31 HIS51 53: SG14 NE264 NE2226 53: HIS31 NE264 1.921 53: HIS51 NE2226 1.498 2.650 53: CYS80 SG477 0.207 1.984 1.570 53: Linking CYS-25 SG-14 and CYS-80 SG-477... 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 150 virtual sites 53: Added 10 dummy masses 53: Added 29 new constraints 53: 53: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 972 pairs 53: Before cleaning: 1270 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 53: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 53: 53: chain #res #atoms 53: 53: 1 'A' 58 488 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 'A' (488 atoms, 58 residues) 53: 53: Identified residue ASN24 as a starting terminus. 53: 53: Identified residue ARG81 as a ending terminus. 53: Start terminus ASN-24: NH3+ 53: End terminus ARG-81: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 58 residues with 639 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 659, now 654 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 321 dihedrals, 354 impropers, 963 angles 53: 972 pairs, 654 bonds and 141 virtual sites 53: 53: Total mass 6908.582 a.m.u. 53: 53: Total charge -6.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 53: 53: The Gromos53a6 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (93 ms) 53: [----------] 20 tests from G53a6/Pdb2gmxTest (1667 ms total) 53: 53: [----------] Global test environment tear-down 53: [==========] 40 tests from 2 test suites ran. (4519 ms total) 53: [ PASSED ] 40 tests. 53/90 Test #53: Pdb2gmx2Test .............................. Passed 4.55 sec test 54 Start 54: Pdb2gmx3Test 54: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/pdb2gmx3-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/Pdb2gmx3Test.xml" 54: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/gmxpreprocess/tests 54: Test timeout computed to be: 1920 54: [==========] Running 39 tests from 6 test suites. 54: [----------] Global test environment set-up. 54: [----------] 10 tests from Amber/Pdb2gmxTest 54: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 54: Before cleaning: 653 pairs 54: Before cleaning: 691 dihedrals 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 128 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 (128 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 252 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 255, now 254 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 691 dihedrals, 51 impropers, 457 angles 54: 650 pairs, 254 bonds and 0 virtual sites 54: 54: Total mass 1846.132 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 54: 54: The Amber99sb-ildn force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (85 ms) 54: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 30 donors and 22 acceptors were found. 54: There are 36 hydrogen bonds 54: Will use HISE for residue 29 54: Will use HISE for residue 32 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS27 HIS29 54: SG90 NE2111 54: HIS29 NE2111 0.987 54: HIS32 NE2135 1.590 1.155 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 54: Before cleaning: 748 pairs 54: Before cleaning: 788 dihedrals 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 149 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 (149 atoms, 16 residues) 54: 54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue PHE33 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 281 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 291, now 290 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 788 dihedrals, 72 impropers, 516 angles 54: 736 pairs, 290 bonds and 0 virtual sites 54: 54: Total mass 2088.366 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 54: 54: The Amber99sb-ildn force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (74 ms) 54: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 22 acceptors were found. 54: There are 26 hydrogen bonds 54: Will use HISE for residue 45 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS45 54: NE295 54: MET46 SD102 1.078 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 54: Before cleaning: 676 pairs 54: Before cleaning: 727 dihedrals 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 132 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 (132 atoms, 16 residues) 54: 54: Identified residue ALA34 as a starting terminus. 54: 54: Identified residue ALA49 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 262, now 261 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 727 dihedrals, 56 impropers, 472 angles 54: 667 pairs, 261 bonds and 0 virtual sites 54: 54: Total mass 1861.124 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 54: 54: The Amber99sb-ildn force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (79 ms) 54: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 21 acceptors were found. 54: There are 30 hydrogen bonds 54: Will use HISE for residue 60 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS60 54: NE285 54: CYS62 SG98 0.803 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 54: Before cleaning: 603 pairs 54: Before cleaning: 634 dihedrals 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 117 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 (117 atoms, 16 residues) 54: 54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue LYS50 as a starting terminus. 54: 54: Identified residue PRO65 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 228 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 233, now 232 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 634 dihedrals, 48 impropers, 419 angles 54: 597 pairs, 232 bonds and 0 virtual sites 54: 54: Total mass 1662.888 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 54: 54: The Amber99sb-ildn force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (58 ms) 54: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 89 donors and 98 acceptors were found. 54: There are 129 hydrogen bonds 54: Will use HISE for residue 31 54: Will use HISE for residue 51 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS25 HIS31 HIS51 54: SG14 NE264 NE2226 54: HIS31 NE264 1.921 54: HIS51 NE2226 1.498 2.650 54: CYS80 SG477 0.207 1.984 1.570 54: Linking CYS-25 SG-14 and CYS-80 SG-477... 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 54: Before cleaning: 2499 pairs 54: Before cleaning: 2631 dihedrals 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 58 488 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 'A' (488 atoms, 58 residues) 54: 54: Identified residue ASN24 as a starting terminus. 54: 54: Identified residue ARG81 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 58 residues with 936 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 952, now 951 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2631 dihedrals, 208 impropers, 1704 angles 54: 2469 pairs, 951 bonds and 0 virtual sites 54: 54: Total mass 6908.576 a.m.u. 54: 54: Total charge -6.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 54: 54: The Amber99sb-ildn force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (146 ms) 54: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 54: Marked 124 virtual sites 54: Added 16 dummy masses 54: Added 26 new constraints 54: Before cleaning: 653 pairs 54: Before cleaning: 691 dihedrals 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 128 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 (128 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 252 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 255, now 254 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 691 dihedrals, 51 impropers, 457 angles 54: 650 pairs, 254 bonds and 130 virtual sites 54: 54: Total mass 1846.132 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 54: 54: The Amber99sb-ildn force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (60 ms) 54: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 30 donors and 22 acceptors were found. 54: There are 36 hydrogen bonds 54: Will use HISE for residue 29 54: Will use HISE for residue 32 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS27 HIS29 54: SG90 NE2111 54: HIS29 NE2111 0.987 54: HIS32 NE2135 1.590 1.155 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 54: Marked 132 virtual sites 54: Added 10 dummy masses 54: Added 19 new constraints 54: Before cleaning: 748 pairs 54: Before cleaning: 788 dihedrals 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 149 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 (149 atoms, 16 residues) 54: 54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue PHE33 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 281 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 291, now 290 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 788 dihedrals, 72 impropers, 516 angles 54: 736 pairs, 290 bonds and 133 virtual sites 54: 54: Total mass 2088.366 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 54: 54: The Amber99sb-ildn force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (67 ms) 54: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 22 acceptors were found. 54: There are 26 hydrogen bonds 54: Will use HISE for residue 45 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS45 54: NE295 54: MET46 SD102 1.078 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 54: Marked 123 virtual sites 54: Added 22 dummy masses 54: Added 35 new constraints 54: Before cleaning: 676 pairs 54: Before cleaning: 727 dihedrals 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 132 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 (132 atoms, 16 residues) 54: 54: Identified residue ALA34 as a starting terminus. 54: 54: Identified residue ALA49 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 262, now 261 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 727 dihedrals, 56 impropers, 472 angles 54: 667 pairs, 261 bonds and 132 virtual sites 54: 54: Total mass 1861.124 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 54: 54: The Amber99sb-ildn force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (105 ms) 54: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 21 acceptors were found. 54: There are 30 hydrogen bonds 54: Will use HISE for residue 60 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS60 54: NE285 54: CYS62 SG98 0.803 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 54: Marked 111 virtual sites 54: Added 18 dummy masses 54: Added 31 new constraints 54: Before cleaning: 603 pairs 54: Before cleaning: 634 dihedrals 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 117 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 (117 atoms, 16 residues) 54: 54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue LYS50 as a starting terminus. 54: 54: Identified residue PRO65 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 228 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 233, now 232 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 634 dihedrals, 48 impropers, 419 angles 54: 597 pairs, 232 bonds and 116 virtual sites 54: 54: Total mass 1662.888 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 54: 54: The Amber99sb-ildn force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (183 ms) 54: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 89 donors and 98 acceptors were found. 54: There are 129 hydrogen bonds 54: Will use HISE for residue 31 54: Will use HISE for residue 51 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS25 HIS31 HIS51 54: SG14 NE264 NE2226 54: HIS31 NE264 1.921 54: HIS51 NE2226 1.498 2.650 54: CYS80 SG477 0.207 1.984 1.570 54: Linking CYS-25 SG-14 and CYS-80 SG-477... 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 54: Marked 447 virtual sites 54: Added 58 dummy masses 54: Added 101 new constraints 54: Before cleaning: 2499 pairs 54: Before cleaning: 2631 dihedrals 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 58 488 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 'A' (488 atoms, 58 residues) 54: 54: Identified residue ASN24 as a starting terminus. 54: 54: Identified residue ARG81 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 58 residues with 936 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 952, now 951 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2631 dihedrals, 208 impropers, 1704 angles 54: 2469 pairs, 951 bonds and 462 virtual sites 54: 54: Total mass 6908.576 a.m.u. 54: 54: Total charge -6.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 54: 54: The Amber99sb-ildn force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (421 ms) 54: [----------] 10 tests from Amber/Pdb2gmxTest (1286 ms total) 54: 54: [----------] 1 test from AmberTip4p/Pdb2gmxTest 54: [ RUN ] AmberTip4p/Pdb2gmxTest.Runs/ff_amber99sbildn_tip4p_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/tip4p.pdb... 54: Read 'TIP4p ice to test that MW is handled correctly', 4 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 0 chains and 1 blocks of water and 2 residues with 4 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 2 4 (only water) 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 (4 atoms, 2 residues) 54: 54: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 2 residues with 8 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 4, now 4 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 0 dihedrals, 0 impropers, 2 angles 54: 0 pairs, 4 bonds and 0 virtual sites 54: 54: Total mass 36.032 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/tip4p.pdb. 54: 54: The Amber99sb-ildn force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] AmberTip4p/Pdb2gmxTest.Runs/ff_amber99sbildn_tip4p_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full (130 ms) 54: [----------] 1 test from AmberTip4p/Pdb2gmxTest (130 ms total) 54: 54: [----------] 12 tests from Charmm/Pdb2gmxTest 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 653 pairs 54: Before cleaning: 663 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 128 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 (128 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 252 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 254, now 254 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 14 cmap torsion pairs 54: 54: There are 663 dihedrals, 48 impropers, 457 angles 54: 650 pairs, 254 bonds and 0 virtual sites 54: 54: Total mass 1846.115 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (703 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 30 donors and 22 acceptors were found. 54: There are 36 hydrogen bonds 54: Will use HISE for residue 29 54: Will use HISE for residue 32 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS27 HIS29 54: SG90 NE2111 54: HIS29 NE2111 0.987 54: HIS32 NE2135 1.590 1.155 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 748 pairs 54: Before cleaning: 778 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 149 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 (149 atoms, 16 residues) 54: 54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue PHE33 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus PHE-33: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 281 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 290, now 290 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 14 cmap torsion pairs 54: 54: There are 778 dihedrals, 49 impropers, 516 angles 54: 736 pairs, 290 bonds and 0 virtual sites 54: 54: Total mass 2088.361 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (112 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 22 acceptors were found. 54: There are 26 hydrogen bonds 54: Will use HISE for residue 45 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS45 54: NE295 54: MET46 SD102 1.078 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 676 pairs 54: Before cleaning: 696 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 132 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 (132 atoms, 16 residues) 54: 54: Identified residue ALA34 as a starting terminus. 54: 54: Identified residue ALA49 as a ending terminus. 54: Start terminus ALA-34: NH3+ 54: End terminus ALA-49: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 261, now 261 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 14 cmap torsion pairs 54: 54: There are 696 dihedrals, 39 impropers, 472 angles 54: 667 pairs, 261 bonds and 0 virtual sites 54: 54: Total mass 1861.130 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (102 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 21 acceptors were found. 54: There are 30 hydrogen bonds 54: Will use HISE for residue 60 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS60 54: NE285 54: CYS62 SG98 0.803 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 603 pairs 54: Before cleaning: 618 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 117 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 (117 atoms, 16 residues) 54: 54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue LYS50 as a starting terminus. 54: 54: Identified residue PRO65 as a ending terminus. 54: Start terminus LYS-50: NH3+ 54: End terminus PRO-65: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 228 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 232, now 232 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 14 cmap torsion pairs 54: 54: There are 618 dihedrals, 38 impropers, 419 angles 54: 597 pairs, 232 bonds and 0 virtual sites 54: 54: Total mass 1662.885 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (61 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 89 donors and 98 acceptors were found. 54: There are 129 hydrogen bonds 54: Will use HISE for residue 31 54: Will use HISE for residue 51 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS25 HIS31 HIS51 54: SG14 NE264 NE2226 54: HIS31 NE264 1.921 54: HIS51 NE2226 1.498 2.650 54: CYS80 SG477 0.207 1.984 1.570 54: Linking CYS-25 SG-14 and CYS-80 SG-477... 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 2499 pairs 54: Before cleaning: 2524 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 58 488 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (488 atoms, 58 residues) 54: 54: Identified residue ASN24 as a starting terminus. 54: 54: Identified residue ARG81 as a ending terminus. 54: Start terminus ASN-24: NH3+ 54: End terminus ARG-81: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 58 residues with 936 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 951, now 951 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 56 cmap torsion pairs 54: 54: There are 2524 dihedrals, 149 impropers, 1704 angles 54: 2469 pairs, 951 bonds and 0 virtual sites 54: 54: Total mass 6908.566 a.m.u. 54: 54: Total charge -6.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (123 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_monomerpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 39 pairs 54: Before cleaning: 39 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/monomer.pdb... 54: Read 'GLU', 9 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 1 residues with 9 atoms 54: 54: chain #res #atoms 54: 54: 1 'X' 1 9 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'X' (9 atoms, 1 residues) 54: 54: Identified residue GLU1 as a starting terminus. 54: 54: Identified residue GLU1 as a ending terminus. 54: Start terminus GLU-1: NH3+ 54: End terminus GLU-1: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 1 residues with 18 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 17, now 17 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 39 dihedrals, 2 impropers, 30 angles 54: 39 pairs, 17 bonds and 0 virtual sites 54: 54: Total mass 146.123 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/monomer.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_monomerpdb_format_gro_match_file (29 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Marked 124 virtual sites 54: Added 16 dummy masses 54: Added 26 new constraints 54: Before cleaning: 653 pairs 54: Before cleaning: 663 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 128 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 (128 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 252 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 254, now 254 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 14 cmap torsion pairs 54: 54: There are 663 dihedrals, 48 impropers, 457 angles 54: 650 pairs, 254 bonds and 130 virtual sites 54: 54: Total mass 1846.115 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (56 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 30 donors and 22 acceptors were found. 54: There are 36 hydrogen bonds 54: Will use HISE for residue 29 54: Will use HISE for residue 32 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS27 HIS29 54: SG90 NE2111 54: HIS29 NE2111 0.987 54: HIS32 NE2135 1.590 1.155 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Marked 132 virtual sites 54: Added 10 dummy masses 54: Added 19 new constraints 54: Before cleaning: 748 pairs 54: Before cleaning: 778 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 149 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 (149 atoms, 16 residues) 54: 54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue PHE33 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus PHE-33: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 281 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 290, now 290 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 14 cmap torsion pairs 54: 54: There are 778 dihedrals, 49 impropers, 516 angles 54: 736 pairs, 290 bonds and 133 virtual sites 54: 54: Total mass 2088.361 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (56 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 22 acceptors were found. 54: There are 26 hydrogen bonds 54: Will use HISE for residue 45 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS45 54: NE295 54: MET46 SD102 1.078 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Marked 123 virtual sites 54: Added 22 dummy masses 54: Added 35 new constraints 54: Before cleaning: 676 pairs 54: Before cleaning: 696 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 132 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 (132 atoms, 16 residues) 54: 54: Identified residue ALA34 as a starting terminus. 54: 54: Identified residue ALA49 as a ending terminus. 54: Start terminus ALA-34: NH3+ 54: End terminus ALA-49: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 261, now 261 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 14 cmap torsion pairs 54: 54: There are 696 dihedrals, 39 impropers, 472 angles 54: 667 pairs, 261 bonds and 132 virtual sites 54: 54: Total mass 1861.130 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (72 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 21 acceptors were found. 54: There are 30 hydrogen bonds 54: Will use HISE for residue 60 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS60 54: NE285 54: CYS62 SG98 0.803 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Marked 111 virtual sites 54: Added 18 dummy masses 54: Added 31 new constraints 54: Before cleaning: 603 pairs 54: Before cleaning: 618 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 117 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 (117 atoms, 16 residues) 54: 54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue LYS50 as a starting terminus. 54: 54: Identified residue PRO65 as a ending terminus. 54: Start terminus LYS-50: NH3+ 54: End terminus PRO-65: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 228 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 232, now 232 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 14 cmap torsion pairs 54: 54: There are 618 dihedrals, 38 impropers, 419 angles 54: 597 pairs, 232 bonds and 116 virtual sites 54: 54: Total mass 1662.885 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (54 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 89 donors and 98 acceptors were found. 54: There are 129 hydrogen bonds 54: Will use HISE for residue 31 54: Will use HISE for residue 51 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS25 HIS31 HIS51 54: SG14 NE264 NE2226 54: HIS31 NE264 1.921 54: HIS51 NE2226 1.498 2.650 54: CYS80 SG477 0.207 1.984 1.570 54: Linking CYS-25 SG-14 and CYS-80 SG-477... 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Marked 447 virtual sites 54: Added 58 dummy masses 54: Added 101 new constraints 54: Before cleaning: 2499 pairs 54: Before cleaning: 2524 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 58 488 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (488 atoms, 58 residues) 54: 54: Identified residue ASN24 as a starting terminus. 54: 54: Identified residue ARG81 as a ending terminus. 54: Start terminus ASN-24: NH3+ 54: End terminus ARG-81: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 58 residues with 936 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 951, now 951 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 56 cmap torsion pairs 54: 54: There are 2524 dihedrals, 149 impropers, 1704 angles 54: 2469 pairs, 951 bonds and 462 virtual sites 54: 54: Total mass 6908.566 a.m.u. 54: 54: Total charge -6.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (134 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_monomerpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Marked 8 virtual sites 54: Added 2 dummy masses 54: Added 3 new constraints 54: Before cleaning: 39 pairs 54: Before cleaning: 39 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/monomer.pdb... 54: Read 'GLU', 9 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 1 residues with 9 atoms 54: 54: chain #res #atoms 54: 54: 1 'X' 1 9 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'X' (9 atoms, 1 residues) 54: 54: Identified residue GLU1 as a starting terminus. 54: 54: Identified residue GLU1 as a ending terminus. 54: Start terminus GLU-1: NH3+ 54: End terminus GLU-1: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 1 residues with 18 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 17, now 17 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 39 dihedrals, 2 impropers, 30 angles 54: 39 pairs, 17 bonds and 9 virtual sites 54: 54: Total mass 146.123 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/monomer.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_monomerpdb_format_gro_match_file (33 ms) 54: [----------] 12 tests from Charmm/Pdb2gmxTest (1541 ms total) 54: 54: [----------] 8 tests from ChainSep/Pdb2gmxTest 54: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_all_chainTerpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 651 pairs 54: Before cleaning: 661 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on changing chain id only (ignoring TER records). 54: 54: Merged chains into joint molecule definitions at 2 places. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 16 127 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (127 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue GLU5 as a ending terminus. 54: 54: Identified residue PHE6 as a starting terminus. 54: 54: Identified residue MET12 as a ending terminus. 54: 54: Identified residue ASN13 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus GLU-5: COO- 54: Start terminus PHE-6: NH3+ 54: End terminus MET-12: COO- 54: Start terminus ASN-13: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 258 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 258, now 258 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 10 cmap torsion pairs 54: 54: There are 661 dihedrals, 46 impropers, 463 angles 54: 648 pairs, 258 bonds and 0 virtual sites 54: 54: Total mass 1882.146 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_all_chainTerpdb_format_gro_match_file (50 ms) 54: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_chainTerpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 123 pairs 54: Before cleaning: 123 dihedrals 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 10 donors and 7 acceptors were found. 54: There are 7 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS8 54: NE223 54: MET12 SD55 0.990 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 317 pairs 54: Before cleaning: 322 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 211 pairs 54: Before cleaning: 216 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on changing chain id only (ignoring TER records). 54: 54: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 4 28 54: 54: 2 'B' 7 58 54: 54: 3 'C' 5 41 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (28 atoms, 4 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue GLU5 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus GLU-5: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 4 residues with 51 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 50, now 50 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2 cmap torsion pairs 54: 54: There are 123 dihedrals, 9 impropers, 88 angles 54: 123 pairs, 50 bonds and 0 virtual sites 54: 54: Total mass 434.421 a.m.u. 54: 54: Total charge -2.000 e 54: 54: Writing topology 54: 54: Processing chain 2 'B' (58 atoms, 7 residues) 54: 54: Identified residue PHE6 as a starting terminus. 54: 54: Identified residue MET12 as a ending terminus. 54: Start terminus PHE-6: NH3+ 54: End terminus MET-12: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 7 residues with 124 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 125, now 125 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 5 cmap torsion pairs 54: 54: There are 322 dihedrals, 19 impropers, 227 angles 54: 314 pairs, 125 bonds and 0 virtual sites 54: 54: Total mass 846.083 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Processing chain 3 'C' (41 atoms, 5 residues) 54: 54: Identified residue ASN13 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ASN-13: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 5 residues with 83 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 83, now 83 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 3 cmap torsion pairs 54: 54: There are 216 dihedrals, 18 impropers, 148 angles 54: 211 pairs, 83 bonds and 0 virtual sites 54: 54: Total mass 601.643 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Including chain 1 in system: 51 atoms 4 residues 54: 54: Including chain 2 in system: 124 atoms 7 residues 54: 54: Including chain 3 in system: 83 atoms 5 residues 54: 54: Now there are 258 atoms and 16 residues 54: 54: Total mass in system 1882.146 a.m.u. 54: 54: Total charge in system 0.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_chainTerpdb_format_gro_match_file (74 ms) 54: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_all_chainTerpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 651 pairs 54: Before cleaning: 661 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records only (ignoring chain id). 54: 54: Merged chains into joint molecule definitions at 2 places. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 16 127 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (127 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue ILE9 as a ending terminus. 54: 54: Identified residue LYS10 as a starting terminus. 54: 54: Identified residue MET12 as a ending terminus. 54: 54: Identified residue ASN13 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus ILE-9: COO- 54: Start terminus LYS-10: NH3+ 54: End terminus MET-12: COO- 54: Start terminus ASN-13: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 258 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 258, now 258 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 10 cmap torsion pairs 54: 54: There are 661 dihedrals, 46 impropers, 463 angles 54: 648 pairs, 258 bonds and 0 virtual sites 54: 54: Total mass 1882.146 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_all_chainTerpdb_format_gro_match_file (73 ms) 54: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_chainTerpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 10 donors and 12 acceptors were found. 54: There are 13 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 54: SG9 54: HIS8 NE251 1.055 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 288 pairs 54: Before cleaning: 293 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 152 pairs 54: Before cleaning: 152 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 211 pairs 54: Before cleaning: 216 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records only (ignoring chain id). 54: 54: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 8 61 54: 54: 2 'B' 3 25 54: 54: 3 'C' 5 41 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (61 atoms, 8 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue ILE9 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus ILE-9: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 8 residues with 114 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 115, now 115 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 6 cmap torsion pairs 54: 54: There are 293 dihedrals, 23 impropers, 203 angles 54: 285 pairs, 115 bonds and 0 virtual sites 54: 54: Total mass 888.952 a.m.u. 54: 54: Total charge -2.000 e 54: 54: Writing topology 54: 54: Processing chain 2 'B' (25 atoms, 3 residues) 54: 54: Identified residue LYS10 as a starting terminus. 54: 54: Identified residue MET12 as a ending terminus. 54: Start terminus LYS-10: NH3+ 54: End terminus MET-12: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 3 residues with 61 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 60, now 60 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 1 cmap torsion pairs 54: 54: There are 152 dihedrals, 5 impropers, 112 angles 54: 152 pairs, 60 bonds and 0 virtual sites 54: 54: Total mass 391.552 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Processing chain 3 'C' (41 atoms, 5 residues) 54: 54: Identified residue ASN13 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ASN-13: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 5 residues with 83 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 83, now 83 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 3 cmap torsion pairs 54: 54: There are 216 dihedrals, 18 impropers, 148 angles 54: 211 pairs, 83 bonds and 0 virtual sites 54: 54: Total mass 601.643 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Including chain 1 in system: 114 atoms 8 residues 54: 54: Including chain 2 in system: 61 atoms 3 residues 54: 54: Including chain 3 in system: 83 atoms 5 residues 54: 54: Now there are 258 atoms and 16 residues 54: 54: Total mass in system 1882.146 a.m.u. 54: 54: Total charge in system 0.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_chainTerpdb_format_gro_match_file (53 ms) 54: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_chainTerpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 650 pairs 54: Before cleaning: 660 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: Merged chains into joint molecule definitions at 3 places. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 16 127 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (127 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue GLU5 as a ending terminus. 54: 54: Identified residue PHE6 as a starting terminus. 54: 54: Identified residue ILE9 as a ending terminus. 54: 54: Identified residue LYS10 as a starting terminus. 54: 54: Identified residue MET12 as a ending terminus. 54: 54: Identified residue ASN13 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus GLU-5: COO- 54: Start terminus PHE-6: NH3+ 54: End terminus ILE-9: COO- 54: Start terminus LYS-10: NH3+ 54: End terminus MET-12: COO- 54: Start terminus ASN-13: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 261 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 260, now 260 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 8 cmap torsion pairs 54: 54: There are 660 dihedrals, 45 impropers, 466 angles 54: 647 pairs, 260 bonds and 0 virtual sites 54: 54: Total mass 1900.162 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_chainTerpdb_format_gro_match_file (52 ms) 54: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_chainTerpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 54: 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 123 pairs 54: Before cleaning: 123 dihedrals 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 6 donors and 4 acceptors were found. 54: There are 3 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 164 pairs 54: Before cleaning: 169 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 152 pairs 54: Before cleaning: 152 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 211 pairs 54: Before cleaning: 216 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 54: 54: There are 4 chains and 0 blocks of water and 16 residues with 127 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 4 28 54: 54: 2 'B' 4 33 54: 54: 3 'B' 3 25 54: 54: 4 'C' 5 41 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (28 atoms, 4 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue GLU5 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus GLU-5: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 4 residues with 51 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 50, now 50 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2 cmap torsion pairs 54: 54: There are 123 dihedrals, 9 impropers, 88 angles 54: 123 pairs, 50 bonds and 0 virtual sites 54: 54: Total mass 434.421 a.m.u. 54: 54: Total charge -2.000 e 54: 54: Writing topology 54: 54: Processing chain 2 'B' (33 atoms, 4 residues) 54: 54: Identified residue PHE6 as a starting terminus. 54: 54: Identified residue ILE9 as a ending terminus. 54: Start terminus PHE-6: NH3+ 54: End terminus ILE-9: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 4 residues with 66 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 67, now 67 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2 cmap torsion pairs 54: 54: There are 169 dihedrals, 13 impropers, 118 angles 54: 161 pairs, 67 bonds and 0 virtual sites 54: 54: Total mass 472.547 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Processing chain 3 'B' (25 atoms, 3 residues) 54: 54: Identified residue LYS10 as a starting terminus. 54: 54: Identified residue MET12 as a ending terminus. 54: Start terminus LYS-10: NH3+ 54: End terminus MET-12: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 3 residues with 61 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 60, now 60 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 1 cmap torsion pairs 54: 54: There are 152 dihedrals, 5 impropers, 112 angles 54: 152 pairs, 60 bonds and 0 virtual sites 54: 54: Total mass 391.552 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Processing chain 4 'C' (41 atoms, 5 residues) 54: 54: Identified residue ASN13 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ASN-13: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 5 residues with 83 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 83, now 83 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 3 cmap torsion pairs 54: 54: There are 216 dihedrals, 18 impropers, 148 angles 54: 211 pairs, 83 bonds and 0 virtual sites 54: 54: Total mass 601.643 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Including chain 1 in system: 51 atoms 4 residues 54: 54: Including chain 2 in system: 66 atoms 4 residues 54: 54: Including chain 3 in system: 61 atoms 3 residues 54: 54: Including chain 4 in system: 83 atoms 5 residues 54: 54: Now there are 261 atoms and 16 residues 54: 54: Total mass in system 1900.162 a.m.u. 54: 54: Total charge in system 0.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_chainTerpdb_format_gro_match_file (66 ms) 54: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_all_chainTerpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 652 pairs 54: Before cleaning: 662 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records and chain id changing. 54: 54: Merged chains into joint molecule definitions at 1 places. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 16 127 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (127 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue MET12 as a ending terminus. 54: 54: Identified residue ASN13 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus MET-12: COO- 54: Start terminus ASN-13: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 256, now 256 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 12 cmap torsion pairs 54: 54: There are 662 dihedrals, 47 impropers, 460 angles 54: 649 pairs, 256 bonds and 0 virtual sites 54: 54: Total mass 1864.131 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_all_chainTerpdb_format_gro_match_file (57 ms) 54: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_chainTerpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 14 donors and 15 acceptors were found. 54: There are 20 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 441 pairs 54: Before cleaning: 446 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 211 pairs 54: Before cleaning: 216 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records and chain id changing. 54: 54: There are 2 chains and 0 blocks of water and 16 residues with 127 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 11 86 54: 54: 2 'C' 5 41 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (86 atoms, 11 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue MET12 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus MET-12: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 11 residues with 172 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 173, now 173 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 9 cmap torsion pairs 54: 54: There are 446 dihedrals, 29 impropers, 312 angles 54: 438 pairs, 173 bonds and 0 virtual sites 54: 54: Total mass 1262.488 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Processing chain 2 'C' (41 atoms, 5 residues) 54: 54: Identified residue ASN13 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ASN-13: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 5 residues with 83 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 83, now 83 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 3 cmap torsion pairs 54: 54: There are 216 dihedrals, 18 impropers, 148 angles 54: 211 pairs, 83 bonds and 0 virtual sites 54: 54: Total mass 601.643 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Including chain 1 in system: 172 atoms 11 residues 54: 54: Including chain 2 in system: 83 atoms 5 residues 54: 54: Now there are 255 atoms and 16 residues 54: 54: Total mass in system 1864.131 a.m.u. 54: 54: Total charge in system 0.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_chainTerpdb_format_gro_match_file (52 ms) 54: [----------] 8 tests from ChainSep/Pdb2gmxTest (481 ms total) 54: 54: [----------] 4 tests from ChainChanges/Pdb2gmxTest 54: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_fragmentspdb_format_pdb_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 83 pairs 54: Before cleaning: 83 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 145 pairs 54: Before cleaning: 150 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/fragments.pdb... 54: Read 'Fragments of peptides and ions', 47 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on changing chain id only (ignoring TER records). 54: 54: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 3 19 54: 54: 2 'B' 3 28 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (19 atoms, 3 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue ASP4 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus ASP-4: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 3 residues with 36 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 35, now 35 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 1 cmap torsion pairs 54: 54: There are 83 dihedrals, 6 impropers, 61 angles 54: 83 pairs, 35 bonds and 0 virtual sites 54: 54: Total mass 306.314 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Processing chain 2 'B' (28 atoms, 3 residues) 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue TRP20 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus TRP-20: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 3 residues with 57 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 58, now 58 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 1 cmap torsion pairs 54: 54: There are 150 dihedrals, 5 impropers, 103 angles 54: 142 pairs, 58 bonds and 0 virtual sites 54: 54: Total mass 404.468 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Including chain 1 in system: 36 atoms 3 residues 54: 54: Including chain 2 in system: 57 atoms 3 residues 54: 54: Now there are 93 atoms and 6 residues 54: 54: Total mass in system 710.782 a.m.u. 54: 54: Total charge in system -1.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/fragments.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_fragmentspdb_format_pdb_match_file (50 ms) 54: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_fragmentspdb_format_pdb_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 83 pairs 54: Before cleaning: 83 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 145 pairs 54: Before cleaning: 150 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/fragments.pdb... 54: Read 'Fragments of peptides and ions', 47 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records only (ignoring chain id). 54: 54: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 3 19 54: 54: 2 'B' 3 28 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (19 atoms, 3 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue ASP4 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus ASP-4: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 3 residues with 36 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 35, now 35 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 1 cmap torsion pairs 54: 54: There are 83 dihedrals, 6 impropers, 61 angles 54: 83 pairs, 35 bonds and 0 virtual sites 54: 54: Total mass 306.314 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Processing chain 2 'B' (28 atoms, 3 residues) 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue TRP20 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus TRP-20: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 3 residues with 57 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 58, now 58 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 1 cmap torsion pairs 54: 54: There are 150 dihedrals, 5 impropers, 103 angles 54: 142 pairs, 58 bonds and 0 virtual sites 54: 54: Total mass 404.468 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Including chain 1 in system: 36 atoms 3 residues 54: 54: Including chain 2 in system: 57 atoms 3 residues 54: 54: Now there are 93 atoms and 6 residues 54: 54: Total mass in system 710.782 a.m.u. 54: 54: Total charge in system -1.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/fragments.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_fragmentspdb_format_pdb_match_file (31 ms) 54: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_fragmentspdb_format_pdb_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 83 pairs 54: Before cleaning: 83 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 145 pairs 54: Before cleaning: 150 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/fragments.pdb... 54: Read 'Fragments of peptides and ions', 47 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 3 19 54: 54: 2 'B' 3 28 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (19 atoms, 3 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue ASP4 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus ASP-4: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 3 residues with 36 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 35, now 35 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 1 cmap torsion pairs 54: 54: There are 83 dihedrals, 6 impropers, 61 angles 54: 83 pairs, 35 bonds and 0 virtual sites 54: 54: Total mass 306.314 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Processing chain 2 'B' (28 atoms, 3 residues) 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue TRP20 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus TRP-20: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 3 residues with 57 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 58, now 58 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 1 cmap torsion pairs 54: 54: There are 150 dihedrals, 5 impropers, 103 angles 54: 142 pairs, 58 bonds and 0 virtual sites 54: 54: Total mass 404.468 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Including chain 1 in system: 36 atoms 3 residues 54: 54: Including chain 2 in system: 57 atoms 3 residues 54: 54: Now there are 93 atoms and 6 residues 54: 54: Total mass in system 710.782 a.m.u. 54: 54: Total charge in system -1.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/fragments.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_fragmentspdb_format_pdb_match_file (30 ms) 54: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_fragmentspdb_format_pdb_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 83 pairs 54: Before cleaning: 83 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 145 pairs 54: Before cleaning: 150 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/fragments.pdb... 54: Read 'Fragments of peptides and ions', 47 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records and chain id changing. 54: 54: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 3 19 54: 54: 2 'B' 3 28 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (19 atoms, 3 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue ASP4 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus ASP-4: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 3 residues with 36 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 35, now 35 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 1 cmap torsion pairs 54: 54: There are 83 dihedrals, 6 impropers, 61 angles 54: 83 pairs, 35 bonds and 0 virtual sites 54: 54: Total mass 306.314 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Processing chain 2 'B' (28 atoms, 3 residues) 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue TRP20 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus TRP-20: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 3 residues with 57 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 58, now 58 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 1 cmap torsion pairs 54: 54: There are 150 dihedrals, 5 impropers, 103 angles 54: 142 pairs, 58 bonds and 0 virtual sites 54: 54: Total mass 404.468 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Including chain 1 in system: 36 atoms 3 residues 54: 54: Including chain 2 in system: 57 atoms 3 residues 54: 54: Now there are 93 atoms and 6 residues 54: 54: Total mass in system 710.782 a.m.u. 54: 54: Total charge in system -1.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/fragments.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_fragmentspdb_format_pdb_match_file (32 ms) 54: [----------] 4 tests from ChainChanges/Pdb2gmxTest (145 ms total) 54: 54: [----------] 4 tests from Cyclic/Pdb2gmxTest 54: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycrnapdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: WARNING: all CONECT records are ignored 54: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 54: 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 6040 pairs 54: Before cleaning: 6605 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 6040 pairs 54: Before cleaning: 6605 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb... 54: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 54: 54: Moved all the water blocks to the end 54: 54: There are 3 chains and 2 blocks of water and 175 residues with 3087 atoms 54: 54: chain #res #atoms 54: 54: 1 'P' 71 1527 54: 54: 2 'Q' 71 1527 54: 54: 3 'Q' 7 7 54: 54: 4 ' ' 10 10 (only water) 54: 54: 5 ' ' 16 16 (only water) 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'P' (1527 atoms, 71 residues) 54: 54: Identified residue G1 as a starting terminus. 54: 54: Identified residue U71 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 71 residues with 2297 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 2481, now 2481 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 6605 dihedrals, 183 impropers, 4434 angles 54: 5827 pairs, 2481 bonds and 0 virtual sites 54: 54: Total mass 22984.514 a.m.u. 54: 54: Total charge -71.000 e 54: 54: Writing topology 54: 54: Processing chain 2 'Q' (1527 atoms, 71 residues) 54: 54: Identified residue G1 as a starting terminus. 54: 54: Identified residue U71 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 71 residues with 2297 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 2481, now 2481 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 6605 dihedrals, 183 impropers, 4434 angles 54: 5827 pairs, 2481 bonds and 0 virtual sites 54: 54: Total mass 22984.514 a.m.u. 54: 54: Total charge -71.000 e 54: 54: Writing topology 54: 54: Processing chain 3 'Q' (7 atoms, 7 residues) 54: 54: Residue MG72 has type 'Ion', assuming it is not linked into a chain. 54: 54: Residue MG73 has type 'Ion', assuming it is not linked into a chain. 54: 54: Residue MG74 has type 'Ion', assuming it is not linked into a chain. 54: 54: Residue MG75 has type 'Ion', assuming it is not linked into a chain. 54: 54: Residue MG76 has type 'Ion', assuming it is not linked into a chain. 54: 54: Disabling further notes about ions. 54: 54: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 7 residues with 7 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: No bonds 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 0 dihedrals, 0 impropers, 0 angles 54: 0 pairs, 0 bonds and 0 virtual sites 54: 54: Total mass 170.135 a.m.u. 54: 54: Total charge 14.000 e 54: 54: Writing topology 54: 54: Processing chain 4 (10 atoms, 10 residues) 54: 54: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 10 residues with 30 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 30, now 30 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 0 dihedrals, 0 impropers, 30 angles 54: 0 pairs, 30 bonds and 0 virtual sites 54: 54: Total mass 180.154 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Processing chain 5 (16 atoms, 16 residues) 54: 54: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 48 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 48, now 48 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 0 dihedrals, 0 impropers, 48 angles 54: 0 pairs, 48 bonds and 0 virtual sites 54: 54: Total mass 288.246 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Including chain 1 in system: 2297 atoms 71 residues 54: 54: Including chain 2 in system: 2297 atoms 71 residues 54: 54: Including chain 3 in system: 7 atoms 7 residues 54: 54: Including chain 4 in system: 30 atoms 10 residues 54: 54: Including chain 5 in system: 48 atoms 16 residues 54: 54: Now there are 4679 atoms and 175 residues 54: 54: Total mass in system 46607.562 a.m.u. 54: 54: Total charge in system -128.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycrnapdb_format_gro_match_file (385 ms) 54: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycprotpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 2325 pairs 54: Before cleaning: 2325 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb... 54: Read 'CARNOCYCLIN-A', 413 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 60 413 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (413 atoms, 60 residues) 54: 54: Identified residue LEU1 as a starting terminus. 54: 54: Identified residue LEU60 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 60 residues with 878 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 880, now 880 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 60 cmap torsion pairs 54: 54: There are 2325 dihedrals, 137 impropers, 1614 angles 54: 2319 pairs, 880 bonds and 0 virtual sites 54: 54: Total mass 5866.087 a.m.u. 54: 54: Total charge 4.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycprotpdb_format_gro_match_file (86 ms) 54: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycrnapdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: WARNING: all CONECT records are ignored 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 12080 pairs 54: Before cleaning: 13210 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb... 54: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: Moved all the water blocks to the end 54: 54: Merged chains into joint molecule definitions at 2 places. 54: 54: There are 1 chains and 2 blocks of water and 175 residues with 3087 atoms 54: 54: chain #res #atoms 54: 54: 1 'P' 149 3061 54: 54: 2 ' ' 10 10 (only water) 54: 54: 3 ' ' 16 16 (only water) 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'P' (3061 atoms, 149 residues) 54: 54: Identified residue G1 as a starting terminus. 54: 54: Identified residue U71 as a ending terminus. 54: 54: Identified residue G1 as a starting terminus. 54: 54: Identified residue U71 as a ending terminus. 54: 54: Residue MG72 has type 'Ion', assuming it is not linked into a chain. 54: 54: Residue MG73 has type 'Ion', assuming it is not linked into a chain. 54: 54: Residue MG74 has type 'Ion', assuming it is not linked into a chain. 54: 54: Residue MG75 has type 'Ion', assuming it is not linked into a chain. 54: 54: Residue MG76 has type 'Ion', assuming it is not linked into a chain. 54: 54: Disabling further notes about ions. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 149 residues with 4601 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 4962, now 4962 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 13210 dihedrals, 366 impropers, 8868 angles 54: 11654 pairs, 4962 bonds and 0 virtual sites 54: 54: Total mass 46139.162 a.m.u. 54: 54: Total charge -128.000 e 54: 54: Writing topology 54: 54: Processing chain 2 (10 atoms, 10 residues) 54: 54: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 10 residues with 30 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 30, now 30 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 0 dihedrals, 0 impropers, 30 angles 54: 0 pairs, 30 bonds and 0 virtual sites 54: 54: Total mass 180.154 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Processing chain 3 (16 atoms, 16 residues) 54: 54: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 48 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 48, now 48 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 0 dihedrals, 0 impropers, 48 angles 54: 0 pairs, 48 bonds and 0 virtual sites 54: 54: Total mass 288.246 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Including chain 1 in system: 4601 atoms 149 residues 54: 54: Including chain 2 in system: 30 atoms 10 residues 54: 54: Including chain 3 in system: 48 atoms 16 residues 54: 54: Now there are 4679 atoms and 175 residues 54: 54: Total mass in system 46607.562 a.m.u. 54: 54: Total charge in system -128.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycrnapdb_format_gro_match_file (492 ms) 54: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycprotpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 2325 pairs 54: Before cleaning: 2325 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb... 54: Read 'CARNOCYCLIN-A', 413 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 60 413 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (413 atoms, 60 residues) 54: 54: Identified residue LEU1 as a starting terminus. 54: 54: Identified residue LEU60 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 60 residues with 878 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 880, now 880 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 60 cmap torsion pairs 54: 54: There are 2325 dihedrals, 137 impropers, 1614 angles 54: 2319 pairs, 880 bonds and 0 virtual sites 54: 54: Total mass 5866.087 a.m.u. 54: 54: Total charge 4.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycprotpdb_format_gro_match_file (91 ms) 54: [----------] 4 tests from Cyclic/Pdb2gmxTest (1055 ms total) 54: 54: [----------] Global test environment tear-down 54: [==========] 39 tests from 6 test suites ran. (4641 ms total) 54: [ PASSED ] 39 tests. 54/90 Test #54: Pdb2gmx3Test .............................. Passed 4.68 sec test 55 Start 55: CorrelationsTest 55: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/correlations-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/CorrelationsTest.xml" 55: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/correlationfunctions/tests 55: Test timeout computed to be: 30 55: [==========] Running 21 tests from 3 test suites. 55: [----------] Global test environment set-up. 55: [----------] 10 tests from AutocorrTest 55: [ RUN ] AutocorrTest.EacNormal 55: [ OK ] AutocorrTest.EacNormal (132 ms) 55: [ RUN ] AutocorrTest.EacNoNormalize 55: [ OK ] AutocorrTest.EacNoNormalize (70 ms) 55: [ RUN ] AutocorrTest.EacCos 55: [ OK ] AutocorrTest.EacCos (129 ms) 55: [ RUN ] AutocorrTest.EacVector 55: [ OK ] AutocorrTest.EacVector (230 ms) 55: [ RUN ] AutocorrTest.EacRcross 55: [ OK ] AutocorrTest.EacRcross (1 ms) 55: [ RUN ] AutocorrTest.EacP0 55: [ OK ] AutocorrTest.EacP0 (246 ms) 55: [ RUN ] AutocorrTest.EacP1 55: [ OK ] AutocorrTest.EacP1 (199 ms) 55: [ RUN ] AutocorrTest.EacP2 55: [ OK ] AutocorrTest.EacP2 (411 ms) 55: [ RUN ] AutocorrTest.EacP3 55: [ OK ] AutocorrTest.EacP3 (3 ms) 55: [ RUN ] AutocorrTest.EacP4 55: [ OK ] AutocorrTest.EacP4 (215 ms) 55: [----------] 10 tests from AutocorrTest (1644 ms total) 55: 55: [----------] 10 tests from ExpfitTest 55: [ RUN ] ExpfitTest.EffnEXP1 55: [ OK ] ExpfitTest.EffnEXP1 (0 ms) 55: [ RUN ] ExpfitTest.EffnEXP2 55: [ OK ] ExpfitTest.EffnEXP2 (0 ms) 55: [ RUN ] ExpfitTest.EffnEXPEXP 55: [ OK ] ExpfitTest.EffnEXPEXP (1 ms) 55: [ RUN ] ExpfitTest.EffnEXP5 55: [ OK ] ExpfitTest.EffnEXP5 (8 ms) 55: [ RUN ] ExpfitTest.EffnEXP7 55: [ OK ] ExpfitTest.EffnEXP7 (7 ms) 55: [ RUN ] ExpfitTest.EffnEXP9 55: [ OK ] ExpfitTest.EffnEXP9 (27 ms) 55: [ RUN ] ExpfitTest.EffnERF 55: [ OK ] ExpfitTest.EffnERF (6 ms) 55: [ RUN ] ExpfitTest.EffnERREST 55: [ OK ] ExpfitTest.EffnERREST (2 ms) 55: [ RUN ] ExpfitTest.EffnVAC 55: [ OK ] ExpfitTest.EffnVAC (14 ms) 55: [ RUN ] ExpfitTest.EffnPRES 55: [ OK ] ExpfitTest.EffnPRES (19 ms) 55: [----------] 10 tests from ExpfitTest (91 ms total) 55: 55: [----------] 1 test from ManyAutocorrelationTest 55: [ RUN ] ManyAutocorrelationTest.Empty 55: [ OK ] ManyAutocorrelationTest.Empty (0 ms) 55: [----------] 1 test from ManyAutocorrelationTest (0 ms total) 55: 55: [----------] Global test environment tear-down 55: [==========] 21 tests from 3 test suites ran. (1741 ms total) 55: [ PASSED ] 21 tests. 55/90 Test #55: CorrelationsTest .......................... Passed 1.77 sec test 56 Start 56: AnalysisDataUnitTests 56: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/analysisdata-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/AnalysisDataUnitTests.xml" 56: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/analysisdata/tests 56: Test timeout computed to be: 30 56: [==========] Running 69 tests from 14 test suites. 56: [----------] Global test environment set-up. 56: [----------] 3 tests from AnalysisDataInitializationTest 56: [ RUN ] AnalysisDataInitializationTest.BasicInitialization 56: [ OK ] AnalysisDataInitializationTest.BasicInitialization (0 ms) 56: [ RUN ] AnalysisDataInitializationTest.ChecksMultiColumnModules 56: [ OK ] AnalysisDataInitializationTest.ChecksMultiColumnModules (0 ms) 56: [ RUN ] AnalysisDataInitializationTest.ChecksMultipointModules 56: [ OK ] AnalysisDataInitializationTest.ChecksMultipointModules (0 ms) 56: [----------] 3 tests from AnalysisDataInitializationTest (0 ms total) 56: 56: [----------] 8 tests from AnalysisDataCommonTest/0, where TypeParam = gmx::test::(anonymous namespace)::SimpleInputData 56: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly 56: [ OK ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames 56: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames (2 ms) 56: [ RUN ] AnalysisDataCommonTest/0.FullStorageWorks 56: [ OK ] AnalysisDataCommonTest/0.FullStorageWorks (0 ms) 56: [ RUN ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData 56: [ OK ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData (0 ms) 56: [ RUN ] AnalysisDataCommonTest/0.LimitedStorageWorks 56: [ OK ] AnalysisDataCommonTest/0.LimitedStorageWorks (0 ms) 56: [----------] 8 tests from AnalysisDataCommonTest/0 (3 ms total) 56: 56: [----------] 8 tests from AnalysisDataCommonTest/1, where TypeParam = gmx::test::(anonymous namespace)::DataSetsInputData 56: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly 56: [ OK ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames 56: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 56: [ RUN ] AnalysisDataCommonTest/1.FullStorageWorks 56: [ OK ] AnalysisDataCommonTest/1.FullStorageWorks (0 ms) 56: [ RUN ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData 56: [ OK ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData (0 ms) 56: [ RUN ] AnalysisDataCommonTest/1.LimitedStorageWorks 56: [ OK ] AnalysisDataCommonTest/1.LimitedStorageWorks (0 ms) 56: [----------] 8 tests from AnalysisDataCommonTest/1 (1 ms total) 56: 56: [----------] 8 tests from AnalysisDataCommonTest/2, where TypeParam = gmx::test::(anonymous namespace)::MultipointInputData 56: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly 56: [ OK ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames 56: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 56: [ RUN ] AnalysisDataCommonTest/2.FullStorageWorks 56: [ OK ] AnalysisDataCommonTest/2.FullStorageWorks (0 ms) 56: [ RUN ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData 56: [ OK ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData (0 ms) 56: [ RUN ] AnalysisDataCommonTest/2.LimitedStorageWorks 56: [ OK ] AnalysisDataCommonTest/2.LimitedStorageWorks (0 ms) 56: [----------] 8 tests from AnalysisDataCommonTest/2 (2 ms total) 56: 56: [----------] 8 tests from AnalysisDataCommonTest/3, where TypeParam = gmx::test::(anonymous namespace)::MultipointDataSetsInputData 56: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly 56: [ OK ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly (4 ms) 56: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames 56: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 56: [ RUN ] AnalysisDataCommonTest/3.FullStorageWorks 56: [ OK ] AnalysisDataCommonTest/3.FullStorageWorks (0 ms) 56: [ RUN ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData 56: [ OK ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData (0 ms) 56: [ RUN ] AnalysisDataCommonTest/3.LimitedStorageWorks 56: [ OK ] AnalysisDataCommonTest/3.LimitedStorageWorks (0 ms) 56: [----------] 8 tests from AnalysisDataCommonTest/3 (6 ms total) 56: 56: [----------] 4 tests from AnalysisArrayDataTest 56: [ RUN ] AnalysisArrayDataTest.CallsModuleCorrectly 56: [ OK ] AnalysisArrayDataTest.CallsModuleCorrectly (0 ms) 56: [ RUN ] AnalysisArrayDataTest.StorageWorks 56: [ OK ] AnalysisArrayDataTest.StorageWorks (0 ms) 56: [ RUN ] AnalysisArrayDataTest.CanSetXAxis 56: [ OK ] AnalysisArrayDataTest.CanSetXAxis (0 ms) 56: [ RUN ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount 56: [ OK ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount (0 ms) 56: [----------] 4 tests from AnalysisArrayDataTest (0 ms total) 56: 56: [----------] 6 tests from AverageModuleTest 56: [ RUN ] AverageModuleTest.BasicTest 56: [ OK ] AverageModuleTest.BasicTest (0 ms) 56: [ RUN ] AverageModuleTest.HandlesMultipointData 56: [ OK ] AverageModuleTest.HandlesMultipointData (1 ms) 56: [ RUN ] AverageModuleTest.HandlesMultipleDataSets 56: [ OK ] AverageModuleTest.HandlesMultipleDataSets (0 ms) 56: [ RUN ] AverageModuleTest.HandlesDataSetAveraging 56: [ OK ] AverageModuleTest.HandlesDataSetAveraging (0 ms) 56: [ RUN ] AverageModuleTest.CanCustomizeXAxis 56: [ OK ] AverageModuleTest.CanCustomizeXAxis (0 ms) 56: [ RUN ] AverageModuleTest.CanCustomizeNonUniformXAxis 56: [ OK ] AverageModuleTest.CanCustomizeNonUniformXAxis (0 ms) 56: [----------] 6 tests from AverageModuleTest (4 ms total) 56: 56: [----------] 2 tests from FrameAverageModuleTest 56: [ RUN ] FrameAverageModuleTest.BasicTest 56: [ OK ] FrameAverageModuleTest.BasicTest (0 ms) 56: [ RUN ] FrameAverageModuleTest.HandlesMultipleDataSets 56: [ OK ] FrameAverageModuleTest.HandlesMultipleDataSets (0 ms) 56: [----------] 2 tests from FrameAverageModuleTest (1 ms total) 56: 56: [----------] 7 tests from AnalysisHistogramSettingsTest 56: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBins 56: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBins (0 ms) 56: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins 56: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins (0 ms) 56: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount 56: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount (0 ms) 56: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth 56: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth (0 ms) 56: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins 56: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins (0 ms) 56: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins 56: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins (0 ms) 56: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange 56: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange (0 ms) 56: [----------] 7 tests from AnalysisHistogramSettingsTest (0 ms total) 56: 56: [----------] 2 tests from SimpleHistogramModuleTest 56: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectly 56: [ OK ] SimpleHistogramModuleTest.ComputesCorrectly (0 ms) 56: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll 56: [ OK ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll (3 ms) 56: [----------] 2 tests from SimpleHistogramModuleTest (3 ms total) 56: 56: [----------] 3 tests from WeightedHistogramModuleTest 56: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectly 56: [ OK ] WeightedHistogramModuleTest.ComputesCorrectly (0 ms) 56: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll 56: [ OK ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll (0 ms) 56: [ RUN ] WeightedHistogramModuleTest.HandlesMultipleDataSets 56: [ OK ] WeightedHistogramModuleTest.HandlesMultipleDataSets (0 ms) 56: [----------] 3 tests from WeightedHistogramModuleTest (2 ms total) 56: 56: [----------] 3 tests from BinAverageModuleTest 56: [ RUN ] BinAverageModuleTest.ComputesCorrectly 56: [ OK ] BinAverageModuleTest.ComputesCorrectly (0 ms) 56: [ RUN ] BinAverageModuleTest.ComputesCorrectlyWithAll 56: [ OK ] BinAverageModuleTest.ComputesCorrectlyWithAll (0 ms) 56: [ RUN ] BinAverageModuleTest.HandlesMultipleDataSets 56: [ OK ] BinAverageModuleTest.HandlesMultipleDataSets (0 ms) 56: [----------] 3 tests from BinAverageModuleTest (1 ms total) 56: 56: [----------] 4 tests from AbstractAverageHistogramTest 56: [ RUN ] AbstractAverageHistogramTest.ClonesCorrectly 56: [ OK ] AbstractAverageHistogramTest.ClonesCorrectly (1 ms) 56: [ RUN ] AbstractAverageHistogramTest.ComputesCumulativeHistogram 56: [ OK ] AbstractAverageHistogramTest.ComputesCumulativeHistogram (0 ms) 56: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth 56: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth (0 ms) 56: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins 56: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins (1 ms) 56: [----------] 4 tests from AbstractAverageHistogramTest (3 ms total) 56: 56: [----------] 3 tests from LifetimeModuleTest 56: [ RUN ] LifetimeModuleTest.BasicTest 56: [ OK ] LifetimeModuleTest.BasicTest (0 ms) 56: [ RUN ] LifetimeModuleTest.CumulativeTest 56: [ OK ] LifetimeModuleTest.CumulativeTest (0 ms) 56: [ RUN ] LifetimeModuleTest.HandlesMultipleDataSets 56: [ OK ] LifetimeModuleTest.HandlesMultipleDataSets (1 ms) 56: [----------] 3 tests from LifetimeModuleTest (2 ms total) 56: 56: [----------] Global test environment tear-down 56: [==========] 69 tests from 14 test suites ran. (36 ms total) 56: [ PASSED ] 69 tests. 56/90 Test #56: AnalysisDataUnitTests ..................... Passed 0.06 sec test 57 Start 57: CoordinateIOTests 57: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/coordinateio-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/CoordinateIOTests.xml" 57: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/coordinateio/tests 57: Test timeout computed to be: 30 57: [==========] Running 67 tests from 20 test suites. 57: [----------] Global test environment set-up. 57: [----------] 1 test from OutputSelectorDeathTest 57: [ RUN ] OutputSelectorDeathTest.RejectsBadSelection 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] OutputSelectorDeathTest.RejectsBadSelection (6 ms) 57: [----------] 1 test from OutputSelectorDeathTest (6 ms total) 57: 57: [----------] 5 tests from TrajectoryFrameWriterTest 57: [ RUN ] TrajectoryFrameWriterTest.RejectsWrongFiletype 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] TrajectoryFrameWriterTest.RejectsWrongFiletype (2 ms) 57: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms (2 ms) 57: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms (2 ms) 57: [ RUN ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms (4 ms) 57: [ RUN ] TrajectoryFrameWriterTest.TNGOutputWorks 57: [ OK ] TrajectoryFrameWriterTest.TNGOutputWorks (0 ms) 57: [----------] 5 tests from TrajectoryFrameWriterTest (10 ms total) 57: 57: [----------] 5 tests from OutputAdapterContainer 57: [ RUN ] OutputAdapterContainer.MakeEmpty 57: [ OK ] OutputAdapterContainer.MakeEmpty (0 ms) 57: [ RUN ] OutputAdapterContainer.AddAdapter 57: [ OK ] OutputAdapterContainer.AddAdapter (0 ms) 57: [ RUN ] OutputAdapterContainer.RejectBadAdapter 57: [ OK ] OutputAdapterContainer.RejectBadAdapter (0 ms) 57: [ RUN ] OutputAdapterContainer.RejectDuplicateAdapter 57: [ OK ] OutputAdapterContainer.RejectDuplicateAdapter (0 ms) 57: [ RUN ] OutputAdapterContainer.AcceptMultipleAdapters 57: [ OK ] OutputAdapterContainer.AcceptMultipleAdapters (0 ms) 57: [----------] 5 tests from OutputAdapterContainer (0 ms total) 57: 57: [----------] 3 tests from RegisterFrameConverterTest 57: [ RUN ] RegisterFrameConverterTest.NoConverterWorks 57: [ OK ] RegisterFrameConverterTest.NoConverterWorks (0 ms) 57: [ RUN ] RegisterFrameConverterTest.RegistrationWorks 57: [ OK ] RegisterFrameConverterTest.RegistrationWorks (0 ms) 57: [ RUN ] RegisterFrameConverterTest.NewConverterCanInvalidateGuarantees 57: [ OK ] RegisterFrameConverterTest.NewConverterCanInvalidateGuarantees (0 ms) 57: [----------] 3 tests from RegisterFrameConverterTest (0 ms total) 57: 57: [----------] 5 tests from FlagTest 57: [ RUN ] FlagTest.CanSetSimpleFlag 57: [ OK ] FlagTest.CanSetSimpleFlag (0 ms) 57: [ RUN ] FlagTest.CanAddNewBox 57: [ OK ] FlagTest.CanAddNewBox (0 ms) 57: [ RUN ] FlagTest.SetsImplicitPrecisionChange 57: [ OK ] FlagTest.SetsImplicitPrecisionChange (0 ms) 57: [ RUN ] FlagTest.SetsImplicitStartTimeChange 57: [ OK ] FlagTest.SetsImplicitStartTimeChange (0 ms) 57: [ RUN ] FlagTest.SetsImplicitTimeStepChange 57: [ OK ] FlagTest.SetsImplicitTimeStepChange (0 ms) 57: [----------] 5 tests from FlagTest (1 ms total) 57: 57: [----------] 5 tests from SetAtomsTest 57: [ RUN ] SetAtomsTest.RemovesExistingAtoms 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] SetAtomsTest.RemovesExistingAtoms (2 ms) 57: [ RUN ] SetAtomsTest.AddsNewAtoms 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] SetAtomsTest.AddsNewAtoms (4 ms) 57: [ RUN ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable (2 ms) 57: [ RUN ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable (2 ms) 57: [ RUN ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible (2 ms) 57: [----------] 5 tests from SetAtomsTest (14 ms total) 57: 57: [----------] 2 tests from SetBothTimeTest 57: [ RUN ] SetBothTimeTest.StartTimeZeroWorks 57: [ OK ] SetBothTimeTest.StartTimeZeroWorks (0 ms) 57: [ RUN ] SetBothTimeTest.SetStartTimeNonZeroWorks 57: [ OK ] SetBothTimeTest.SetStartTimeNonZeroWorks (0 ms) 57: [----------] 2 tests from SetBothTimeTest (0 ms total) 57: 57: [----------] 2 tests from SetStartTimeTest 57: [ RUN ] SetStartTimeTest.WorksWithNonZeroStart 57: [ OK ] SetStartTimeTest.WorksWithNonZeroStart (0 ms) 57: [ RUN ] SetStartTimeTest.WorksWithZeroStart 57: [ OK ] SetStartTimeTest.WorksWithZeroStart (0 ms) 57: [----------] 2 tests from SetStartTimeTest (0 ms total) 57: 57: [----------] 1 test from SetTimeStepTest 57: [ RUN ] SetTimeStepTest.SetTimeStepWorks 57: [ OK ] SetTimeStepTest.SetTimeStepWorks (0 ms) 57: [----------] 1 test from SetTimeStepTest (0 ms total) 57: 57: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest 57: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 (2 ms) 57: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 (2 ms) 57: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 (1 ms) 57: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 (2 ms) 57: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 (2 ms) 57: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 (1 ms) 57: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest (12 ms total) 57: 57: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles 57: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/0 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/0 (2 ms) 57: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/1 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/1 (2 ms) 57: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/2 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/2 (2 ms) 57: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles (6 ms total) 57: 57: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles 57: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 57: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 (0 ms) 57: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 57: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 (0 ms) 57: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 57: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 (0 ms) 57: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles (0 ms total) 57: 57: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles 57: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/0 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/0 (4 ms) 57: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/1 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/1 (3 ms) 57: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/2 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/2 (3 ms) 57: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/3 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/3 (4 ms) 57: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles (16 ms total) 57: 57: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles 57: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/0 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/0 (1 ms) 57: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/1 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/1 (1 ms) 57: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/2 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/2 (1 ms) 57: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles (5 ms total) 57: 57: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles 57: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 57: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 (0 ms) 57: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 57: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 (0 ms) 57: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 57: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 (0 ms) 57: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles (0 ms total) 57: 57: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles 57: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/0 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/0 (1 ms) 57: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/1 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/1 (1 ms) 57: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles (3 ms total) 57: 57: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles 57: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 57: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 (0 ms) 57: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 57: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 (0 ms) 57: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 57: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 (0 ms) 57: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 57: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 (0 ms) 57: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles (0 ms total) 57: 57: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles 57: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 (2 ms) 57: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 (1 ms) 57: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles (3 ms total) 57: 57: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles 57: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 57: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 (0 ms) 57: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 57: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 (0 ms) 57: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 57: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 (0 ms) 57: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 57: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 (0 ms) 57: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles (0 ms total) 57: 57: [----------] 4 tests from ModuleSupported/NoOptionalOutput 57: [ RUN ] ModuleSupported/NoOptionalOutput.Works/0 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/NoOptionalOutput.Works/0 (2 ms) 57: [ RUN ] ModuleSupported/NoOptionalOutput.Works/1 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/NoOptionalOutput.Works/1 (1 ms) 57: [ RUN ] ModuleSupported/NoOptionalOutput.Works/2 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/NoOptionalOutput.Works/2 (1 ms) 57: [ RUN ] ModuleSupported/NoOptionalOutput.Works/3 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/NoOptionalOutput.Works/3 (1 ms) 57: [----------] 4 tests from ModuleSupported/NoOptionalOutput (7 ms total) 57: 57: [----------] Global test environment tear-down 57: [==========] 67 tests from 20 test suites ran. (91 ms total) 57: [ PASSED ] 67 tests. 57/90 Test #57: CoordinateIOTests ......................... Passed 0.11 sec test 58 Start 58: TrajectoryAnalysisUnitTests 58: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/trajectoryanalysis-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/TrajectoryAnalysisUnitTests.xml" 58: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests 58: Test timeout computed to be: 1920 58: [==========] Running 393 tests from 21 test suites. 58: [----------] Global test environment set-up. 58: [----------] 11 tests from AngleModuleTest 58: [ RUN ] AngleModuleTest.ComputesSimpleAngles 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.ComputesSimpleAngles (4 ms) 58: [ RUN ] AngleModuleTest.ComputesDihedrals 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.ComputesDihedrals (2 ms) 58: [ RUN ] AngleModuleTest.ComputesVectorPairAngles 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.ComputesVectorPairAngles (2 ms) 58: [ RUN ] AngleModuleTest.ComputesVectorPlanePairAngles 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.ComputesVectorPlanePairAngles (2 ms) 58: [ RUN ] AngleModuleTest.ComputesPlaneZAxisAngles 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.ComputesPlaneZAxisAngles (1 ms) 58: [ RUN ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles (2 ms) 58: [ RUN ] AngleModuleTest.ComputesVectorTimeZeroAngles 58: Reading frames from gro file 'Test system for different angles', 33 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.ComputesVectorTimeZeroAngles (2 ms) 58: [ RUN ] AngleModuleTest.ComputesMultipleAngles 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.ComputesMultipleAngles (2 ms) 58: [ RUN ] AngleModuleTest.HandlesDynamicSelections 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.HandlesDynamicSelections (1 ms) 58: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorAngles 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorAngles (1 ms) 58: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles (2 ms) 58: [----------] 11 tests from AngleModuleTest (25 ms total) 58: 58: [----------] 5 tests from ClustsizeTest 58: [ RUN ] ClustsizeTest.NoMolDefaultCutoff 58: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 58: There is one group in the index 58: '', 24 atoms 58: Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Total number of atoms in clusters = 24 58: cmid: 2, cmax: 4, max_size: 6 58: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 58: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolDefaultCutoff (2 ms) 58: [ RUN ] ClustsizeTest.NoMolShortCutoff 58: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 58: There is one group in the index 58: '', 24 atoms 58: Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Total number of atoms in clusters = 24 58: cmid: 1, cmax: 6, max_size: 6 58: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 58: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolShortCutoff (2 ms) 58: [ RUN ] ClustsizeTest.MolDefaultCutoff 58: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 58: '', 24 atoms 58: Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Total number of atoms in clusters = 8 58: cmid: 2, cmax: 4, max_size: 2 58: 50%100%cmid: 2, cmax: 6, max_size: 2 58: 50%100%[ OK ] ClustsizeTest.MolDefaultCutoff (2 ms) 58: [ RUN ] ClustsizeTest.MolShortCutoff 58: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 58: '', 24 atoms 58: Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Total number of atoms in clusters = 8 58: cmid: 1, cmax: 6, max_size: 2 58: 50%100%cmid: 2, cmax: 6, max_size: 2 58: 50%100%[ OK ] ClustsizeTest.MolShortCutoff (3 ms) 58: [ RUN ] ClustsizeTest.MolCSize 58: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 58: '', 24 atoms 58: Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Total number of atoms in clusters = 8 58: cmid: 2, cmax: 4, max_size: 2 58: 50%100%cmid: 2, cmax: 6, max_size: 2 58: 50%100%[ OK ] ClustsizeTest.MolCSize (2 ms) 58: [----------] 5 tests from ClustsizeTest (12 ms total) 58: 58: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest 58: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp 58: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp (0 ms) 58: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory 58: Reading frames from gro file 'Test system', 8 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory (2 ms) 58: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset 58: Reading frames from gro file 'Test system', 8 atoms. 58: Reading frame 0 time 0.000 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset (2 ms) 58: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory 58: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory (0 ms) 58: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest (5 ms total) 58: 58: [----------] 4 tests from ConvertTrjModuleTest 58: [ RUN ] ConvertTrjModuleTest.WritesNormalOutput 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 58: Reading frame 0 time 0.000 Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: [ OK ] ConvertTrjModuleTest.WritesNormalOutput (9 ms) 58: [ RUN ] ConvertTrjModuleTest.WritesAtomSubset 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 58: Reading frame 0 time 0.000 Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: [ OK ] ConvertTrjModuleTest.WritesAtomSubset (9 ms) 58: [ RUN ] ConvertTrjModuleTest.WorksWithAtomAdding 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms 58: Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: [ OK ] ConvertTrjModuleTest.WorksWithAtomAdding (2 ms) 58: [ RUN ] ConvertTrjModuleTest.WorksWithAtomsAndSelection 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms 58: Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: [ OK ] ConvertTrjModuleTest.WorksWithAtomsAndSelection (3 ms) 58: [----------] 4 tests from ConvertTrjModuleTest (24 ms total) 58: 58: [----------] 6 tests from DistanceModuleTest 58: [ RUN ] DistanceModuleTest.ComputesDistances 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: atomname S1 S2: 58: Number of samples: 5 58: Average distance: 1.43246 nm 58: Standard deviation: 0.96700 nm 58: [ OK ] DistanceModuleTest.ComputesDistances (2 ms) 58: [ RUN ] DistanceModuleTest.ComputesMultipleDistances 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: atomname S1 S2: 58: Number of samples: 5 58: Average distance: 1.43246 nm 58: Standard deviation: 0.96700 nm 58: resindex 1 to 4 and atomname CB merge resindex 2 to 5 and atomname CB: 58: Number of samples: 4 58: Average distance: 1.81066 nm 58: Standard deviation: 0.79289 nm 58: [ OK ] DistanceModuleTest.ComputesMultipleDistances (2 ms) 58: [ RUN ] DistanceModuleTest.HandlesDynamicSelections 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: atomname S1 S2 and res_cog x < 2.8: 58: Number of samples: 3 58: Average distance: 1.72076 nm 58: Standard deviation: 1.24839 nm 58: [ OK ] DistanceModuleTest.HandlesDynamicSelections (2 ms) 58: [ RUN ] DistanceModuleTest.HandlesSelectionFromGroup 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: Contacts: 58: Number of samples: 2 58: Average distance: 1.00000 nm 58: Standard deviation: 0.00000 nm 58: [ OK ] DistanceModuleTest.HandlesSelectionFromGroup (6 ms) 58: [ RUN ] DistanceModuleTest.HandlesSelectionFromGroupWithSuccessiveIndices 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: SuccessiveContacts: 58: Number of samples: 2 58: Average distance: 1.00000 nm 58: Standard deviation: 0.00000 nm 58: [ OK ] DistanceModuleTest.HandlesSelectionFromGroupWithSuccessiveIndices (6 ms) 58: [ RUN ] DistanceModuleTest.HandlesSelectionFromLargeGroup 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: ManyContacts: 58: Number of samples: 10 58: Average distance: 1.82913 nm 58: Standard deviation: 0.78478 nm 58: [ OK ] DistanceModuleTest.HandlesSelectionFromLargeGroup (7 ms) 58: [----------] 6 tests from DistanceModuleTest (30 ms total) 58: 58: [----------] 2 tests from ExtractClusterModuleTest 58: [ RUN ] ExtractClusterModuleTest.WorksWithAllAtoms 58: trr version: GMX_trn_file (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 58: Analyzed 26 frames, last time 0.050 58: There are 8 clusters containing 26 structures, highest framenr is 25 58: [ OK ] ExtractClusterModuleTest.WorksWithAllAtoms (2 ms) 58: [ RUN ] ExtractClusterModuleTest.WorksWithAtomSubset 58: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 58: Analyzed 26 frames, last time 0.050 58: There are 8 clusters containing 26 structures, highest framenr is 25 58: [ OK ] ExtractClusterModuleTest.WorksWithAtomSubset (2 ms) 58: [----------] 2 tests from ExtractClusterModuleTest (5 ms total) 58: 58: [----------] 2 tests from FreeVolumeModuleTest 58: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolume 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 58: from the source below. This means the results may be different 58: compared to previous GROMACS versions. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. (1964) 58: DOI: 10.1021/j100785a001 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Could not determine VDW radius for CO2-RM. Set to zero. 58: Could not determine VDW radius for CO2-RM. Set to zero. 58: Could not determine VDW radius for CO2-RM. Set to zero. 58: Could not determine VDW radius for CO2-RM. Set to zero. 58: Could not determine VDW radius for CO2-RM. Set to zero. 58: Could not determine VDW radius for CO2-RM. Set to zero. 58: Could not determine VDW radius for CO2-RM. Set to zero. 58: Could not determine VDW radius for CO2-RM. Set to zero. 58: Could not determine VDW radius for CO2-RM. Set to zero. 58: Could not determine VDW radius for 40 particles. These were set to zero. 58: Reading frame 0 time 0.000 Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: cutoff = 0.18 nm 58: probe_radius = 0 nm 58: seed = 13 58: ninsert = 1000 probes per nm^3 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. (1964) 58: DOI: 10.1021/j100785a001 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: Tuanan C. Lourenco, Mariny F. C. Coelho, Teodorico C. Ramalho, David van der 58: Spoel, Luciano T. Costa 58: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 58: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 58: Environ. Sci. Technol. (2013) 58: DOI: 10.1021/es4020986 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Free volume 38.02 +/- 0.00 % 58: Total volume 68.92 +/- 0.00 nm^3 58: Number of molecules 340 total mass 63491.38 Dalton 58: Average molar mass: 186.74 Dalton 58: Density rho: 1529.71 +/- 0.00 nm^3 58: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 58: Molecular van der Waals volume assuming homogeneity: 0.1256 +/- 0.0000 nm^3 58: Fractional free volume 0.194 +/- 0.000 58: [ OK ] FreeVolumeModuleTest.ComputesFreeVolume (79 ms) 58: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolumeSelection 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 58: from the source below. This means the results may be different 58: compared to previous GROMACS versions. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. (1964) 58: DOI: 10.1021/j100785a001 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Reading frame 0 time 0.000 Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: cutoff = 0.18 nm 58: probe_radius = 0 nm 58: seed = 17 58: ninsert = 1000 probes per nm^3 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. (1964) 58: DOI: 10.1021/j100785a001 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: Tuanan C. Lourenco, Mariny F. C. Coelho, Teodorico C. Ramalho, David van der 58: Spoel, Luciano T. Costa 58: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 58: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 58: Environ. Sci. Technol. (2013) 58: DOI: 10.1021/es4020986 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Free volume 38.48 +/- 0.00 % 58: Total volume 68.92 +/- 0.00 nm^3 58: Number of molecules 340 total mass 63491.38 Dalton 58: Average molar mass: 186.74 Dalton 58: Density rho: 1529.71 +/- 0.00 nm^3 58: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 58: Molecular van der Waals volume assuming homogeneity: 0.1247 +/- 0.0000 nm^3 58: Fractional free volume 0.200 +/- 0.000 58: [ OK ] FreeVolumeModuleTest.ComputesFreeVolumeSelection (83 ms) 58: [----------] 2 tests from FreeVolumeModuleTest (163 ms total) 58: 58: [----------] 13 tests from MsdModuleTest 58: [ RUN ] MsdModuleTest.threeDimensionalDiffusion 58: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 58: Analyzed 10 frames, last time 9.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] MsdModuleTest.threeDimensionalDiffusion (3 ms) 58: [ RUN ] MsdModuleTest.twoDimensionalDiffusion 58: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 58: Analyzed 10 frames, last time 9.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] MsdModuleTest.twoDimensionalDiffusion (2 ms) 58: [ RUN ] MsdModuleTest.oneDimensionalDiffusion 58: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 58: Analyzed 10 frames, last time 9.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] MsdModuleTest.oneDimensionalDiffusion (2 ms) 58: [ RUN ] MsdModuleTest.oneDimensionalDiffusionWithMaxTau 58: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 58: Analyzed 10 frames, last time 9.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] MsdModuleTest.oneDimensionalDiffusionWithMaxTau (4 ms) 58: [ RUN ] MsdModuleTest.multipleGroupsWork 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 58: For energy conservation with LINCS, lincs_iter should be 2 or larger. 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 1818.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 58: NVE simulation: will use the initial temperature of 288.764 K for 58: determining the Verlet buffer size 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 58: There are 9 non-linear virtual site constructions. Their contribution to 58: the energy error is approximated. In most cases this does not affect the 58: error significantly. 58: 58: 58: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 5 NOTEs 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 2.000 58: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 58: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 58: Analyzed 21 frames, last time 40.000 58: Setting the LD random seed to -33571475 58: 58: Generated 2145 of the 2145 non-bonded parameter combinations 58: 58: Generated 2145 of the 2145 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 58: 58: Cleaning up constraints and constant bonded interactions with virtual sites 58: 58: Converted 15 Bonds with virtual sites to connections, 7 left 58: 58: Removed 18 Angles with virtual sites, 21 left 58: 58: Removed 10 Proper Dih.s with virtual sites, 44 left 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 58: 58: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: [ OK ] MsdModuleTest.multipleGroupsWork (32 ms) 58: [ RUN ] MsdModuleTest.subPicosecondTrajectoryWorks 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 58: For energy conservation with LINCS, lincs_iter should be 2 or larger. 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 1818.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 58: NVE simulation: will use the initial temperature of 288.764 K for 58: determining the Verlet buffer size 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 58: There are 9 non-linear virtual site constructions. Their contribution to 58: the energy error is approximated. In most cases this does not affect the 58: error significantly. 58: 58: 58: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 5 NOTEs 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 0.100 58: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 58: Reading frame 2 time 0.200 Reading frame 3 time 0.300 Reading frame 4 time 0.400 Reading frame 5 time 0.500 Reading frame 6 time 0.600 Reading frame 7 time 0.700 Reading frame 8 time 0.800 Reading frame 9 time 0.900 Reading frame 10 time 1.000 Reading frame 11 time 1.100 Reading frame 12 time 1.200 Reading frame 13 time 1.300 Reading frame 14 time 1.400 Reading frame 15 time 1.500 Reading frame 16 time 1.600 Reading frame 17 time 1.700 Reading frame 18 time 1.800 Reading frame 19 time 1.900 Reading frame 20 time 2.000 Last frame 20 time 2.000 58: Analyzed 21 frames, last time 2.000 58: Setting the LD random seed to -1084491778 58: 58: Generated 2145 of the 2145 non-bonded parameter combinations 58: 58: Generated 2145 of the 2145 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 58: 58: Cleaning up constraints and constant bonded interactions with virtual sites 58: 58: Converted 15 Bonds with virtual sites to connections, 7 left 58: 58: Removed 18 Angles with virtual sites, 21 left 58: 58: Removed 10 Proper Dih.s with virtual sites, 44 left 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 58: 58: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: [ OK ] MsdModuleTest.subPicosecondTrajectoryWorks (32 ms) 58: [ RUN ] MsdModuleTest.trestartLessThanDt 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 58: For energy conservation with LINCS, lincs_iter should be 2 or larger. 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 1818.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 58: NVE simulation: will use the initial temperature of 288.764 K for 58: determining the Verlet buffer size 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 58: There are 9 non-linear virtual site constructions. Their contribution to 58: the energy error is approximated. In most cases this does not affect the 58: error significantly. 58: 58: 58: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 5 NOTEs 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Setting the LD random seed to -134611970 58: 58: Generated 2145 of the 2145 non-bonded parameter combinations 58: 58: Generated 2145 of the 2145 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 58: 58: Cleaning up constraints and constant bonded interactions with virtual sites 58: 58: Converted 15 Bonds with virtual sites to connections, 7 left 58: 58: Removed 18 Angles with virtual sites, 21 left 58: 58: Removed 10 Proper Dih.s with virtual sites, 44 left 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 58: 58: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: [ OK ] MsdModuleTest.trestartLessThanDt (28 ms) 58: [ RUN ] MsdModuleTest.trestartGreaterThanDt 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 58: For energy conservation with LINCS, lincs_iter should be 2 or larger. 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 1818.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 58: NVE simulation: will use the initial temperature of 288.764 K for 58: determining the Verlet buffer size 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 58: There are 9 non-linear virtual site constructions. Their contribution to 58: the energy error is approximated. In most cases this does not affect the 58: error significantly. 58: 58: 58: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 5 NOTEs 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 58: Analyzed 21 frames, last time 40.000 58: Setting the LD random seed to -815301450 58: 58: Generated 2145 of the 2145 non-bonded parameter combinations 58: 58: Generated 2145 of the 2145 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 58: 58: Cleaning up constraints and constant bonded interactions with virtual sites 58: 58: Converted 15 Bonds with virtual sites to connections, 7 left 58: 58: Removed 18 Angles with virtual sites, 21 left 58: 58: Removed 10 Proper Dih.s with virtual sites, 44 left 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 58: 58: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: [ OK ] MsdModuleTest.trestartGreaterThanDt (32 ms) 58: [ RUN ] MsdModuleTest.trestartGreaterThanDtAndNotAMultipleOfDt 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 58: For energy conservation with LINCS, lincs_iter should be 2 or larger. 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 1818.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 58: NVE simulation: will use the initial temperature of 288.764 K for 58: determining the Verlet buffer size 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 58: There are 9 non-linear virtual site constructions. Their contribution to 58: the energy error is approximated. In most cases this does not affect the 58: error significantly. 58: 58: 58: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 5 NOTEs 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Setting the LD random seed to -17665583 58: 58: Generated 2145 of the 2145 non-bonded parameter combinations 58: 58: Generated 2145 of the 2145 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 58: 58: Cleaning up constraints and constant bonded interactions with virtual sites 58: 58: Converted 15 Bonds with virtual sites to connections, 7 left 58: 58: Removed 18 Angles with virtual sites, 21 left 58: 58: Removed 10 Proper Dih.s with virtual sites, 44 left 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 58: 58: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: [ OK ] MsdModuleTest.trestartGreaterThanDtAndNotAMultipleOfDt (29 ms) 58: [ RUN ] MsdModuleTest.molTest 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 58: For energy conservation with LINCS, lincs_iter should be 2 or larger. 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 1818.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 58: NVE simulation: will use the initial temperature of 288.764 K for 58: determining the Verlet buffer size 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 58: There are 9 non-linear virtual site constructions. Their contribution to 58: the energy error is approximated. In most cases this does not affect the 58: error significantly. 58: 58: 58: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 5 NOTEs 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 58: Analyzed 21 frames, last time 40.000 58: Setting the LD random seed to -26503298 58: 58: Generated 2145 of the 2145 non-bonded parameter combinations 58: 58: Generated 2145 of the 2145 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 58: 58: Cleaning up constraints and constant bonded interactions with virtual sites 58: 58: Converted 15 Bonds with virtual sites to connections, 7 left 58: 58: Removed 18 Angles with virtual sites, 21 left 58: 58: Removed 10 Proper Dih.s with virtual sites, 44 left 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 58: 58: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: [ OK ] MsdModuleTest.molTest (38 ms) 58: [ RUN ] MsdModuleTest.beginFit 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 58: For energy conservation with LINCS, lincs_iter should be 2 or larger. 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 1818.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 58: NVE simulation: will use the initial temperature of 288.764 K for 58: determining the Verlet buffer size 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 58: There are 9 non-linear virtual site constructions. Their contribution to 58: the energy error is approximated. In most cases this does not affect the 58: error significantly. 58: 58: 58: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 5 NOTEs 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 2.000 58: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 58: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 58: Analyzed 21 frames, last time 40.000 58: Setting the LD random seed to -322451393 58: 58: Generated 2145 of the 2145 non-bonded parameter combinations 58: 58: Generated 2145 of the 2145 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 58: 58: Cleaning up constraints and constant bonded interactions with virtual sites 58: 58: Converted 15 Bonds with virtual sites to connections, 7 left 58: 58: Removed 18 Angles with virtual sites, 21 left 58: 58: Removed 10 Proper Dih.s with virtual sites, 44 left 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 58: 58: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: [ OK ] MsdModuleTest.beginFit (29 ms) 58: [ RUN ] MsdModuleTest.endFit 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 58: For energy conservation with LINCS, lincs_iter should be 2 or larger. 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 1818.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 58: NVE simulation: will use the initial temperature of 288.764 K for 58: determining the Verlet buffer size 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 58: There are 9 non-linear virtual site constructions. Their contribution to 58: the energy error is approximated. In most cases this does not affect the 58: error significantly. 58: 58: 58: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 5 NOTEs 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 2.000 58: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 58: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 58: Analyzed 21 frames, last time 40.000 58: Setting the LD random seed to -715148289 58: 58: Generated 2145 of the 2145 non-bonded parameter combinations 58: 58: Generated 2145 of the 2145 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 58: 58: Cleaning up constraints and constant bonded interactions with virtual sites 58: 58: Converted 15 Bonds with virtual sites to connections, 7 left 58: 58: Removed 18 Angles with virtual sites, 21 left 58: 58: Removed 10 Proper Dih.s with virtual sites, 44 left 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 58: 58: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: [ OK ] MsdModuleTest.endFit (28 ms) 58: [ RUN ] MsdModuleTest.notEnoughPointsForFitErrorEstimate 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 58: For energy conservation with LINCS, lincs_iter should be 2 or larger. 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 1818.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 58: NVE simulation: will use the initial temperature of 288.764 K for 58: determining the Verlet buffer size 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 58: There are 9 non-linear virtual site constructions. Their contribution to 58: the energy error is approximated. In most cases this does not affect the 58: error significantly. 58: 58: 58: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 5 NOTEs 58: NOTE: You provided an index file 58: /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_solvated.ndx 58: (with -n), but it was not used by any selection. 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 2.000 58: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 58: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 58: Analyzed 21 frames, last time 40.000 58: Setting the LD random seed to -25186597 58: 58: Generated 2145 of the 2145 non-bonded parameter combinations 58: 58: Generated 2145 of the 2145 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 58: 58: Cleaning up constraints and constant bonded interactions with virtual sites 58: 58: Converted 15 Bonds with virtual sites to connections, 7 left 58: 58: Removed 18 Angles with virtual sites, 21 left 58: 58: Removed 10 Proper Dih.s with virtual sites, 44 left 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 58: 58: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: [ OK ] MsdModuleTest.notEnoughPointsForFitErrorEstimate (30 ms) 58: [----------] 13 tests from MsdModuleTest (296 ms total) 58: 58: [----------] 9 tests from PairDistanceModuleTest 58: [ RUN ] PairDistanceModuleTest.ComputesAllDistances 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] PairDistanceModuleTest.ComputesAllDistances (2 ms) 58: [ RUN ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff (1 ms) 58: [ RUN ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff (2 ms) 58: [ RUN ] PairDistanceModuleTest.ComputesMaxDistance 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] PairDistanceModuleTest.ComputesMaxDistance (2 ms) 58: [ RUN ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff (1 ms) 58: [ RUN ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff (2 ms) 58: [ RUN ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff (2 ms) 58: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten (1 ms) 58: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup (1 ms) 58: [----------] 9 tests from PairDistanceModuleTest (18 ms total) 58: 58: [----------] 5 tests from RdfModuleTest 58: [ RUN ] RdfModuleTest.BasicTest 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] RdfModuleTest.BasicTest (21 ms) 58: [ RUN ] RdfModuleTest.SelectionsSolelyFromIndexFileWork 58: Reading frames from gro file '216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984', 648 atoms. 58: Reading frame 0 time 0.000 Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: [ OK ] RdfModuleTest.SelectionsSolelyFromIndexFileWork (17 ms) 58: [ RUN ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork (19 ms) 58: [ RUN ] RdfModuleTest.CalculatesSurf 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] RdfModuleTest.CalculatesSurf (9 ms) 58: [ RUN ] RdfModuleTest.CalculatesXY 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] RdfModuleTest.CalculatesXY (22 ms) 58: [----------] 5 tests from RdfModuleTest (90 ms total) 58: 58: [----------] 5 tests from SasaModuleTest 58: [ RUN ] SasaModuleTest.BasicTest 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 58: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 58: of Surface Area and Volume and to Dot Surface Contouring of Molecular 58: Assemblies 58: J. Comp. Chem. (1995) 58: DOI: 10.1002/jcc.540160303 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 58: from the source below. This means the results may be different 58: compared to previous GROMACS versions. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. (1964) 58: DOI: 10.1021/j100785a001 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Analyzed topology coordinates 58: [ OK ] SasaModuleTest.BasicTest (12 ms) 58: [ RUN ] SasaModuleTest.HandlesSelectedResidues 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 58: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 58: of Surface Area and Volume and to Dot Surface Contouring of Molecular 58: Assemblies 58: J. Comp. Chem. (1995) 58: DOI: 10.1002/jcc.540160303 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 58: from the source below. This means the results may be different 58: compared to previous GROMACS versions. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. (1964) 58: DOI: 10.1021/j100785a001 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Analyzed topology coordinates 58: [ OK ] SasaModuleTest.HandlesSelectedResidues (5 ms) 58: [ RUN ] SasaModuleTest.WritesConnollySurfaceWithSolute 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 58: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 58: of Surface Area and Volume and to Dot Surface Contouring of Molecular 58: Assemblies 58: J. Comp. Chem. (1995) 58: DOI: 10.1002/jcc.540160303 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 58: from the source below. This means the results may be different 58: compared to previous GROMACS versions. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. (1964) 58: DOI: 10.1021/j100785a001 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Analyzed topology coordinates 58: [ OK ] SasaModuleTest.WritesConnollySurfaceWithSolute (4 ms) 58: [ RUN ] SasaModuleTest.HandlesDynamicOutputGroup 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 58: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 58: of Surface Area and Volume and to Dot Surface Contouring of Molecular 58: Assemblies 58: J. Comp. Chem. (1995) 58: DOI: 10.1002/jcc.540160303 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 58: from the source below. This means the results may be different 58: compared to previous GROMACS versions. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. (1964) 58: DOI: 10.1021/j100785a001 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Analyzed topology coordinates 58: [ OK ] SasaModuleTest.HandlesDynamicOutputGroup (6 ms) 58: [ RUN ] SasaModuleTest.HandlesDynamicCalculationGroup 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 58: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 58: of Surface Area and Volume and to Dot Surface Contouring of Molecular 58: Assemblies 58: J. Comp. Chem. (1995) 58: DOI: 10.1002/jcc.540160303 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 58: from the source below. This means the results may be different 58: compared to previous GROMACS versions. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. (1964) 58: DOI: 10.1021/j100785a001 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Analyzed topology coordinates 58: [ OK ] SasaModuleTest.HandlesDynamicCalculationGroup (6 ms) 58: [----------] 5 tests from SasaModuleTest (37 ms total) 58: 58: [----------] 8 tests from SelectModuleTest 58: [ RUN ] SelectModuleTest.BasicTest 58: Reading frames from gro file 'Test system', 15 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] SelectModuleTest.BasicTest (5 ms) 58: [ RUN ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput 58: Reading frames from gro file 'Test system', 15 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput (2 ms) 58: [ RUN ] SelectModuleTest.HandlesPDBOutputWithPDBInput 58: Reading frames from gro file 'Test system', 15 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] SelectModuleTest.HandlesPDBOutputWithPDBInput (2 ms) 58: [ RUN ] SelectModuleTest.HandlesMaxPDBOutput 58: Reading frames from gro file 'Test system', 15 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] SelectModuleTest.HandlesMaxPDBOutput (2 ms) 58: [ RUN ] SelectModuleTest.HandlesSelectedPDBOutput 58: Reading frames from gro file 'Test system', 15 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] SelectModuleTest.HandlesSelectedPDBOutput (2 ms) 58: [ RUN ] SelectModuleTest.NormalizesSizes 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] SelectModuleTest.NormalizesSizes (1 ms) 58: [ RUN ] SelectModuleTest.WritesResidueNumbers 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] SelectModuleTest.WritesResidueNumbers (1 ms) 58: [ RUN ] SelectModuleTest.WritesResidueIndices 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] SelectModuleTest.WritesResidueIndices (1 ms) 58: [----------] 8 tests from SelectModuleTest (22 ms total) 58: 58: [----------] 10 tests from SurfaceAreaTest 58: [ RUN ] SurfaceAreaTest.ComputesSinglePoint 58: [ OK ] SurfaceAreaTest.ComputesSinglePoint (0 ms) 58: [ RUN ] SurfaceAreaTest.ComputesTwoPoints 58: [ OK ] SurfaceAreaTest.ComputesTwoPoints (0 ms) 58: [ RUN ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius 58: [ OK ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius (1 ms) 58: [ RUN ] SurfaceAreaTest.SurfacePoints12 58: [ OK ] SurfaceAreaTest.SurfacePoints12 (0 ms) 58: [ RUN ] SurfaceAreaTest.SurfacePoints32 58: [ OK ] SurfaceAreaTest.SurfacePoints32 (0 ms) 58: [ RUN ] SurfaceAreaTest.SurfacePoints42 58: [ OK ] SurfaceAreaTest.SurfacePoints42 (0 ms) 58: [ RUN ] SurfaceAreaTest.SurfacePoints122 58: [ OK ] SurfaceAreaTest.SurfacePoints122 (0 ms) 58: [ RUN ] SurfaceAreaTest.Computes100Points 58: [ OK ] SurfaceAreaTest.Computes100Points (0 ms) 58: [ RUN ] SurfaceAreaTest.Computes100PointsWithRectangularPBC 58: [ OK ] SurfaceAreaTest.Computes100PointsWithRectangularPBC (2 ms) 58: [ RUN ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC 58: [ OK ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC (4 ms) 58: [----------] 10 tests from SurfaceAreaTest (11 ms total) 58: 58: [----------] 4 tests from TopologyInformation 58: [ RUN ] TopologyInformation.CantWorkWithoutReadingAFile 58: [ OK ] TopologyInformation.CantWorkWithoutReadingAFile (0 ms) 58: [ RUN ] TopologyInformation.WorksWithGroFile 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] TopologyInformation.WorksWithGroFile (1 ms) 58: [ RUN ] TopologyInformation.WorksWithPdbFile 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] TopologyInformation.WorksWithPdbFile (2 ms) 58: [ RUN ] TopologyInformation.WorksWithTprFromPdbFile 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file lysozyme.top, line 1465]: 58: System has non-zero total charge: 2.000000 58: Total charge should normally be an integer. See 58: https://manual.gromacs.org/current/user-guide/floating-point.html 58: for discussion on how close it should be to an integer. 58: 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 465.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 58: NVE simulation with an initial temperature of zero: will use a Verlet 58: buffer of 10%. Check your energy drift! 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 4 NOTEs 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 58: Setting the LD random seed to -553652357 58: 58: Generated 330891 of the 330891 non-bonded parameter combinations 58: 58: Generated 330891 of the 330891 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 58: 58: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 58: Analysing residue names: 58: There are: 10 Protein residues 58: Analysing Protein... 58: 58: This run will generate roughly 0 Mb of data 58: [ OK ] TopologyInformation.WorksWithTprFromPdbFile (650 ms) 58: [----------] 4 tests from TopologyInformation (655 ms total) 58: 58: [----------] 4 tests from TrajectoryModuleTest 58: [ RUN ] TrajectoryModuleTest.BasicTest 58: Reading frames from gro file 'Test system', 15 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] TrajectoryModuleTest.BasicTest (3 ms) 58: [ RUN ] TrajectoryModuleTest.PlotsXOnly 58: Reading frames from gro file 'Test system', 15 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] TrajectoryModuleTest.PlotsXOnly (3 ms) 58: [ RUN ] TrajectoryModuleTest.HandlesNoVelocities 58: Reading frames from gro file 'Test system', 15 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] TrajectoryModuleTest.HandlesNoVelocities (2 ms) 58: [ RUN ] TrajectoryModuleTest.HandlesNoForces 58: Reading frames from gro file 'Test system', 15 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] TrajectoryModuleTest.HandlesNoForces (1 ms) 58: [----------] 4 tests from TrajectoryModuleTest (10 ms total) 58: 58: [----------] 5 tests from UnionFinderTest 58: [ RUN ] UnionFinderTest.WorksEmpty 58: [ OK ] UnionFinderTest.WorksEmpty (0 ms) 58: [ RUN ] UnionFinderTest.BasicMerges 58: [ OK ] UnionFinderTest.BasicMerges (0 ms) 58: [ RUN ] UnionFinderTest.LargerMerges 58: [ OK ] UnionFinderTest.LargerMerges (0 ms) 58: [ RUN ] UnionFinderTest.LongRightMerge 58: [ OK ] UnionFinderTest.LongRightMerge (0 ms) 58: [ RUN ] UnionFinderTest.LongLeftMerge 58: [ OK ] UnionFinderTest.LongLeftMerge (0 ms) 58: [----------] 5 tests from UnionFinderTest (0 ms total) 58: 58: [----------] 1 test from MappedUnionFinderTest 58: [ RUN ] MappedUnionFinderTest.BasicMerges 58: [ OK ] MappedUnionFinderTest.BasicMerges (0 ms) 58: [----------] 1 test from MappedUnionFinderTest (0 ms total) 58: 58: [----------] 192 tests from MoleculeTests/DsspModuleTest 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/0 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/0 (23 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/1 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/1 (23 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/2 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/2 (23 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/3 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/3 (23 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/4 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/4 (22 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/5 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/5 (22 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/6 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/6 (22 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/7 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/7 (22 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/8 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/8 (23 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/9 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/9 (22 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/10 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/10 (29 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/11 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/11 (24 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/12 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/12 (24 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/13 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/13 (23 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/14 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/14 (23 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/15 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/15 (26 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/16 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/16 (23 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/17 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/17 (23 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/18 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/18 (24 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/19 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/19 (22 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/20 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/20 (23 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/21 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/21 (22 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/22 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/22 (23 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/23 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/23 (22 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/24 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/24 (21 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/25 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/25 (22 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/26 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/26 (23 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/27 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/27 (23 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/28 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/28 (23 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/29 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/29 (24 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/30 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/30 (23 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/31 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/31 (22 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/32 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/32 (22 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/33 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/33 (22 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/34 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/34 (22 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/35 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/35 (24 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/36 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/36 (25 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/37 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/37 (23 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/38 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/38 (21 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/39 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/39 (22 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/40 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/40 (22 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/41 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/41 (25 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/42 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/42 (23 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/43 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/43 (23 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/44 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/44 (22 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/45 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/45 (22 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/46 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/46 (22 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/47 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/47 (23 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/48 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/48 (21 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/49 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/49 (22 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/50 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/50 (22 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/51 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/51 (22 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/52 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/52 (21 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/53 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/53 (22 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/54 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/54 (22 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/55 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/55 (22 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/56 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/56 (23 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/57 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/57 (23 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/58 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/58 (23 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/59 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/59 (23 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/60 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/60 (24 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/61 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/61 (23 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/62 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/62 (22 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/63 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/63 (24 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/64 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/64 (22 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/65 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/65 (21 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/66 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/66 (21 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/67 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/67 (22 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/68 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/68 (23 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/69 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/69 (27 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/70 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/70 (30 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/71 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/71 (31 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/72 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/72 (29 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/73 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/73 (24 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/74 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/74 (21 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/75 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/75 (22 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/76 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/76 (21 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/77 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/77 (23 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/78 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/78 (22 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/79 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/79 (21 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/80 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/80 (21 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/81 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/81 (21 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/82 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/82 (24 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/83 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/83 (22 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/84 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/84 (21 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/85 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/85 (22 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/86 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/86 (21 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/87 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/87 (20 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/88 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/88 (23 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/89 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/89 (25 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/90 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/90 (22 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/91 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/91 (22 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/92 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/92 (21 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/93 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/93 (22 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/94 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/94 (22 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/95 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/95 (21 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/96 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/96 (21 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/97 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/97 (22 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/98 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/98 (22 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/99 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/99 (21 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/100 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/100 (21 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/101 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/101 (21 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/102 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/102 (21 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/103 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/103 (20 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/104 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/104 (21 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/105 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/105 (21 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/106 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/106 (22 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/107 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/107 (22 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/108 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/108 (21 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/109 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/109 (21 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/110 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/110 (22 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/111 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/111 (22 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/112 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/112 (20 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/113 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/113 (21 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/114 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/114 (23 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/115 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/115 (21 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/116 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/116 (22 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/117 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/117 (21 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/118 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/118 (22 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/119 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/119 (20 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/120 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/120 (21 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/121 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/121 (23 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/122 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/122 (20 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/123 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/123 (21 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/124 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/124 (20 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/125 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/125 (20 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/126 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/126 (21 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/127 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/127 (21 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/128 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/128 (17 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/129 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/129 (17 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/130 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/130 (16 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/131 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/131 (16 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/132 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/132 (16 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/133 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/133 (18 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/134 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/134 (17 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/135 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/135 (15 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/136 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/136 (16 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/137 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/137 (16 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/138 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/138 (17 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/139 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/139 (16 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/140 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/140 (16 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/141 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/141 (16 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/142 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/142 (16 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/143 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/143 (17 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/144 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/144 (17 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/145 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/145 (17 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/146 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/146 (17 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/147 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/147 (16 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/148 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/148 (15 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/149 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/149 (16 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/150 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/150 (16 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/151 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/151 (20 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/152 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/152 (28 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/153 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/153 (19 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/154 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/154 (20 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/155 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/155 (20 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/156 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/156 (20 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/157 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/157 (19 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/158 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/158 (19 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/159 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/159 (18 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/160 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/160 (21 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/161 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/161 (19 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/162 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/162 (25 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/163 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/163 (18 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/164 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/164 (24 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/165 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/165 (30 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/166 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/166 (30 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/167 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/167 (21 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/168 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/168 (23 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/169 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/169 (98 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/170 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/170 (21 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/171 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/171 (26 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/172 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/172 (139 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/173 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/173 (20 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/174 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/174 (52 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/175 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/175 (20 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/176 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/176 (31 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/177 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/177 (31 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/178 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/178 (27 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/179 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/179 (24 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/180 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/180 (18 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/181 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/181 (21 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/182 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/182 (20 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/183 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/183 (19 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/184 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/184 (18 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/185 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/185 (18 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/186 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/186 (18 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/187 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/187 (19 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/188 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/188 (20 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/189 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/189 (24 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/190 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/190 (19 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/191 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/191 (18 ms) 58: [----------] 192 tests from MoleculeTests/DsspModuleTest (4468 ms total) 58: 58: [----------] 3 tests from GyrateTests/GyrateModuleTest 58: [ RUN ] GyrateTests/GyrateModuleTest.Works/0 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: [ OK ] GyrateTests/GyrateModuleTest.Works/0 (8 ms) 58: [ RUN ] GyrateTests/GyrateModuleTest.Works/1 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: [ OK ] GyrateTests/GyrateModuleTest.Works/1 (7 ms) 58: [ RUN ] GyrateTests/GyrateModuleTest.Works/2 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: [ OK ] GyrateTests/GyrateModuleTest.Works/2 (7 ms) 58: [----------] 3 tests from GyrateTests/GyrateModuleTest (24 ms total) 58: 58: [----------] 96 tests from HBondTests/HbondModuleTest 58: [ RUN ] HBondTests/HbondModuleTest.Works/0 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 56 acceptors and 27 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/0 (15 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/1 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 29 acceptors and 27 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/1 (15 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/2 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 56 acceptors and 4 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/2 (14 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/3 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 29 acceptors and 4 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/3 (14 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/4 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 56 acceptors and 27 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/4 (87 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/5 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 29 acceptors and 27 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/5 (139 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/6 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 56 acceptors and 4 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/6 (16 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/7 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 29 acceptors and 4 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/7 (14 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/8 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 56 acceptors and 27 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/8 (15 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/9 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 29 acceptors and 27 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/9 (15 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/10 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 56 acceptors and 4 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/10 (14 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/11 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 29 acceptors and 4 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/11 (14 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/12 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 56 acceptors and 27 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/12 (15 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/13 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 29 acceptors and 27 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/13 (15 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/14 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 56 acceptors and 4 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/14 (18 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/15 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 29 acceptors and 4 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/15 (14 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/16 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 56 acceptors and 27 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/16 (16 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/17 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 29 acceptors and 27 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/17 (16 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/18 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 56 acceptors and 4 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/18 (15 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/19 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 29 acceptors and 4 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/19 (16 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/20 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 56 acceptors and 27 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/20 (16 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/21 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 29 acceptors and 27 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/21 (17 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/22 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 56 acceptors and 4 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/22 (13 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/23 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 29 acceptors and 4 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/23 (14 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/24 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 56 acceptors and 27 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/24 (16 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/25 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 29 acceptors and 27 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/25 (17 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/26 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 56 acceptors and 4 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/26 (14 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/27 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 29 acceptors and 4 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/27 (16 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/28 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 56 acceptors and 27 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/28 (18 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/29 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 29 acceptors and 27 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/29 (18 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/30 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 56 acceptors and 4 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/30 (16 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/31 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 29 acceptors and 4 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/31 (15 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/32 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 56 acceptors and 27 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/32 (97 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/33 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 29 acceptors and 27 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/33 (100 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/34 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 56 acceptors and 4 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/34 (100 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/35 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 29 acceptors and 4 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/35 (94 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/36 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 56 acceptors and 27 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/36 (96 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/37 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 29 acceptors and 27 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/37 (95 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/38 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 56 acceptors and 4 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/38 (93 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/39 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 29 acceptors and 4 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/39 (92 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/40 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 56 acceptors and 27 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/40 (93 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/41 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 29 acceptors and 27 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/41 (86 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/42 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 56 acceptors and 4 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/42 (92 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/43 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 29 acceptors and 4 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/43 (90 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/44 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 56 acceptors and 27 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/44 (97 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/45 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 29 acceptors and 27 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/45 (93 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/46 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 56 acceptors and 4 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/46 (119 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/47 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 29 acceptors and 4 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/47 (87 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/48 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 56 acceptors and 27 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/48 (89 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/49 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 29 acceptors and 27 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/49 (86 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/50 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 56 acceptors and 4 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/50 (93 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/51 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 29 acceptors and 4 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/51 (82 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/52 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 56 acceptors and 27 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/52 (87 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/53 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 29 acceptors and 27 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/53 (86 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/54 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 56 acceptors and 4 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/54 (84 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/55 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 29 acceptors and 4 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/55 (85 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/56 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 56 acceptors and 27 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/56 (89 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/57 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 29 acceptors and 27 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/57 (85 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/58 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 56 acceptors and 4 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/58 (98 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/59 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 29 acceptors and 4 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/59 (198 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/60 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 56 acceptors and 27 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/60 (120 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/61 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 29 acceptors and 27 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/61 (104 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/62 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 56 acceptors and 4 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/62 (110 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/63 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 29 acceptors and 4 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/63 (105 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/64 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/64 (105 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/65 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/65 (107 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/66 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/66 (93 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/67 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/67 (88 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/68 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/68 (96 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/69 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/69 (90 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/70 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/70 (97 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/71 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/71 (96 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/72 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/72 (95 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/73 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/73 (91 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/74 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/74 (94 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/75 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/75 (88 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/76 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/76 (96 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/77 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/77 (223 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/78 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/78 (85 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/79 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/79 (82 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/80 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/80 (79 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/81 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/81 (128 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/82 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/82 (85 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/83 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/83 (247 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/84 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/84 (91 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/85 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/85 (274 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/86 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/86 (400 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/87 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/87 (85 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/88 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/88 (89 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/89 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/89 (89 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/90 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/90 (90 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/91 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/91 (93 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/92 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/92 (158 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/93 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/93 (209 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/94 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/94 (448 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/95 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/95 (298 ms) 58: [----------] 96 tests from HBondTests/HbondModuleTest (9373 ms total) 58: 58: [----------] 4 tests from MoleculeTests/ScatteringModule 58: [ RUN ] MoleculeTests/ScatteringModule.DirectMode/0 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 58: Method for calculating small-angle neutron scattering spectra using all-atom 58: molecular dynamics trajectories 58: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 58: DOI: 10.1134/S1027451013060372 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/ScatteringModule.DirectMode/0 (23 ms) 58: [ RUN ] MoleculeTests/ScatteringModule.DirectMode/1 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 58: Method for calculating small-angle neutron scattering spectra using all-atom 58: molecular dynamics trajectories 58: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 58: DOI: 10.1134/S1027451013060372 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: D. T. Cromer, J. B. Mann 58: X-ray scattering factors computed from numerical Hartree-Fock wave functions 58: Acta Cryst. A (1968) 58: DOI: 10.1107/S0567739468000550 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/ScatteringModule.DirectMode/1 (449 ms) 58: [ RUN ] MoleculeTests/ScatteringModule.MCMode/0 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 58: Method for calculating small-angle neutron scattering spectra using all-atom 58: molecular dynamics trajectories 58: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 58: DOI: 10.1134/S1027451013060372 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/ScatteringModule.MCMode/0 (14 ms) 58: [ RUN ] MoleculeTests/ScatteringModule.MCMode/1 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 58: Method for calculating small-angle neutron scattering spectra using all-atom 58: molecular dynamics trajectories 58: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 58: DOI: 10.1134/S1027451013060372 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: D. T. Cromer, J. B. Mann 58: X-ray scattering factors computed from numerical Hartree-Fock wave functions 58: Acta Cryst. A (1968) 58: DOI: 10.1107/S0567739468000550 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/ScatteringModule.MCMode/1 (104 ms) 58: [----------] 4 tests from MoleculeTests/ScatteringModule (594 ms total) 58: 58: [----------] Global test environment tear-down 58: [==========] 393 tests from 21 test suites ran. (15870 ms total) 58: [ PASSED ] 393 tests. 58/90 Test #58: TrajectoryAnalysisUnitTests ............... Passed 15.92 sec test 59 Start 59: EnergyAnalysisUnitTests 59: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/energyanalysis-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/EnergyAnalysisUnitTests.xml" 59: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/energyanalysis/tests 59: Test timeout computed to be: 30 59: [==========] Running 12 tests from 5 test suites. 59: [----------] Global test environment set-up. 59: [----------] 2 tests from EnergyTermTest 59: [ RUN ] EnergyTermTest.ConstructWorks 59: [ OK ] EnergyTermTest.ConstructWorks (0 ms) 59: [ RUN ] EnergyTermTest.AddFrameWorks 59: [ OK ] EnergyTermTest.AddFrameWorks (0 ms) 59: [----------] 2 tests from EnergyTermTest (0 ms total) 59: 59: [----------] 1 test from DhdlTest 59: [ RUN ] DhdlTest.ExtractDhdl 59: Opened /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/dhdl.edr as double precision energy file 59: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/dhdl.tpr, VERSION 2016-dev-20160810-e3ded7f (double precision) 59: Note: file tpx version 110, software tpx version 137 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Reading energy frame 6 time 0.060 Reading energy frame 7 time 0.070 Reading energy frame 8 time 0.080 Reading energy frame 9 time 0.090 Reading energy frame 10 time 0.100 Reading energy frame 11 time 0.110 Reading energy frame 12 time 0.120 Reading energy frame 13 time 0.130 Reading energy frame 14 time 0.140 Reading energy frame 15 time 0.150 Reading energy frame 16 time 0.160 Reading energy frame 17 time 0.170 Reading energy frame 18 time 0.180 Reading energy frame 19 time 0.190 Reading energy frame 20 time 0.200 Reading energy frame 30 time 0.300 Reading energy frame 40 time 0.400 Reading energy frame 50 time 0.500 Reading energy frame 60 time 0.600 Reading energy frame 70 time 0.700 Reading energy frame 80 time 0.800 Reading energy frame 90 time 0.900 Reading energy frame 100 time 1.000 Last energy frame read 100 time 1.000 59: 59: 59: Wrote 8 lambda values with 101 samples as 808 dH data blocks to /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary/DhdlTest_ExtractDhdl_dhdl.xvg 59: [ OK ] DhdlTest.ExtractDhdl (171 ms) 59: [----------] 1 test from DhdlTest (171 ms total) 59: 59: [----------] 1 test from OriresTest 59: [ RUN ] OriresTest.ExtractOrires 59: Opened /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/orires.edr as single precision energy file 59: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/orires.tpr, VERSION 2017-dev-20170725-fea8651 (single precision) 59: Note: file tpx version 111, software tpx version 137 59: Found 7 orientation restraints with 1 experimentsSelect the orientation restraint labels you want (-1 is all) 59: End your selection with 0 59: Selecting all 7 orientation restraints 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Reading energy frame 3 time 0.006 Reading energy frame 4 time 0.008 Reading energy frame 5 time 0.010 Reading energy frame 6 time 0.012 Reading energy frame 7 time 0.014 Reading energy frame 8 time 0.016 Reading energy frame 9 time 0.018 Reading energy frame 10 time 0.020 Last energy frame read 10 time 0.020 59: [ OK ] OriresTest.ExtractOrires (14 ms) 59: [----------] 1 test from OriresTest (14 ms total) 59: 59: [----------] 5 tests from EnergyTest 59: [ RUN ] EnergyTest.ExtractEnergy 59: Opened /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 59: 59: Select the terms you want from the following list by 59: selecting either (part of) the name or the number or a combination. 59: End your selection with an empty line or a zero. 59: ------------------------------------------------------------------- 59: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 59: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 59: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 59: 13 Box-Z 14 Volume 15 Density 16 pV 59: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 59: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 59: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 59: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 59: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 59: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 59: 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 59: 59: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 59: All statistics are over 5001 points 59: 59: Energy Average Err.Est. RMSD Tot-Drift 59: ------------------------------------------------------------------------------- 59: Potential -34142.2 39 228.993 -62.8906 (kJ/mol) 59: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 59: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 59: [ OK ] EnergyTest.ExtractEnergy (6 ms) 59: [ RUN ] EnergyTest.ExtractEnergyByNumber 59: Opened /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 59: 59: Select the terms you want from the following list by 59: selecting either (part of) the name or the number or a combination. 59: End your selection with an empty line or a zero. 59: ------------------------------------------------------------------- 59: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 59: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 59: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 59: 13 Box-Z 14 Volume 15 Density 16 pV 59: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 59: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 59: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 59: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 59: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 59: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 59: 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 59: 59: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 59: All statistics are over 5001 points 59: 59: Energy Average Err.Est. RMSD Tot-Drift 59: ------------------------------------------------------------------------------- 59: Coul. recip. 302.771 2.8 17.5152 12.5403 (kJ/mol) 59: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 59: Pres. DC -268.49 3 8.52175 13.2804 (bar) 59: [ OK ] EnergyTest.ExtractEnergyByNumber (2 ms) 59: [ RUN ] EnergyTest.ExtractEnergyMixed 59: Opened /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 59: 59: Select the terms you want from the following list by 59: selecting either (part of) the name or the number or a combination. 59: End your selection with an empty line or a zero. 59: ------------------------------------------------------------------- 59: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 59: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 59: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 59: 13 Box-Z 14 Volume 15 Density 16 pV 59: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 59: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 59: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 59: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 59: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 59: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 59: 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 59: 59: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 4 data sets 59: All statistics are over 5001 points 59: 59: Energy Average Err.Est. RMSD Tot-Drift 59: ------------------------------------------------------------------------------- 59: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 59: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 59: Box-Z 2.92457 0.0054 0.0151558 0.0234974 (nm) 59: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 59: [ OK ] EnergyTest.ExtractEnergyMixed (8 ms) 59: [ RUN ] EnergyTest.ExtractEnergyWithNumberInName 59: Opened /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/ener_numberInName.edr as single precision energy file 59: 59: Select the terms you want from the following list by 59: selecting either (part of) the name or the number or a combination. 59: End your selection with an empty line or a zero. 59: ------------------------------------------------------------------- 59: 1 Bond 2 Angle 3 Proper-Dih. 4 Per.-Imp.-Dih. 59: 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 Coulomb-(SR) 59: 9 Coul.-recip. 10 Potential 11 Kinetic-En. 12 Total-Energy 59: 13 Conserved-En. 14 Temperature 15 Pressure 16 Constr.-rmsd 59: 17 Vir-XX 18 Vir-XY 19 Vir-XZ 20 Vir-YX 59: 21 Vir-YY 22 Vir-YZ 23 Vir-ZX 24 Vir-ZY 59: 25 Vir-ZZ 26 Pres-XX 27 Pres-XY 28 Pres-XZ 59: 29 Pres-YX 30 Pres-YY 31 Pres-YZ 32 Pres-ZX 59: 33 Pres-ZY 34 Pres-ZZ 35 #Surf*SurfTen 36 2CosZ*Vel-X 59: 37 1/Viscosity 38 T-System 39 Lamb-System 59: 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Last energy frame read 2 time 0.004 59: 59: Statistics over 3 steps [ 0.0000 through 0.0040 ps ], 1 data sets 59: All statistics are over 3 points (frames) 59: 59: Energy Average Err.Est. RMSD Tot-Drift 59: ------------------------------------------------------------------------------- 59: 1/Viscosity 57767.2 -- 10666.2 -25998 (m s/kg) 59: [ OK ] EnergyTest.ExtractEnergyWithNumberInName (1 ms) 59: [ RUN ] EnergyTest.ExtractEnergyWithNumberInNameAndAlsoByNumber 59: Opened /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/ener_numberInName.edr as single precision energy file 59: 59: Select the terms you want from the following list by 59: selecting either (part of) the name or the number or a combination. 59: End your selection with an empty line or a zero. 59: ------------------------------------------------------------------- 59: 1 Bond 2 Angle 3 Proper-Dih. 4 Per.-Imp.-Dih. 59: 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 Coulomb-(SR) 59: 9 Coul.-recip. 10 Potential 11 Kinetic-En. 12 Total-Energy 59: 13 Conserved-En. 14 Temperature 15 Pressure 16 Constr.-rmsd 59: 17 Vir-XX 18 Vir-XY 19 Vir-XZ 20 Vir-YX 59: 21 Vir-YY 22 Vir-YZ 23 Vir-ZX 24 Vir-ZY 59: 25 Vir-ZZ 26 Pres-XX 27 Pres-XY 28 Pres-XZ 59: 29 Pres-YX 30 Pres-YY 31 Pres-YZ 32 Pres-ZX 59: 33 Pres-ZY 34 Pres-ZZ 35 #Surf*SurfTen 36 2CosZ*Vel-X 59: 37 1/Viscosity 38 T-System 39 Lamb-System 59: 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Last energy frame read 2 time 0.004 59: 59: Statistics over 3 steps [ 0.0000 through 0.0040 ps ], 2 data sets 59: All statistics are over 3 points (frames) 59: 59: Energy Average Err.Est. RMSD Tot-Drift 59: ------------------------------------------------------------------------------- 59: LJ (SR) -14.1095 -- 0.384124 0.932214 (kJ/mol) 59: 1/Viscosity 57767.2 -- 10666.2 -25998 (m s/kg) 59: [ OK ] EnergyTest.ExtractEnergyWithNumberInNameAndAlsoByNumber (1 ms) 59: [----------] 5 tests from EnergyTest (22 ms total) 59: 59: [----------] 3 tests from ViscosityTest 59: [ RUN ] ViscosityTest.EinsteinViscosity 59: Opened /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 59: 59: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 59: All statistics are over 5001 points 59: 59: Energy Average Err.Est. RMSD Tot-Drift 59: ------------------------------------------------------------------------------- 59: Pres-XX 20.2092 65 717.193 185.978 (bar) 59: Pres-XY -47.7351 39 372.522 207.456 (bar) 59: Pres-XZ 11.477 31 379.79 6.80818 (bar) 59: Pres-YX -47.7106 39 372.525 207.5 (bar) 59: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 59: Pres-YZ -41.3534 45 401.216 114.663 (bar) 59: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 59: Pres-ZY -41.3119 45 401.196 114.743 (bar) 59: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 59: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 59: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 59: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 59: 59: Computing shear viscosity using the Einstein relation with 6 start points separated by 0.2 ps 59: [ OK ] ViscosityTest.EinsteinViscosity (593 ms) 59: [ RUN ] ViscosityTest.EinsteinViscosityIntegral 59: Opened /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 59: 59: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 59: All statistics are over 5001 points 59: 59: Energy Average Err.Est. RMSD Tot-Drift 59: ------------------------------------------------------------------------------- 59: Pres-XX 20.2092 65 717.193 185.978 (bar) 59: Pres-XY -47.7351 39 372.522 207.456 (bar) 59: Pres-XZ 11.477 31 379.79 6.80818 (bar) 59: Pres-YX -47.7106 39 372.525 207.5 (bar) 59: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 59: Pres-YZ -41.3534 45 401.216 114.663 (bar) 59: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 59: Pres-ZY -41.3119 45 401.196 114.743 (bar) 59: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 59: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 59: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 59: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 59: 59: Computing shear viscosity using the Einstein relation with 6 start points separated by 0.2 ps 59: [ OK ] ViscosityTest.EinsteinViscosityIntegral (305 ms) 59: [ RUN ] ViscosityTest.EinsteinViscosityDefaultArguments 59: Opened /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 59: 59: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 59: All statistics are over 5001 points 59: 59: Energy Average Err.Est. RMSD Tot-Drift 59: ------------------------------------------------------------------------------- 59: Pres-XX 20.2092 65 717.193 185.978 (bar) 59: Pres-XY -47.7351 39 372.522 207.456 (bar) 59: Pres-XZ 11.477 31 379.79 6.80818 (bar) 59: Pres-YX -47.7106 39 372.525 207.5 (bar) 59: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 59: Pres-YZ -41.3534 45 401.216 114.663 (bar) 59: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 59: Pres-ZY -41.3119 45 401.196 114.743 (bar) 59: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 59: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 59: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 59: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 59: 59: Computing shear viscosity using the Einstein relation with 6 start points separated by 0.2 ps 59: [ OK ] ViscosityTest.EinsteinViscosityDefaultArguments (308 ms) 59: [----------] 3 tests from ViscosityTest (1207 ms total) 59: 59: [----------] Global test environment tear-down 59: [==========] 12 tests from 5 test suites ran. (1416 ms total) 59: [ PASSED ] 12 tests. 59/90 Test #59: EnergyAnalysisUnitTests ................... Passed 1.44 sec test 60 Start 60: ToolUnitTests 60: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/tool-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/ToolUnitTests.xml" 60: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests 60: Test timeout computed to be: 1920 60: [==========] Running 63 tests from 8 test suites. 60: [----------] Global test environment set-up. 60: [----------] 2 tests from DumpTest 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file lysozyme.top, line 1465]: 60: System has non-zero total charge: 2.000000 60: Total charge should normally be an integer. See 60: https://manual.gromacs.org/current/user-guide/floating-point.html 60: for discussion on how close it should be to an integer. 60: 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 465.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 60: NVE simulation with an initial temperature of zero: will use a Verlet 60: buffer of 10%. Check your energy drift! 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 NOTEs 60: Setting the LD random seed to -37882913 60: 60: Generated 330891 of the 330891 non-bonded parameter combinations 60: 60: Generated 330891 of the 330891 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 60: Analysing residue names: 60: There are: 10 Protein residues 60: Analysing Protein... 60: 60: This run will generate roughly 0 Mb of data 60: [ RUN ] DumpTest.WorksWithTpr 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr: 60: inputrec: 60: integrator = md 60: tinit = 0 60: dt = 0.001 60: nsteps = 0 60: init-step = 0 60: simulation-part = 1 60: mts = false 60: mass-repartition-factor = 1 60: comm-mode = Linear 60: nstcomm = 100 60: bd-fric = 0 60: ld-seed = -37882913 60: emtol = 10 60: emstep = 0.01 60: niter = 20 60: fcstep = 0 60: nstcgsteep = 1000 60: nbfgscorr = 10 60: rtpi = 0.05 60: nstxout = 0 60: nstvout = 0 60: nstfout = 0 60: nstlog = 1000 60: nstcalcenergy = 100 60: nstenergy = 1000 60: nstxout-compressed = 0 60: compressed-x-precision = 1000 60: cutoff-scheme = Verlet 60: nstlist = 10 60: pbc = xyz 60: periodic-molecules = false 60: verlet-buffer-tolerance = -1 60: verlet-buffer-pressure-tolerance = 0.5 60: rlist = 1.1 60: coulombtype = Cut-off 60: coulomb-modifier = Potential-shift 60: rcoulomb-switch = 0 60: rcoulomb = 1 60: epsilon-r = 1 60: epsilon-rf = inf 60: vdw-type = Cut-off 60: vdw-modifier = Potential-shift 60: rvdw-switch = 0 60: rvdw = 1 60: DispCorr = No 60: table-extension = 1 60: fourierspacing = 0.12 60: fourier-nx = 0 60: fourier-ny = 0 60: fourier-nz = 0 60: pme-order = 4 60: ewald-rtol = 1e-05 60: ewald-rtol-lj = 0.001 60: lj-pme-comb-rule = Geometric 60: ewald-geometry = 3d 60: epsilon-surface = 0 60: ensemble-temperature-setting = not available 60: tcoupl = No 60: nsttcouple = -1 60: nh-chain-length = 0 60: print-nose-hoover-chain-variables = false 60: pcoupl = No 60: refcoord-scaling = No 60: posres-com: not available 60: posres-comB: not available 60: QMMM = false 60: qm-opts: 60: ngQM = 0 60: constraint-algorithm = Lincs 60: continuation = false 60: Shake-SOR = false 60: shake-tol = 0.0001 60: lincs-order = 4 60: lincs-iter = 1 60: lincs-warnangle = 30 60: nwall = 0 60: wall-type = 9-3 60: wall-r-linpot = -1 60: wall-atomtype[0] = -1 60: wall-atomtype[1] = -1 60: wall-density[0] = 0 60: wall-density[1] = 0 60: wall-ewald-zfac = 3 60: pull = false 60: awh = false 60: rotation = false 60: interactiveMD = false 60: disre = No 60: disre-weighting = Conservative 60: disre-mixed = false 60: dr-fc = 1000 60: dr-tau = 0 60: nstdisreout = 100 60: orire-fc = 0 60: orire-tau = 0 60: nstorireout = 100 60: free-energy = no 60: cos-acceleration = 0 60: deform (3x3): 60: deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: simulated-tempering = false 60: swapcoords = no 60: userint1 = 0 60: userint2 = 0 60: userint3 = 0 60: userint4 = 0 60: userreal1 = 0 60: userreal2 = 0 60: userreal3 = 0 60: userreal4 = 0 60: applied-forces: 60: electric-field: 60: x: 60: E0 = 0 60: omega = 0 60: t0 = 0 60: sigma = 0 60: y: 60: E0 = 0 60: omega = 0 60: t0 = 0 60: sigma = 0 60: z: 60: E0 = 0 60: omega = 0 60: t0 = 0 60: sigma = 0 60: density-guided-simulation: 60: active = false 60: group = protein 60: similarity-measure = inner-product 60: atom-spreading-weight = unity 60: force-constant = 1e+09 60: gaussian-transform-spreading-width = 0.2 60: gaussian-transform-spreading-range-in-multiples-of-width = 4 60: reference-density-filename = reference.mrc 60: nst = 1 60: normalize-densities = true 60: adaptive-force-scaling = false 60: adaptive-force-scaling-time-constant = 4 60: shift-vector = 60: transformation-matrix = 60: qmmm-cp2k: 60: active = false 60: qmgroup = System 60: qmmethod = PBE 60: qmfilenames = 60: qmcharge = 0 60: qmmultiplicity = 1 60: colvars: 60: active = false 60: configfile = 60: seed = -1 60: nnpot: 60: active = false 60: modelfile = model.pt 60: input-group = System 60: model-input1 = 60: model-input2 = 60: model-input3 = 60: model-input4 = 60: grpopts: 60: nrdf: 465 60: ref-t: 0 60: tau-t: 0 60: annealing: No 60: annealing-npoints: 0 60: acc: 0 0 0 60: nfreeze: N N N 60: energygrp-flags[ 0]: 0 60: header: 60: bIr = present 60: bBox = present 60: bTop = present 60: bX = present 60: bV = present 60: bF = not present 60: natoms = 156 60: lambda = 0.000000e+00 60: buffer size = 46382 60: topology: 60: name="First 10 residues from 1AKI" 60: #atoms = 156 60: #molblock = 1 60: molblock (0): 60: moltype = 0 "Protein_chain_B" 60: #molecules = 1 60: #posres_xA = 0 60: #posres_xB = 0 60: bIntermolecularInteractions = false 60: ffparams: 60: atnr=10 60: ntypes=212 60: functype[0]=LJ_SR, c6= 3.35274590e-03, c12= 3.95094276e-06 60: functype[1]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[2]=LJ_SR, c6= 2.60916958e-03, c12= 3.84022405e-06 60: functype[3]=LJ_SR, c6= 6.41072227e-04, c12= 3.43856414e-07 60: functype[4]=LJ_SR, c6= 4.04775795e-03, c12= 7.32754188e-06 60: functype[5]=LJ_SR, c6= 2.81521026e-03, c12= 2.50631660e-06 60: functype[6]=LJ_SR, c6= 2.80388421e-03, c12= 4.30620821e-06 60: functype[7]=LJ_SR, c6= 5.81477652e-04, c12= 2.82897616e-07 60: functype[8]=LJ_SR, c6= 6.03335386e-04, c12= 2.35915493e-07 60: functype[9]=LJ_SR, c6= 7.20490469e-03, c12= 1.15394714e-05 60: functype[10]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[11]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[12]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[13]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[14]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[15]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[16]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[17]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[18]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[19]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[20]=LJ_SR, c6= 2.60916958e-03, c12= 3.84022405e-06 60: functype[21]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[22]=LJ_SR, c6= 2.03050394e-03, c12= 3.73260514e-06 60: functype[23]=LJ_SR, c6= 4.98894195e-04, c12= 3.34220175e-07 60: functype[24]=LJ_SR, c6= 3.15004122e-03, c12= 7.12220026e-06 60: functype[25]=LJ_SR, c6= 2.19085021e-03, c12= 2.43608270e-06 60: functype[26]=LJ_SR, c6= 2.18203571e-03, c12= 4.18553600e-06 60: functype[27]=LJ_SR, c6= 4.52516542e-04, c12= 2.74969580e-07 60: functype[28]=LJ_SR, c6= 4.69526683e-04, c12= 2.29304163e-07 60: functype[29]=LJ_SR, c6= 5.60698984e-03, c12= 1.12160897e-05 60: functype[30]=LJ_SR, c6= 6.41072227e-04, c12= 3.43856414e-07 60: functype[31]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[32]=LJ_SR, c6= 4.98894195e-04, c12= 3.34220175e-07 60: functype[33]=LJ_SR, c6= 1.22578131e-04, c12= 2.99263014e-08 60: functype[34]=LJ_SR, c6= 7.73964217e-04, c12= 6.37726998e-07 60: functype[35]=LJ_SR, c6= 5.38290828e-04, c12= 2.18128321e-07 60: functype[36]=LJ_SR, c6= 5.36125386e-04, c12= 3.74775709e-07 60: functype[37]=LJ_SR, c6= 1.11183173e-04, c12= 2.46209719e-08 60: functype[38]=LJ_SR, c6= 1.15362534e-04, c12= 2.05320472e-08 60: functype[39]=LJ_SR, c6= 1.37763575e-03, c12= 1.00429668e-06 60: functype[40]=LJ_SR, c6= 4.04775795e-03, c12= 7.32754188e-06 60: functype[41]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[42]=LJ_SR, c6= 3.15004122e-03, c12= 7.12220026e-06 60: functype[43]=LJ_SR, c6= 7.73964217e-04, c12= 6.37726998e-07 60: functype[44]=LJ_SR, c6= 4.88684513e-03, c12= 1.35898972e-05 60: functype[45]=LJ_SR, c6= 3.39879468e-03, c12= 4.64829736e-06 60: functype[46]=LJ_SR, c6= 3.38512054e-03, c12= 7.98643487e-06 60: functype[47]=LJ_SR, c6= 7.02015939e-04, c12= 5.24670895e-07 60: functype[48]=LJ_SR, c6= 7.28404266e-04, c12= 4.37535846e-07 60: functype[49]=LJ_SR, c6= 8.69845692e-03, c12= 2.14014708e-05 60: functype[50]=LJ_SR, c6= 2.81521026e-03, c12= 2.50631660e-06 60: functype[51]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[52]=LJ_SR, c6= 2.19085021e-03, c12= 2.43608270e-06 60: functype[53]=LJ_SR, c6= 5.38290828e-04, c12= 2.18128321e-07 60: functype[54]=LJ_SR, c6= 3.39879468e-03, c12= 4.64829736e-06 60: functype[55]=LJ_SR, c6= 2.36385735e-03, c12= 1.58990645e-06 60: functype[56]=LJ_SR, c6= 2.35434738e-03, c12= 2.73168575e-06 60: functype[57]=LJ_SR, c6= 4.88250953e-04, c12= 1.79458596e-07 60: functype[58]=LJ_SR, c6= 5.06604381e-04, c12= 1.49655136e-07 60: functype[59]=LJ_SR, c6= 6.04976481e-03, c12= 7.32016997e-06 60: functype[60]=LJ_SR, c6= 2.80388421e-03, c12= 4.30620821e-06 60: functype[61]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[62]=LJ_SR, c6= 2.18203571e-03, c12= 4.18553600e-06 60: functype[63]=LJ_SR, c6= 5.36125386e-04, c12= 3.74775709e-07 60: functype[64]=LJ_SR, c6= 3.38512054e-03, c12= 7.98643487e-06 60: functype[65]=LJ_SR, c6= 2.35434738e-03, c12= 2.73168575e-06 60: functype[66]=LJ_SR, c6= 2.34487536e-03, c12= 4.69342376e-06 60: functype[67]=LJ_SR, c6= 4.86286852e-04, c12= 3.08335643e-07 60: functype[68]=LJ_SR, c6= 5.04566357e-04, c12= 2.57128875e-07 60: functype[69]=LJ_SR, c6= 6.02542516e-03, c12= 1.25770912e-05 60: functype[70]=LJ_SR, c6= 5.81477652e-04, c12= 2.82897616e-07 60: functype[71]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[72]=LJ_SR, c6= 4.52516542e-04, c12= 2.74969580e-07 60: functype[73]=LJ_SR, c6= 1.11183173e-04, c12= 2.46209719e-08 60: functype[74]=LJ_SR, c6= 7.02015939e-04, c12= 5.24670895e-07 60: functype[75]=LJ_SR, c6= 4.88250953e-04, c12= 1.79458596e-07 60: functype[76]=LJ_SR, c6= 4.86286852e-04, c12= 3.08335643e-07 60: functype[77]=LJ_SR, c6= 1.00847494e-04, c12= 2.02561683e-08 60: functype[78]=LJ_SR, c6= 1.04638377e-04, c12= 1.68921392e-08 60: functype[79]=LJ_SR, c6= 1.24956947e-03, c12= 8.26254961e-07 60: functype[80]=LJ_SR, c6= 6.03335386e-04, c12= 2.35915493e-07 60: functype[81]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[82]=LJ_SR, c6= 4.69526683e-04, c12= 2.29304163e-07 60: functype[83]=LJ_SR, c6= 1.15362534e-04, c12= 2.05320472e-08 60: functype[84]=LJ_SR, c6= 7.28404266e-04, c12= 4.37535846e-07 60: functype[85]=LJ_SR, c6= 5.06604381e-04, c12= 1.49655136e-07 60: functype[86]=LJ_SR, c6= 5.04566357e-04, c12= 2.57128875e-07 60: functype[87]=LJ_SR, c6= 1.04638377e-04, c12= 1.68921392e-08 60: functype[88]=LJ_SR, c6= 1.08571716e-04, c12= 1.40867806e-08 60: functype[89]=LJ_SR, c6= 1.29654107e-03, c12= 6.89035176e-07 60: functype[90]=LJ_SR, c6= 7.20490469e-03, c12= 1.15394714e-05 60: functype[91]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[92]=LJ_SR, c6= 5.60698984e-03, c12= 1.12160897e-05 60: functype[93]=LJ_SR, c6= 1.37763575e-03, c12= 1.00429668e-06 60: functype[94]=LJ_SR, c6= 8.69845692e-03, c12= 2.14014708e-05 60: functype[95]=LJ_SR, c6= 6.04976481e-03, c12= 7.32016997e-06 60: functype[96]=LJ_SR, c6= 6.02542516e-03, c12= 1.25770912e-05 60: functype[97]=LJ_SR, c6= 1.24956947e-03, c12= 8.26254961e-07 60: functype[98]=LJ_SR, c6= 1.29654107e-03, c12= 6.89035176e-07 60: functype[99]=LJ_SR, c6= 1.54830217e-02, c12= 3.37031743e-05 60: functype[100]=BONDS, b0A= 1.01000e-01, cbA= 3.63171e+05, b0B= 1.01000e-01, cbB= 3.63171e+05 60: functype[101]=BONDS, b0A= 1.47100e-01, cbA= 3.07106e+05, b0B= 1.47100e-01, cbB= 3.07106e+05 60: functype[102]=BONDS, b0A= 1.09000e-01, cbA= 2.84512e+05, b0B= 1.09000e-01, cbB= 2.84512e+05 60: functype[103]=BONDS, b0A= 1.52900e-01, cbA= 2.24262e+05, b0B= 1.52900e-01, cbB= 2.24262e+05 60: functype[104]=BONDS, b0A= 1.52200e-01, cbA= 2.65266e+05, b0B= 1.52200e-01, cbB= 2.65266e+05 60: functype[105]=BONDS, b0A= 1.22900e-01, cbA= 4.76976e+05, b0B= 1.22900e-01, cbB= 4.76976e+05 60: functype[106]=BONDS, b0A= 1.33500e-01, cbA= 4.10032e+05, b0B= 1.33500e-01, cbB= 4.10032e+05 60: functype[107]=BONDS, b0A= 1.44900e-01, cbA= 2.82002e+05, b0B= 1.44900e-01, cbB= 2.82002e+05 60: functype[108]=BONDS, b0A= 1.51000e-01, cbA= 2.65266e+05, b0B= 1.51000e-01, cbB= 2.65266e+05 60: functype[109]=BONDS, b0A= 1.40000e-01, cbA= 3.92459e+05, b0B= 1.40000e-01, cbB= 3.92459e+05 60: functype[110]=BONDS, b0A= 1.08000e-01, cbA= 3.07106e+05, b0B= 1.08000e-01, cbB= 3.07106e+05 60: functype[111]=BONDS, b0A= 1.46300e-01, cbA= 2.82002e+05, b0B= 1.46300e-01, cbB= 2.82002e+05 60: functype[112]=BONDS, b0A= 1.34000e-01, cbA= 4.02501e+05, b0B= 1.34000e-01, cbB= 4.02501e+05 60: functype[113]=BONDS, b0A= 1.81000e-01, cbA= 1.85770e+05, b0B= 1.81000e-01, cbB= 1.85770e+05 60: functype[114]=BONDS, b0A= 1.33600e-01, cbA= 2.29283e+05, b0B= 1.33600e-01, cbB= 2.29283e+05 60: functype[115]=BONDS, b0A= 1.25000e-01, cbA= 5.48941e+05, b0B= 1.25000e-01, cbB= 5.48941e+05 60: functype[116]=ANGLES, thA= 1.09500e+02, ctA= 2.92880e+02, thB= 1.09500e+02, ctB= 2.92880e+02 60: functype[117]=ANGLES, thA= 1.11200e+02, ctA= 6.69440e+02, thB= 1.11200e+02, ctB= 6.69440e+02 60: functype[118]=ANGLES, thA= 1.10700e+02, ctA= 3.13800e+02, thB= 1.10700e+02, ctB= 3.13800e+02 60: functype[119]=ANGLES, thA= 1.11100e+02, ctA= 5.27184e+02, thB= 1.11100e+02, ctB= 5.27184e+02 60: functype[120]=ANGLES, thA= 1.12700e+02, ctA= 4.88273e+02, thB= 1.12700e+02, ctB= 4.88273e+02 60: functype[121]=ANGLES, thA= 1.07800e+02, ctA= 2.76144e+02, thB= 1.07800e+02, ctB= 2.76144e+02 60: functype[122]=ANGLES, thA= 1.20400e+02, ctA= 6.69440e+02, thB= 1.20400e+02, ctB= 6.69440e+02 60: functype[123]=ANGLES, thA= 1.16600e+02, ctA= 5.85760e+02, thB= 1.16600e+02, ctB= 5.85760e+02 60: functype[124]=ANGLES, thA= 1.22900e+02, ctA= 6.69440e+02, thB= 1.22900e+02, ctB= 6.69440e+02 60: functype[125]=ANGLES, thA= 1.19800e+02, ctA= 2.92880e+02, thB= 1.19800e+02, ctB= 2.92880e+02 60: functype[126]=ANGLES, thA= 1.21900e+02, ctA= 4.18400e+02, thB= 1.21900e+02, ctB= 4.18400e+02 60: functype[127]=ANGLES, thA= 1.18400e+02, ctA= 3.17984e+02, thB= 1.18400e+02, ctB= 3.17984e+02 60: functype[128]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09700e+02, ctB= 6.69440e+02 60: functype[129]=ANGLES, thA= 1.10100e+02, ctA= 5.27184e+02, thB= 1.10100e+02, ctB= 5.27184e+02 60: functype[130]=ANGLES, thA= 1.14000e+02, ctA= 5.27184e+02, thB= 1.14000e+02, ctB= 5.27184e+02 60: functype[131]=ANGLES, thA= 1.20000e+02, ctA= 5.85760e+02, thB= 1.20000e+02, ctB= 5.85760e+02 60: functype[132]=ANGLES, thA= 1.20000e+02, ctA= 5.27184e+02, thB= 1.20000e+02, ctB= 5.27184e+02 60: functype[133]=ANGLES, thA= 1.20000e+02, ctA= 2.92880e+02, thB= 1.20000e+02, ctB= 2.92880e+02 60: functype[134]=ANGLES, thA= 1.18400e+02, ctA= 2.92880e+02, thB= 1.18400e+02, ctB= 2.92880e+02 60: functype[135]=ANGLES, thA= 1.23200e+02, ctA= 4.18400e+02, thB= 1.23200e+02, ctB= 4.18400e+02 60: functype[136]=ANGLES, thA= 1.08600e+02, ctA= 4.18400e+02, thB= 1.08600e+02, ctB= 4.18400e+02 60: functype[137]=ANGLES, thA= 9.60000e+01, ctA= 3.68192e+02, thB= 9.60000e+01, ctB= 3.68192e+02 60: functype[138]=ANGLES, thA= 1.17000e+02, ctA= 5.85760e+02, thB= 1.17000e+02, ctB= 5.85760e+02 60: functype[139]=ANGLES, thA= 1.26000e+02, ctA= 6.69440e+02, thB= 1.26000e+02, ctB= 6.69440e+02 60: functype[140]=PDIHS, phiA= 1.80000000e+02, cpA= 4.39319992e+01, phiB= 1.80000000e+02, cpB= 4.39319992e+01, mult=2 60: functype[141]=PDIHS, phiA= 1.80000000e+02, cpA= 4.18400002e+00, phiB= 1.80000000e+02, cpB= 4.18400002e+00, mult=2 60: functype[142]=PDIHS, phiA= 1.80000000e+02, cpA= 4.60239983e+00, phiB= 1.80000000e+02, cpB= 4.60239983e+00, mult=2 60: functype[143]=RBDIHS, rbcA[0]= 5.46010017e-01, rbcA[1]= 1.63803005e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.18405008e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 5.46010017e-01, rbcB[1]= 1.63803005e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.18405008e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[144]=RBDIHS, rbcA[0]= 7.25920022e-01, rbcA[1]= 2.17776990e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.90370011e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 7.25920022e-01, rbcB[1]= 2.17776990e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.90370011e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[145]=RBDIHS, rbcA[0]= 1.27611995e+00, rbcA[1]= 1.16734004e+00, rbcA[2]= 8.95380020e-01, rbcA[3]=-3.33884001e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 1.27611995e+00, rbcB[1]= 1.16734004e+00, rbcB[2]= 8.95380020e-01, rbcB[3]=-3.33884001e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[146]=RBDIHS, rbcA[0]=-6.91824007e+00, rbcA[1]= 4.67562008e+00, rbcA[2]= 2.24261999e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-6.91824007e+00, rbcB[1]= 4.67562008e+00, rbcB[2]= 2.24261999e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[147]=RBDIHS, rbcA[0]= 9.70690012e-01, rbcA[1]= 2.91206002e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.88275003e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 9.70690012e-01, rbcB[1]= 2.91206002e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.88275003e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[148]=RBDIHS, rbcA[0]= 6.27600014e-01, rbcA[1]= 1.88279998e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.51040006e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 6.27600014e-01, rbcB[1]= 1.88279998e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.51040006e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[149]=RBDIHS, rbcA[0]=-1.58989996e-01, rbcA[1]=-4.76980001e-01, rbcA[2]= 0.00000000e+00, rbcA[3]= 6.35959983e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-1.58989996e-01, rbcB[1]=-4.76980001e-01, rbcB[2]= 0.00000000e+00, rbcB[3]= 6.35959983e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[150]=RBDIHS, rbcA[0]= 1.03637600e+01, rbcA[1]=-6.60654020e+00, rbcA[2]=-1.04934702e+01, rbcA[3]= 6.73623991e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 1.03637600e+01, rbcB[1]=-6.60654020e+00, rbcB[2]=-1.04934702e+01, rbcB[3]= 6.73623991e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[151]=RBDIHS, rbcA[0]= 5.00825024e+00, rbcA[1]=-1.69869995e+00, rbcA[2]=-3.72379988e-01, rbcA[3]=-2.93716002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 5.00825024e+00, rbcB[1]=-1.69869995e+00, rbcB[2]=-3.72379988e-01, rbcB[3]=-2.93716002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[152]=RBDIHS, rbcA[0]= 2.92880011e+00, rbcA[1]=-1.46440005e+00, rbcA[2]= 2.09199995e-01, rbcA[3]=-1.67359996e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 2.92880011e+00, rbcB[1]=-1.46440005e+00, rbcB[2]= 2.09199995e-01, rbcB[3]=-1.67359996e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[153]=RBDIHS, rbcA[0]= 5.77183008e+00, rbcA[1]=-2.67147994e+00, rbcA[2]= 9.58140016e-01, rbcA[3]=-4.05847979e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 5.77183008e+00, rbcB[1]=-2.67147994e+00, rbcB[2]= 9.58140016e-01, rbcB[3]=-4.05847979e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[154]=RBDIHS, rbcA[0]= 8.03330004e-01, rbcA[1]= 2.40999007e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.21331000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 8.03330004e-01, rbcB[1]= 2.40999007e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.21331000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[155]=RBDIHS, rbcA[0]= 2.05016003e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.05016003e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 2.05016003e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.05016003e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[156]=RBDIHS, rbcA[0]= 3.02879791e+01, rbcA[1]=-4.81160021e+00, rbcA[2]=-2.54763794e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 3.02879791e+01, rbcB[1]=-4.81160021e+00, rbcB[2]=-2.54763794e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[157]=RBDIHS, rbcA[0]= 2.54763794e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.54763794e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 2.54763794e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.54763794e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[158]=RBDIHS, rbcA[0]= 1.57025499e+01, rbcA[1]= 3.17565594e+01, rbcA[2]=-3.66935992e+00, rbcA[3]=-4.37897491e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 1.57025499e+01, rbcB[1]= 3.17565594e+01, rbcB[2]=-3.66935992e+00, rbcB[3]=-4.37897491e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[159]=RBDIHS, rbcA[0]=-1.03574896e+01, rbcA[1]=-2.95871601e+01, rbcA[2]=-1.16734004e+00, rbcA[3]= 4.11119919e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-1.03574896e+01, rbcB[1]=-2.95871601e+01, rbcB[2]=-1.16734004e+00, rbcB[3]= 4.11119919e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[160]=RBDIHS, rbcA[0]= 4.50198984e+00, rbcA[1]= 7.82410026e-01, rbcA[2]=-1.60247004e+00, rbcA[3]=-3.68192005e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 4.50198984e+00, rbcB[1]= 7.82410026e-01, rbcB[2]=-1.60247004e+00, rbcB[3]=-3.68192005e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[161]=RBDIHS, rbcA[0]= 4.22589988e-01, rbcA[1]= 2.70705009e+00, rbcA[2]=-3.12964010e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 4.22589988e-01, rbcB[1]= 2.70705009e+00, rbcB[2]=-3.12964010e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[162]=RBDIHS, rbcA[0]=-7.65670002e-01, rbcA[1]= 2.70705009e+00, rbcA[2]= 4.02501011e+00, rbcA[3]=-5.96639013e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-7.65670002e-01, rbcB[1]= 2.70705009e+00, rbcB[2]= 4.02501011e+00, rbcB[3]=-5.96639013e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[163]=RBDIHS, rbcA[0]= 9.66499984e-01, rbcA[1]= 2.89950991e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.86600995e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 9.66499984e-01, rbcB[1]= 2.89950991e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.86600995e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[164]=RBDIHS, rbcA[0]=-4.23421001e+00, rbcA[1]= 7.22159004e+00, rbcA[2]= 1.90789998e+00, rbcA[3]=-4.89527988e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-4.23421001e+00, rbcB[1]= 7.22159004e+00, rbcB[2]= 1.90789998e+00, rbcB[3]=-4.89527988e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[165]=RBDIHS, rbcA[0]= 3.03339996e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.03339996e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 3.03339996e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.03339996e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[166]=RBDIHS, rbcA[0]= 1.02319698e+01, rbcA[1]= 3.52082992e+00, rbcA[2]=-3.97899008e+00, rbcA[3]=-9.77381992e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 1.02319698e+01, rbcB[1]= 3.52082992e+00, rbcB[2]=-3.97899008e+00, rbcB[3]=-9.77381992e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[167]=RBDIHS, rbcA[0]= 5.49777985e+00, rbcA[1]= 1.41838002e+00, rbcA[2]=-6.91615009e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 5.49777985e+00, rbcB[1]= 1.41838002e+00, rbcB[2]=-6.91615009e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[168]=RBDIHS, rbcA[0]=-1.21755004e+00, rbcA[1]=-3.65264010e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 4.87018013e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-1.21755004e+00, rbcB[1]=-3.65264010e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 4.87018013e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[169]=RBDIHS, rbcA[0]=-1.26775002e+00, rbcA[1]= 3.02084994e+00, rbcA[2]= 1.74473000e+00, rbcA[3]=-3.49781990e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-1.26775002e+00, rbcB[1]= 3.02084994e+00, rbcB[2]= 1.74473000e+00, rbcB[3]=-3.49781990e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[170]=RBDIHS, rbcA[0]= 3.80117011e+00, rbcA[1]=-6.95172024e+00, rbcA[2]=-1.01671004e+00, rbcA[3]= 4.16726017e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 3.80117011e+00, rbcB[1]=-6.95172024e+00, rbcB[2]=-1.01671004e+00, rbcB[3]= 4.16726017e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[171]=RBDIHS, rbcA[0]= 3.70279998e-01, rbcA[1]= 1.11085999e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-1.48114002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 3.70279998e-01, rbcB[1]= 1.11085999e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-1.48114002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[172]=RBDIHS, rbcA[0]= 3.32042198e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.32042198e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 3.32042198e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.32042198e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[173]=RBDIHS, rbcA[0]= 1.63176003e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-1.63176003e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 1.63176003e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-1.63176003e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[174]=RBDIHS, rbcA[0]= 3.40787005e+00, rbcA[1]=-2.80537009e+00, rbcA[2]=-3.59820008e-01, rbcA[3]=-2.42670000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 3.40787005e+00, rbcB[1]=-2.80537009e+00, rbcB[2]=-3.59820008e-01, rbcB[3]=-2.42670000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[175]=RBDIHS, rbcA[0]=-1.62590199e+01, rbcA[1]= 9.08765030e+00, rbcA[2]= 7.17138004e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-1.62590199e+01, rbcB[1]= 9.08765030e+00, rbcB[2]= 7.17138004e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[176]=RBDIHS, rbcA[0]= 9.45590019e-01, rbcA[1]= 2.83675003e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.78234005e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 9.45590019e-01, rbcB[1]= 2.83675003e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.78234005e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[177]=RBDIHS, rbcA[0]=-1.50624001e+00, rbcA[1]= 5.37225008e+00, rbcA[2]= 1.17989004e+00, rbcA[3]=-5.04589987e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-1.50624001e+00, rbcB[1]= 5.37225008e+00, rbcB[2]= 1.17989004e+00, rbcB[3]=-5.04589987e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[178]=RBDIHS, rbcA[0]= 1.00416005e+00, rbcA[1]= 3.01248002e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-4.01664019e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 1.00416005e+00, rbcB[1]= 3.01248002e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-4.01664019e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[179]=RBDIHS, rbcA[0]= 8.79267979e+00, rbcA[1]=-1.18344402e+01, rbcA[2]= 1.07528996e+00, rbcA[3]= 1.96648002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 8.79267979e+00, rbcB[1]=-1.18344402e+01, rbcB[2]= 1.07528996e+00, rbcB[3]= 1.96648002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[180]=RBDIHS, rbcA[0]=-5.77392006e+00, rbcA[1]= 3.38485003e+00, rbcA[2]= 2.38906002e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-5.77392006e+00, rbcB[1]= 3.38485003e+00, rbcB[2]= 2.38906002e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[181]=RBDIHS, rbcA[0]=-9.08345985e+00, rbcA[1]= 9.75708961e+00, rbcA[2]= 3.45180011e+00, rbcA[3]=-4.12542009e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-9.08345985e+00, rbcB[1]= 9.75708961e+00, rbcB[2]= 3.45180011e+00, rbcB[3]=-4.12542009e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[182]=RBDIHS, rbcA[0]=-4.70699996e-01, rbcA[1]=-1.41209996e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 1.88279998e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-4.70699996e-01, rbcB[1]=-1.41209996e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 1.88279998e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[183]=RBDIHS, rbcA[0]= 3.43088007e+00, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.43088007e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 3.43088007e+00, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.43088007e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[184]=RBDIHS, rbcA[0]= 2.57315993e+00, rbcA[1]= 3.49781990e+00, rbcA[2]=-1.10038996e+00, rbcA[3]=-4.97059011e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 2.57315993e+00, rbcB[1]= 3.49781990e+00, rbcB[2]=-1.10038996e+00, rbcB[3]=-4.97059011e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[185]=RBDIHS, rbcA[0]=-8.22160006e-01, rbcA[1]= 1.12758994e+00, rbcA[2]=-3.05440009e-01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-8.22160006e-01, rbcB[1]= 1.12758994e+00, rbcB[2]=-3.05440009e-01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[186]=LJ14, c6A= 3.20536114e-04, c12A= 1.71928207e-07, c6B= 3.20536114e-04, c12B= 1.71928207e-07 60: functype[187]=LJ14, c6A= 1.30458479e-03, c12A= 1.92011203e-06, c6B= 1.30458479e-03, c12B= 1.92011203e-06 60: functype[188]=LJ14, c6A= 1.40760513e-03, c12A= 1.25315830e-06, c6B= 1.40760513e-03, c12B= 1.25315830e-06 60: functype[189]=LJ14, c6A= 1.67637295e-03, c12A= 1.97547138e-06, c6B= 1.67637295e-03, c12B= 1.97547138e-06 60: functype[190]=LJ14, c6A= 0.00000000e+00, c12A= 0.00000000e+00, c6B= 0.00000000e+00, c12B= 0.00000000e+00 60: functype[191]=LJ14, c6A= 2.49447097e-04, c12A= 1.67110088e-07, c6B= 2.49447097e-04, c12B= 1.67110088e-07 60: functype[192]=LJ14, c6A= 1.01525197e-03, c12A= 1.86630257e-06, c6B= 1.01525197e-03, c12B= 1.86630257e-06 60: functype[193]=LJ14, c6A= 6.12890653e-05, c12A= 1.49631507e-08, c6B= 6.12890653e-05, c12B= 1.49631507e-08 60: functype[194]=LJ14, c6A= 2.69145414e-04, c12A= 1.09064160e-07, c6B= 2.69145414e-04, c12B= 1.09064160e-07 60: functype[195]=LJ14, c6A= 1.09542510e-03, c12A= 1.21804135e-06, c6B= 1.09542510e-03, c12B= 1.21804135e-06 60: functype[196]=LJ14, c6A= 3.86982108e-04, c12A= 3.18863499e-07, c6B= 3.86982108e-04, c12B= 3.18863499e-07 60: functype[197]=LJ14, c6A= 1.57502061e-03, c12A= 3.56110013e-06, c6B= 1.57502061e-03, c12B= 3.56110013e-06 60: functype[198]=LJ14, c6A= 2.44342256e-03, c12A= 6.79494860e-06, c6B= 2.44342256e-03, c12B= 6.79494860e-06 60: functype[199]=LJ14, c6A= 1.40194211e-03, c12A= 2.15310411e-06, c6B= 1.40194211e-03, c12B= 2.15310411e-06 60: functype[200]=LJ14, c6A= 1.09101785e-03, c12A= 2.09276800e-06, c6B= 1.09101785e-03, c12B= 2.09276800e-06 60: functype[201]=LJ14, c6A= 2.68062693e-04, c12A= 1.87387855e-07, c6B= 2.68062693e-04, c12B= 1.87387855e-07 60: functype[202]=LJ14, c6A= 2.26258271e-04, c12A= 1.37484790e-07, c6B= 2.26258271e-04, c12B= 1.37484790e-07 60: functype[203]=LJ14, c6A= 2.43143426e-04, c12A= 1.54167822e-07, c6B= 2.43143426e-04, c12B= 1.54167822e-07 60: functype[204]=LJ14, c6A= 1.17243768e-03, c12A= 2.34671188e-06, c6B= 1.17243768e-03, c12B= 2.34671188e-06 60: functype[205]=LJ14, c6A= 1.69256027e-03, c12A= 3.99321743e-06, c6B= 1.69256027e-03, c12B= 3.99321743e-06 60: functype[206]=LJ14, c6A= 5.04237469e-05, c12A= 1.01280841e-08, c6B= 5.04237469e-05, c12B= 1.01280841e-08 60: functype[207]=LJ14, c6A= 2.34763342e-04, c12A= 1.14652082e-07, c6B= 2.34763342e-04, c12B= 1.14652082e-07 60: functype[208]=LJ14, c6A= 5.76812672e-05, c12A= 1.02660236e-08, c6B= 5.76812672e-05, c12B= 1.02660236e-08 60: functype[209]=LJ14, c6A= 3.60245234e-03, c12A= 5.76973571e-06, c6B= 3.60245234e-03, c12B= 5.76973571e-06 60: functype[210]=LJ14, c6A= 6.88817876e-04, c12A= 5.02148339e-07, c6B= 6.88817876e-04, c12B= 5.02148339e-07 60: functype[211]=LJ14, c6A= 4.34922846e-03, c12A= 1.07007354e-05, c6B= 4.34922846e-03, c12B= 1.07007354e-05 60: reppow = 12 60: fudgeQQ = 0.5 60: cmap 60: moltype (0): 60: name="Protein_chain_B" 60: atoms: 60: atom (156): 60: atom[ 0]={type= 0, typeB= 0, ptype= Atom, m= 1.40027e+01, q=-3.00000e-01, mB= 1.40027e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} 60: atom[ 1]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 60: atom[ 2]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 60: atom[ 3]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 60: atom[ 4]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 2.50000e-01, mB= 1.20110e+01, qB= 2.50000e-01, resind= 0, atomnumber= 6} 60: atom[ 5]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 60: atom[ 6]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 60: atom[ 7]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 60: atom[ 8]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 60: atom[ 9]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 60: atom[ 10]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 60: atom[ 11]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 60: atom[ 12]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 60: atom[ 13]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 60: atom[ 14]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 60: atom[ 15]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 0, atomnumber= 6} 60: atom[ 16]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 60: atom[ 17]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 60: atom[ 18]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-3.00000e-01, mB= 1.40067e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} 60: atom[ 19]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 60: atom[ 20]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 60: atom[ 21]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 60: atom[ 22]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 0, atomnumber= 6} 60: atom[ 23]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 0, atomnumber= 8} 60: atom[ 24]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 1, atomnumber= 7} 60: atom[ 25]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 1, atomnumber= 1} 60: atom[ 26]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 1, atomnumber= 6} 60: atom[ 27]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 60: atom[ 28]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 1, atomnumber= 6} 60: atom[ 29]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 60: atom[ 30]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} 60: atom[ 31]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 60: atom[ 32]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 60: atom[ 33]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 60: atom[ 34]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} 60: atom[ 35]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 60: atom[ 36]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 60: atom[ 37]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 60: atom[ 38]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 1, atomnumber= 6} 60: atom[ 39]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 1, atomnumber= 8} 60: atom[ 40]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 2, atomnumber= 7} 60: atom[ 41]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 2, atomnumber= 1} 60: atom[ 42]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 2, atomnumber= 6} 60: atom[ 43]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 60: atom[ 44]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-03, mB= 1.20110e+01, qB=-5.00000e-03, resind= 2, atomnumber= 6} 60: atom[ 45]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 60: atom[ 46]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 60: atom[ 47]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 60: atom[ 48]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 60: atom[ 49]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 60: atom[ 50]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 60: atom[ 51]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 60: atom[ 52]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 60: atom[ 53]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 60: atom[ 54]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 60: atom[ 55]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 60: atom[ 56]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 60: atom[ 57]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 60: atom[ 58]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 2, atomnumber= 6} 60: atom[ 59]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 2, atomnumber= 8} 60: atom[ 60]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 3, atomnumber= 7} 60: atom[ 61]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 3, atomnumber= 1} 60: atom[ 62]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 8.00000e-02, mB= 1.20110e+01, qB= 8.00000e-02, resind= 3, atomnumber= 6} 60: atom[ 63]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} 60: atom[ 64]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} 60: atom[ 65]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 3, atomnumber= 6} 60: atom[ 66]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 3, atomnumber= 8} 60: atom[ 67]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 4, atomnumber= 7} 60: atom[ 68]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 4, atomnumber= 1} 60: atom[ 69]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 4, atomnumber= 6} 60: atom[ 70]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 60: atom[ 71]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 4, atomnumber= 6} 60: atom[ 72]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 60: atom[ 73]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 60: atom[ 74]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-02, mB= 1.20110e+01, qB=-5.00000e-02, resind= 4, atomnumber= 6} 60: atom[ 75]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 60: atom[ 76]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 60: atom[ 77]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 4, atomnumber= 6} 60: atom[ 78]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 60: atom[ 79]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 60: atom[ 80]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-7.00000e-01, mB= 1.40067e+01, qB=-7.00000e-01, resind= 4, atomnumber= 7} 60: atom[ 81]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.40000e-01, mB= 1.00800e+00, qB= 4.40000e-01, resind= 4, atomnumber= 1} 60: atom[ 82]={type= 8, typeB= 8, ptype= Atom, m= 1.20110e+01, q= 6.40000e-01, mB= 1.20110e+01, qB= 6.40000e-01, resind= 4, atomnumber= 6} 60: atom[ 83]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} 60: atom[ 84]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 60: atom[ 85]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 60: atom[ 86]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} 60: atom[ 87]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 60: atom[ 88]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 60: atom[ 89]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 4, atomnumber= 6} 60: atom[ 90]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 4, atomnumber= 8} 60: atom[ 91]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 5, atomnumber= 7} 60: atom[ 92]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 5, atomnumber= 1} 60: atom[ 93]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 5, atomnumber= 6} 60: atom[ 94]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 60: atom[ 95]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 6.00000e-02, mB= 1.20110e+01, qB= 6.00000e-02, resind= 5, atomnumber= 6} 60: atom[ 96]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 60: atom[ 97]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 60: atom[ 98]={type= 9, typeB= 9, ptype= Atom, m= 3.20600e+01, q=-3.35000e-01, mB= 3.20600e+01, qB=-3.35000e-01, resind= 5, atomnumber= 16} 60: atom[ 99]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 1.55000e-01, mB= 1.00800e+00, qB= 1.55000e-01, resind= 5, atomnumber= 1} 60: atom[ 100]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 5, atomnumber= 6} 60: atom[ 101]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 5, atomnumber= 8} 60: atom[ 102]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 6, atomnumber= 7} 60: atom[ 103]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 6, atomnumber= 1} 60: atom[ 104]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 6, atomnumber= 6} 60: atom[ 105]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 60: atom[ 106]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 6, atomnumber= 6} 60: atom[ 107]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 60: atom[ 108]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 60: atom[ 109]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-2.20000e-01, mB= 1.20110e+01, qB=-2.20000e-01, resind= 6, atomnumber= 6} 60: atom[ 110]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 60: atom[ 111]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 60: atom[ 112]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 7.00000e-01, mB= 1.20110e+01, qB= 7.00000e-01, resind= 6, atomnumber= 6} 60: atom[ 113]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} 60: atom[ 114]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} 60: atom[ 115]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 6, atomnumber= 6} 60: atom[ 116]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 6, atomnumber= 8} 60: atom[ 117]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 7, atomnumber= 7} 60: atom[ 118]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 7, atomnumber= 1} 60: atom[ 119]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 7, atomnumber= 6} 60: atom[ 120]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 60: atom[ 121]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 7, atomnumber= 6} 60: atom[ 122]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 60: atom[ 123]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 60: atom[ 124]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 7, atomnumber= 6} 60: atom[ 125]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 60: atom[ 126]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} 60: atom[ 127]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 60: atom[ 128]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 60: atom[ 129]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 60: atom[ 130]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} 60: atom[ 131]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 60: atom[ 132]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 60: atom[ 133]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 60: atom[ 134]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 7, atomnumber= 6} 60: atom[ 135]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 7, atomnumber= 8} 60: atom[ 136]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 8, atomnumber= 7} 60: atom[ 137]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 8, atomnumber= 1} 60: atom[ 138]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 8, atomnumber= 6} 60: atom[ 139]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 60: atom[ 140]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 8, atomnumber= 6} 60: atom[ 141]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 60: atom[ 142]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 60: atom[ 143]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 60: atom[ 144]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 8, atomnumber= 6} 60: atom[ 145]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 8, atomnumber= 8} 60: atom[ 146]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 9, atomnumber= 7} 60: atom[ 147]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 9, atomnumber= 1} 60: atom[ 148]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 9, atomnumber= 6} 60: atom[ 149]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 60: atom[ 150]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 9, atomnumber= 6} 60: atom[ 151]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 60: atom[ 152]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 60: atom[ 153]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 60: atom[ 154]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 9, atomnumber= 6} 60: atom[ 155]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 9, atomnumber= 8} 60: atom (156): 60: atom[0]={name="N"} 60: atom[1]={name="H1"} 60: atom[2]={name="H2"} 60: atom[3]={name="H3"} 60: atom[4]={name="CA"} 60: atom[5]={name="HA"} 60: atom[6]={name="CB"} 60: atom[7]={name="HB1"} 60: atom[8]={name="HB2"} 60: atom[9]={name="CG"} 60: atom[10]={name="HG1"} 60: atom[11]={name="HG2"} 60: atom[12]={name="CD"} 60: atom[13]={name="HD1"} 60: atom[14]={name="HD2"} 60: atom[15]={name="CE"} 60: atom[16]={name="HE1"} 60: atom[17]={name="HE2"} 60: atom[18]={name="NZ"} 60: atom[19]={name="HZ1"} 60: atom[20]={name="HZ2"} 60: atom[21]={name="HZ3"} 60: atom[22]={name="C"} 60: atom[23]={name="O"} 60: atom[24]={name="N"} 60: atom[25]={name="H"} 60: atom[26]={name="CA"} 60: atom[27]={name="HA"} 60: atom[28]={name="CB"} 60: atom[29]={name="HB"} 60: atom[30]={name="CG1"} 60: atom[31]={name="HG11"} 60: atom[32]={name="HG12"} 60: atom[33]={name="HG13"} 60: atom[34]={name="CG2"} 60: atom[35]={name="HG21"} 60: atom[36]={name="HG22"} 60: atom[37]={name="HG23"} 60: atom[38]={name="C"} 60: atom[39]={name="O"} 60: atom[40]={name="N"} 60: atom[41]={name="H"} 60: atom[42]={name="CA"} 60: atom[43]={name="HA"} 60: atom[44]={name="CB"} 60: atom[45]={name="HB1"} 60: atom[46]={name="HB2"} 60: atom[47]={name="CG"} 60: atom[48]={name="CD1"} 60: atom[49]={name="HD1"} 60: atom[50]={name="CD2"} 60: atom[51]={name="HD2"} 60: atom[52]={name="CE1"} 60: atom[53]={name="HE1"} 60: atom[54]={name="CE2"} 60: atom[55]={name="HE2"} 60: atom[56]={name="CZ"} 60: atom[57]={name="HZ"} 60: atom[58]={name="C"} 60: atom[59]={name="O"} 60: atom[60]={name="N"} 60: atom[61]={name="H"} 60: atom[62]={name="CA"} 60: atom[63]={name="HA1"} 60: atom[64]={name="HA2"} 60: atom[65]={name="C"} 60: atom[66]={name="O"} 60: atom[67]={name="N"} 60: atom[68]={name="H"} 60: atom[69]={name="CA"} 60: atom[70]={name="HA"} 60: atom[71]={name="CB"} 60: atom[72]={name="HB1"} 60: atom[73]={name="HB2"} 60: atom[74]={name="CG"} 60: atom[75]={name="HG1"} 60: atom[76]={name="HG2"} 60: atom[77]={name="CD"} 60: atom[78]={name="HD1"} 60: atom[79]={name="HD2"} 60: atom[80]={name="NE"} 60: atom[81]={name="HE"} 60: atom[82]={name="CZ"} 60: atom[83]={name="NH1"} 60: atom[84]={name="HH11"} 60: atom[85]={name="HH12"} 60: atom[86]={name="NH2"} 60: atom[87]={name="HH21"} 60: atom[88]={name="HH22"} 60: atom[89]={name="C"} 60: atom[90]={name="O"} 60: atom[91]={name="N"} 60: atom[92]={name="H"} 60: atom[93]={name="CA"} 60: atom[94]={name="HA"} 60: atom[95]={name="CB"} 60: atom[96]={name="HB1"} 60: atom[97]={name="HB2"} 60: atom[98]={name="SG"} 60: atom[99]={name="HG"} 60: atom[100]={name="C"} 60: atom[101]={name="O"} 60: atom[102]={name="N"} 60: atom[103]={name="H"} 60: atom[104]={name="CA"} 60: atom[105]={name="HA"} 60: atom[106]={name="CB"} 60: atom[107]={name="HB1"} 60: atom[108]={name="HB2"} 60: atom[109]={name="CG"} 60: atom[110]={name="HG1"} 60: atom[111]={name="HG2"} 60: atom[112]={name="CD"} 60: atom[113]={name="OE1"} 60: atom[114]={name="OE2"} 60: atom[115]={name="C"} 60: atom[116]={name="O"} 60: atom[117]={name="N"} 60: atom[118]={name="H"} 60: atom[119]={name="CA"} 60: atom[120]={name="HA"} 60: atom[121]={name="CB"} 60: atom[122]={name="HB1"} 60: atom[123]={name="HB2"} 60: atom[124]={name="CG"} 60: atom[125]={name="HG"} 60: atom[126]={name="CD1"} 60: atom[127]={name="HD11"} 60: atom[128]={name="HD12"} 60: atom[129]={name="HD13"} 60: atom[130]={name="CD2"} 60: atom[131]={name="HD21"} 60: atom[132]={name="HD22"} 60: atom[133]={name="HD23"} 60: atom[134]={name="C"} 60: atom[135]={name="O"} 60: atom[136]={name="N"} 60: atom[137]={name="H"} 60: atom[138]={name="CA"} 60: atom[139]={name="HA"} 60: atom[140]={name="CB"} 60: atom[141]={name="HB1"} 60: atom[142]={name="HB2"} 60: atom[143]={name="HB3"} 60: atom[144]={name="C"} 60: atom[145]={name="O"} 60: atom[146]={name="N"} 60: atom[147]={name="H"} 60: atom[148]={name="CA"} 60: atom[149]={name="HA"} 60: atom[150]={name="CB"} 60: atom[151]={name="HB1"} 60: atom[152]={name="HB2"} 60: atom[153]={name="HB3"} 60: atom[154]={name="C"} 60: atom[155]={name="O"} 60: type (156): 60: type[0]={name="opls_287",nameB="opls_287"} 60: type[1]={name="opls_290",nameB="opls_290"} 60: type[2]={name="opls_290",nameB="opls_290"} 60: type[3]={name="opls_290",nameB="opls_290"} 60: type[4]={name="opls_293B",nameB="opls_293B"} 60: type[5]={name="opls_140",nameB="opls_140"} 60: type[6]={name="opls_136",nameB="opls_136"} 60: type[7]={name="opls_140",nameB="opls_140"} 60: type[8]={name="opls_140",nameB="opls_140"} 60: type[9]={name="opls_136",nameB="opls_136"} 60: type[10]={name="opls_140",nameB="opls_140"} 60: type[11]={name="opls_140",nameB="opls_140"} 60: type[12]={name="opls_136",nameB="opls_136"} 60: type[13]={name="opls_140",nameB="opls_140"} 60: type[14]={name="opls_140",nameB="opls_140"} 60: type[15]={name="opls_292",nameB="opls_292"} 60: type[16]={name="opls_140",nameB="opls_140"} 60: type[17]={name="opls_140",nameB="opls_140"} 60: type[18]={name="opls_287",nameB="opls_287"} 60: type[19]={name="opls_290",nameB="opls_290"} 60: type[20]={name="opls_290",nameB="opls_290"} 60: type[21]={name="opls_290",nameB="opls_290"} 60: type[22]={name="opls_235",nameB="opls_235"} 60: type[23]={name="opls_236",nameB="opls_236"} 60: type[24]={name="opls_238",nameB="opls_238"} 60: type[25]={name="opls_241",nameB="opls_241"} 60: type[26]={name="opls_224B",nameB="opls_224B"} 60: type[27]={name="opls_140",nameB="opls_140"} 60: type[28]={name="opls_137",nameB="opls_137"} 60: type[29]={name="opls_140",nameB="opls_140"} 60: type[30]={name="opls_135",nameB="opls_135"} 60: type[31]={name="opls_140",nameB="opls_140"} 60: type[32]={name="opls_140",nameB="opls_140"} 60: type[33]={name="opls_140",nameB="opls_140"} 60: type[34]={name="opls_135",nameB="opls_135"} 60: type[35]={name="opls_140",nameB="opls_140"} 60: type[36]={name="opls_140",nameB="opls_140"} 60: type[37]={name="opls_140",nameB="opls_140"} 60: type[38]={name="opls_235",nameB="opls_235"} 60: type[39]={name="opls_236",nameB="opls_236"} 60: type[40]={name="opls_238",nameB="opls_238"} 60: type[41]={name="opls_241",nameB="opls_241"} 60: type[42]={name="opls_224B",nameB="opls_224B"} 60: type[43]={name="opls_140",nameB="opls_140"} 60: type[44]={name="opls_149",nameB="opls_149"} 60: type[45]={name="opls_140",nameB="opls_140"} 60: type[46]={name="opls_140",nameB="opls_140"} 60: type[47]={name="opls_145",nameB="opls_145"} 60: type[48]={name="opls_145",nameB="opls_145"} 60: type[49]={name="opls_146",nameB="opls_146"} 60: type[50]={name="opls_145",nameB="opls_145"} 60: type[51]={name="opls_146",nameB="opls_146"} 60: type[52]={name="opls_145",nameB="opls_145"} 60: type[53]={name="opls_146",nameB="opls_146"} 60: type[54]={name="opls_145",nameB="opls_145"} 60: type[55]={name="opls_146",nameB="opls_146"} 60: type[56]={name="opls_145",nameB="opls_145"} 60: type[57]={name="opls_146",nameB="opls_146"} 60: type[58]={name="opls_235",nameB="opls_235"} 60: type[59]={name="opls_236",nameB="opls_236"} 60: type[60]={name="opls_238",nameB="opls_238"} 60: type[61]={name="opls_241",nameB="opls_241"} 60: type[62]={name="opls_223B",nameB="opls_223B"} 60: type[63]={name="opls_140",nameB="opls_140"} 60: type[64]={name="opls_140",nameB="opls_140"} 60: type[65]={name="opls_235",nameB="opls_235"} 60: type[66]={name="opls_236",nameB="opls_236"} 60: type[67]={name="opls_238",nameB="opls_238"} 60: type[68]={name="opls_241",nameB="opls_241"} 60: type[69]={name="opls_224B",nameB="opls_224B"} 60: type[70]={name="opls_140",nameB="opls_140"} 60: type[71]={name="opls_136",nameB="opls_136"} 60: type[72]={name="opls_140",nameB="opls_140"} 60: type[73]={name="opls_140",nameB="opls_140"} 60: type[74]={name="opls_308",nameB="opls_308"} 60: type[75]={name="opls_140",nameB="opls_140"} 60: type[76]={name="opls_140",nameB="opls_140"} 60: type[77]={name="opls_307",nameB="opls_307"} 60: type[78]={name="opls_140",nameB="opls_140"} 60: type[79]={name="opls_140",nameB="opls_140"} 60: type[80]={name="opls_303",nameB="opls_303"} 60: type[81]={name="opls_304",nameB="opls_304"} 60: type[82]={name="opls_302",nameB="opls_302"} 60: type[83]={name="opls_300",nameB="opls_300"} 60: type[84]={name="opls_301",nameB="opls_301"} 60: type[85]={name="opls_301",nameB="opls_301"} 60: type[86]={name="opls_300",nameB="opls_300"} 60: type[87]={name="opls_301",nameB="opls_301"} 60: type[88]={name="opls_301",nameB="opls_301"} 60: type[89]={name="opls_235",nameB="opls_235"} 60: type[90]={name="opls_236",nameB="opls_236"} 60: type[91]={name="opls_238",nameB="opls_238"} 60: type[92]={name="opls_241",nameB="opls_241"} 60: type[93]={name="opls_224B",nameB="opls_224B"} 60: type[94]={name="opls_140",nameB="opls_140"} 60: type[95]={name="opls_206",nameB="opls_206"} 60: type[96]={name="opls_140",nameB="opls_140"} 60: type[97]={name="opls_140",nameB="opls_140"} 60: type[98]={name="opls_200",nameB="opls_200"} 60: type[99]={name="opls_204",nameB="opls_204"} 60: type[100]={name="opls_235",nameB="opls_235"} 60: type[101]={name="opls_236",nameB="opls_236"} 60: type[102]={name="opls_238",nameB="opls_238"} 60: type[103]={name="opls_241",nameB="opls_241"} 60: type[104]={name="opls_224B",nameB="opls_224B"} 60: type[105]={name="opls_140",nameB="opls_140"} 60: type[106]={name="opls_136",nameB="opls_136"} 60: type[107]={name="opls_140",nameB="opls_140"} 60: type[108]={name="opls_140",nameB="opls_140"} 60: type[109]={name="opls_274",nameB="opls_274"} 60: type[110]={name="opls_140",nameB="opls_140"} 60: type[111]={name="opls_140",nameB="opls_140"} 60: type[112]={name="opls_271",nameB="opls_271"} 60: type[113]={name="opls_272",nameB="opls_272"} 60: type[114]={name="opls_272",nameB="opls_272"} 60: type[115]={name="opls_235",nameB="opls_235"} 60: type[116]={name="opls_236",nameB="opls_236"} 60: type[117]={name="opls_238",nameB="opls_238"} 60: type[118]={name="opls_241",nameB="opls_241"} 60: type[119]={name="opls_224B",nameB="opls_224B"} 60: type[120]={name="opls_140",nameB="opls_140"} 60: type[121]={name="opls_136",nameB="opls_136"} 60: type[122]={name="opls_140",nameB="opls_140"} 60: type[123]={name="opls_140",nameB="opls_140"} 60: type[124]={name="opls_137",nameB="opls_137"} 60: type[125]={name="opls_140",nameB="opls_140"} 60: type[126]={name="opls_135",nameB="opls_135"} 60: type[127]={name="opls_140",nameB="opls_140"} 60: type[128]={name="opls_140",nameB="opls_140"} 60: type[129]={name="opls_140",nameB="opls_140"} 60: type[130]={name="opls_135",nameB="opls_135"} 60: type[131]={name="opls_140",nameB="opls_140"} 60: type[132]={name="opls_140",nameB="opls_140"} 60: type[133]={name="opls_140",nameB="opls_140"} 60: type[134]={name="opls_235",nameB="opls_235"} 60: type[135]={name="opls_236",nameB="opls_236"} 60: type[136]={name="opls_238",nameB="opls_238"} 60: type[137]={name="opls_241",nameB="opls_241"} 60: type[138]={name="opls_224B",nameB="opls_224B"} 60: type[139]={name="opls_140",nameB="opls_140"} 60: type[140]={name="opls_135",nameB="opls_135"} 60: type[141]={name="opls_140",nameB="opls_140"} 60: type[142]={name="opls_140",nameB="opls_140"} 60: type[143]={name="opls_140",nameB="opls_140"} 60: type[144]={name="opls_235",nameB="opls_235"} 60: type[145]={name="opls_236",nameB="opls_236"} 60: type[146]={name="opls_238",nameB="opls_238"} 60: type[147]={name="opls_241",nameB="opls_241"} 60: type[148]={name="opls_224B",nameB="opls_224B"} 60: type[149]={name="opls_140",nameB="opls_140"} 60: type[150]={name="opls_135",nameB="opls_135"} 60: type[151]={name="opls_140",nameB="opls_140"} 60: type[152]={name="opls_140",nameB="opls_140"} 60: type[153]={name="opls_140",nameB="opls_140"} 60: type[154]={name="opls_235",nameB="opls_235"} 60: type[155]={name="opls_236",nameB="opls_236"} 60: residue (10): 60: residue[0]={name="LYS", nr=1, ic=' '} 60: residue[1]={name="VAL", nr=2, ic=' '} 60: residue[2]={name="PHE", nr=3, ic=' '} 60: residue[3]={name="GLY", nr=4, ic=' '} 60: residue[4]={name="ARG", nr=5, ic=' '} 60: residue[5]={name="CYS", nr=6, ic=' '} 60: residue[6]={name="GLU", nr=7, ic=' '} 60: residue[7]={name="LEU", nr=8, ic=' '} 60: residue[8]={name="ALA", nr=9, ic=' '} 60: residue[9]={name="ALA", nr=10, ic=' '} 60: excls: 60: numLists=156 60: numElements=1828 60: excls[0][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} 60: excls[1][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 60: excls[2][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 60: excls[3][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 60: excls[4][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 60: 23, 24, 25, 26} 60: excls[5][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} 60: excls[6][num=19]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 60: 14, 15, 22, 23, 24} 60: excls[7][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} 60: excls[8][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} 60: excls[9][num=17]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 60: 16, 17, 18, 22} 60: excls[10][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} 60: excls[11][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} 60: excls[12][num=17]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 60: 17, 18, 19, 20, 21} 60: excls[13][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} 60: excls[14][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} 60: excls[15][num=14]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 60: 20, 21} 60: excls[16][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 60: excls[17][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 60: excls[18][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 60: excls[19][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 60: excls[20][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 60: excls[21][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 60: excls[22][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 60: 26, 27, 28, 38} 60: excls[23][num=9]={0, 4, 5, 6, 22, 23, 24, 25, 26} 60: excls[24][num=17]={0, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 60: 30, 34, 38, 39, 40} 60: excls[25][num=9]={4, 22, 23, 24, 25, 26, 27, 28, 38} 60: excls[26][num=22]={4, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 60: 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42} 60: excls[27][num=12]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, 60: 40} 60: excls[28][num=18]={22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 60: 34, 35, 36, 37, 38, 39, 40} 60: excls[29][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 60: 36, 37, 38} 60: excls[30][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 60: 36, 37, 38} 60: excls[31][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 60: excls[32][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 60: excls[33][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 60: excls[34][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 60: 36, 37, 38} 60: excls[35][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 60: excls[36][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 60: excls[37][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 60: excls[38][num=17]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, 60: 40, 41, 42, 43, 44, 58} 60: excls[39][num=9]={24, 26, 27, 28, 38, 39, 40, 41, 42} 60: excls[40][num=17]={24, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 60: 45, 46, 47, 58, 59, 60} 60: excls[41][num=9]={26, 38, 39, 40, 41, 42, 43, 44, 58} 60: excls[42][num=18]={26, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 60: 48, 50, 58, 59, 60, 61, 62} 60: excls[43][num=12]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 60: 60} 60: excls[44][num=18]={38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 60: 50, 51, 52, 54, 58, 59, 60} 60: excls[45][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} 60: excls[46][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} 60: excls[47][num=17]={40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 60: 52, 53, 54, 55, 56, 58} 60: excls[48][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 60: 54, 56, 57} 60: excls[49][num=8]={44, 47, 48, 49, 50, 52, 53, 56} 60: excls[50][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 60: 55, 56, 57} 60: excls[51][num=8]={44, 47, 48, 50, 51, 54, 55, 56} 60: excls[52][num=11]={44, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57} 60: excls[53][num=8]={47, 48, 49, 52, 53, 54, 56, 57} 60: excls[54][num=11]={44, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57} 60: excls[55][num=8]={47, 50, 51, 52, 54, 55, 56, 57} 60: excls[56][num=11]={47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57} 60: excls[57][num=8]={48, 50, 52, 53, 54, 55, 56, 57} 60: excls[58][num=17]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 60: 60, 61, 62, 63, 64, 65} 60: excls[59][num=9]={40, 42, 43, 44, 58, 59, 60, 61, 62} 60: excls[60][num=14]={40, 42, 43, 44, 58, 59, 60, 61, 62, 63, 64, 60: 65, 66, 67} 60: excls[61][num=9]={42, 58, 59, 60, 61, 62, 63, 64, 65} 60: excls[62][num=13]={42, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 60: 68, 69} 60: excls[63][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67} 60: excls[64][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67} 60: excls[65][num=14]={58, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 60: 70, 71, 89} 60: excls[66][num=9]={60, 62, 63, 64, 65, 66, 67, 68, 69} 60: excls[67][num=17]={60, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 60: 72, 73, 74, 89, 90, 91} 60: excls[68][num=9]={62, 65, 66, 67, 68, 69, 70, 71, 89} 60: excls[69][num=19]={62, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 60: 75, 76, 77, 89, 90, 91, 92, 93} 60: excls[70][num=12]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, 60: 91} 60: excls[71][num=18]={65, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 60: 77, 78, 79, 80, 89, 90, 91} 60: excls[72][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} 60: excls[73][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} 60: excls[74][num=16]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 60: 79, 80, 81, 82, 89} 60: excls[75][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} 60: excls[76][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} 60: excls[77][num=15]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 60: 81, 82, 83, 86} 60: excls[78][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} 60: excls[79][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} 60: excls[80][num=16]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 60: 84, 85, 86, 87, 88} 60: excls[81][num=9]={74, 77, 78, 79, 80, 81, 82, 83, 86} 60: excls[82][num=13]={74, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 60: 87, 88} 60: excls[83][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} 60: excls[84][num=6]={80, 82, 83, 84, 85, 86} 60: excls[85][num=6]={80, 82, 83, 84, 85, 86} 60: excls[86][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} 60: excls[87][num=6]={80, 82, 83, 86, 87, 88} 60: excls[88][num=6]={80, 82, 83, 86, 87, 88} 60: excls[89][num=17]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, 60: 91, 92, 93, 94, 95, 100} 60: excls[90][num=9]={67, 69, 70, 71, 89, 90, 91, 92, 93} 60: excls[91][num=17]={67, 69, 70, 71, 89, 90, 91, 92, 93, 94, 95, 60: 96, 97, 98, 100, 101, 102} 60: excls[92][num=9]={69, 89, 90, 91, 92, 93, 94, 95, 100} 60: excls[93][num=17]={69, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 60: 99, 100, 101, 102, 103, 104} 60: excls[94][num=12]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101, 60: 102} 60: excls[95][num=13]={89, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 60: 101, 102} 60: excls[96][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 60: excls[97][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 60: excls[98][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 60: excls[99][num=6]={93, 95, 96, 97, 98, 99} 60: excls[100][num=17]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101, 60: 102, 103, 104, 105, 106, 115} 60: excls[101][num=9]={91, 93, 94, 95, 100, 101, 102, 103, 104} 60: excls[102][num=17]={91, 93, 94, 95, 100, 101, 102, 103, 104, 105, 60: 106, 107, 108, 109, 115, 116, 117} 60: excls[103][num=9]={93, 100, 101, 102, 103, 104, 105, 106, 115} 60: excls[104][num=19]={93, 100, 101, 102, 103, 104, 105, 106, 107, 60: 108, 109, 110, 111, 112, 115, 116, 117, 118, 119} 60: excls[105][num=12]={100, 102, 103, 104, 105, 106, 107, 108, 109, 60: 115, 116, 117} 60: excls[106][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109, 60: 110, 111, 112, 113, 114, 115, 116, 117} 60: excls[107][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111, 60: 112, 115} 60: excls[108][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111, 60: 112, 115} 60: excls[109][num=13]={102, 104, 105, 106, 107, 108, 109, 110, 111, 60: 112, 113, 114, 115} 60: excls[110][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 60: 114} 60: excls[111][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 60: 114} 60: excls[112][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 60: 114} 60: excls[113][num=7]={106, 109, 110, 111, 112, 113, 114} 60: excls[114][num=7]={106, 109, 110, 111, 112, 113, 114} 60: excls[115][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109, 60: 115, 116, 117, 118, 119, 120, 121, 134} 60: excls[116][num=9]={102, 104, 105, 106, 115, 116, 117, 118, 119} 60: excls[117][num=17]={102, 104, 105, 106, 115, 116, 117, 118, 119, 60: 120, 121, 122, 123, 124, 134, 135, 136} 60: excls[118][num=9]={104, 115, 116, 117, 118, 119, 120, 121, 134} 60: excls[119][num=19]={104, 115, 116, 117, 118, 119, 120, 121, 122, 60: 123, 124, 125, 126, 130, 134, 135, 136, 137, 138} 60: excls[120][num=12]={115, 117, 118, 119, 120, 121, 122, 123, 124, 60: 134, 135, 136} 60: excls[121][num=21]={115, 117, 118, 119, 120, 121, 122, 123, 124, 60: 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136} 60: excls[122][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126, 60: 130, 134} 60: excls[123][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126, 60: 130, 134} 60: excls[124][num=17]={117, 119, 120, 121, 122, 123, 124, 125, 126, 60: 127, 128, 129, 130, 131, 132, 133, 134} 60: excls[125][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 60: 129, 130, 131, 132, 133} 60: excls[126][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 60: 129, 130, 131, 132, 133} 60: excls[127][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 60: excls[128][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 60: excls[129][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 60: excls[130][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 60: 129, 130, 131, 132, 133} 60: excls[131][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 60: excls[132][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 60: excls[133][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 60: excls[134][num=17]={115, 117, 118, 119, 120, 121, 122, 123, 124, 60: 134, 135, 136, 137, 138, 139, 140, 144} 60: excls[135][num=9]={117, 119, 120, 121, 134, 135, 136, 137, 138} 60: excls[136][num=17]={117, 119, 120, 121, 134, 135, 136, 137, 138, 60: 139, 140, 141, 142, 143, 144, 145, 146} 60: excls[137][num=9]={119, 134, 135, 136, 137, 138, 139, 140, 144} 60: excls[138][num=16]={119, 134, 135, 136, 137, 138, 139, 140, 141, 60: 142, 143, 144, 145, 146, 147, 148} 60: excls[139][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143, 60: 144, 145, 146} 60: excls[140][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143, 60: 144, 145, 146} 60: excls[141][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 60: excls[142][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 60: excls[143][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 60: excls[144][num=17]={134, 136, 137, 138, 139, 140, 141, 142, 143, 60: 144, 145, 146, 147, 148, 149, 150, 154} 60: excls[145][num=9]={136, 138, 139, 140, 144, 145, 146, 147, 148} 60: excls[146][num=16]={136, 138, 139, 140, 144, 145, 146, 147, 148, 60: 149, 150, 151, 152, 153, 154, 155} 60: excls[147][num=9]={138, 144, 145, 146, 147, 148, 149, 150, 154} 60: excls[148][num=13]={138, 144, 145, 146, 147, 148, 149, 150, 151, 60: 152, 153, 154, 155} 60: excls[149][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 60: 154, 155} 60: excls[150][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 60: 154, 155} 60: excls[151][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 60: excls[152][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 60: excls[153][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 60: excls[154][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 60: 154, 155} 60: excls[155][num=6]={146, 148, 149, 150, 154, 155} 60: Bond: 60: nr: 468 60: iatoms: 60: 0 type=100 (BONDS) 0 1 60: 1 type=100 (BONDS) 0 2 60: 2 type=100 (BONDS) 0 3 60: 3 type=101 (BONDS) 0 4 60: 4 type=102 (BONDS) 4 5 60: 5 type=103 (BONDS) 4 6 60: 6 type=104 (BONDS) 4 22 60: 7 type=102 (BONDS) 6 7 60: 8 type=102 (BONDS) 6 8 60: 9 type=103 (BONDS) 6 9 60: 10 type=102 (BONDS) 9 10 60: 11 type=102 (BONDS) 9 11 60: 12 type=103 (BONDS) 9 12 60: 13 type=102 (BONDS) 12 13 60: 14 type=102 (BONDS) 12 14 60: 15 type=103 (BONDS) 12 15 60: 16 type=102 (BONDS) 15 16 60: 17 type=102 (BONDS) 15 17 60: 18 type=101 (BONDS) 15 18 60: 19 type=100 (BONDS) 18 19 60: 20 type=100 (BONDS) 18 20 60: 21 type=100 (BONDS) 18 21 60: 22 type=105 (BONDS) 22 23 60: 23 type=106 (BONDS) 22 24 60: 24 type=100 (BONDS) 24 25 60: 25 type=107 (BONDS) 24 26 60: 26 type=102 (BONDS) 26 27 60: 27 type=103 (BONDS) 26 28 60: 28 type=104 (BONDS) 26 38 60: 29 type=102 (BONDS) 28 29 60: 30 type=103 (BONDS) 28 30 60: 31 type=103 (BONDS) 28 34 60: 32 type=102 (BONDS) 30 31 60: 33 type=102 (BONDS) 30 32 60: 34 type=102 (BONDS) 30 33 60: 35 type=102 (BONDS) 34 35 60: 36 type=102 (BONDS) 34 36 60: 37 type=102 (BONDS) 34 37 60: 38 type=105 (BONDS) 38 39 60: 39 type=106 (BONDS) 38 40 60: 40 type=100 (BONDS) 40 41 60: 41 type=107 (BONDS) 40 42 60: 42 type=102 (BONDS) 42 43 60: 43 type=103 (BONDS) 42 44 60: 44 type=104 (BONDS) 42 58 60: 45 type=102 (BONDS) 44 45 60: 46 type=102 (BONDS) 44 46 60: 47 type=108 (BONDS) 44 47 60: 48 type=109 (BONDS) 47 48 60: 49 type=109 (BONDS) 47 50 60: 50 type=110 (BONDS) 48 49 60: 51 type=109 (BONDS) 48 52 60: 52 type=110 (BONDS) 50 51 60: 53 type=109 (BONDS) 50 54 60: 54 type=110 (BONDS) 52 53 60: 55 type=109 (BONDS) 52 56 60: 56 type=110 (BONDS) 54 55 60: 57 type=109 (BONDS) 54 56 60: 58 type=110 (BONDS) 56 57 60: 59 type=105 (BONDS) 58 59 60: 60 type=106 (BONDS) 58 60 60: 61 type=100 (BONDS) 60 61 60: 62 type=107 (BONDS) 60 62 60: 63 type=102 (BONDS) 62 63 60: 64 type=102 (BONDS) 62 64 60: 65 type=104 (BONDS) 62 65 60: 66 type=105 (BONDS) 65 66 60: 67 type=106 (BONDS) 65 67 60: 68 type=100 (BONDS) 67 68 60: 69 type=107 (BONDS) 67 69 60: 70 type=102 (BONDS) 69 70 60: 71 type=103 (BONDS) 69 71 60: 72 type=104 (BONDS) 69 89 60: 73 type=102 (BONDS) 71 72 60: 74 type=102 (BONDS) 71 73 60: 75 type=103 (BONDS) 71 74 60: 76 type=102 (BONDS) 74 75 60: 77 type=102 (BONDS) 74 76 60: 78 type=103 (BONDS) 74 77 60: 79 type=102 (BONDS) 77 78 60: 80 type=102 (BONDS) 77 79 60: 81 type=111 (BONDS) 77 80 60: 82 type=100 (BONDS) 80 81 60: 83 type=112 (BONDS) 80 82 60: 84 type=112 (BONDS) 82 83 60: 85 type=112 (BONDS) 82 86 60: 86 type=100 (BONDS) 83 84 60: 87 type=100 (BONDS) 83 85 60: 88 type=100 (BONDS) 86 87 60: 89 type=100 (BONDS) 86 88 60: 90 type=105 (BONDS) 89 90 60: 91 type=106 (BONDS) 89 91 60: 92 type=100 (BONDS) 91 92 60: 93 type=107 (BONDS) 91 93 60: 94 type=102 (BONDS) 93 94 60: 95 type=103 (BONDS) 93 95 60: 96 type=104 (BONDS) 93 100 60: 97 type=102 (BONDS) 95 96 60: 98 type=102 (BONDS) 95 97 60: 99 type=113 (BONDS) 95 98 60: 100 type=114 (BONDS) 98 99 60: 101 type=105 (BONDS) 100 101 60: 102 type=106 (BONDS) 100 102 60: 103 type=100 (BONDS) 102 103 60: 104 type=107 (BONDS) 102 104 60: 105 type=102 (BONDS) 104 105 60: 106 type=103 (BONDS) 104 106 60: 107 type=104 (BONDS) 104 115 60: 108 type=102 (BONDS) 106 107 60: 109 type=102 (BONDS) 106 108 60: 110 type=103 (BONDS) 106 109 60: 111 type=102 (BONDS) 109 110 60: 112 type=102 (BONDS) 109 111 60: 113 type=104 (BONDS) 109 112 60: 114 type=115 (BONDS) 112 113 60: 115 type=115 (BONDS) 112 114 60: 116 type=105 (BONDS) 115 116 60: 117 type=106 (BONDS) 115 117 60: 118 type=100 (BONDS) 117 118 60: 119 type=107 (BONDS) 117 119 60: 120 type=102 (BONDS) 119 120 60: 121 type=103 (BONDS) 119 121 60: 122 type=104 (BONDS) 119 134 60: 123 type=102 (BONDS) 121 122 60: 124 type=102 (BONDS) 121 123 60: 125 type=103 (BONDS) 121 124 60: 126 type=102 (BONDS) 124 125 60: 127 type=103 (BONDS) 124 126 60: 128 type=103 (BONDS) 124 130 60: 129 type=102 (BONDS) 126 127 60: 130 type=102 (BONDS) 126 128 60: 131 type=102 (BONDS) 126 129 60: 132 type=102 (BONDS) 130 131 60: 133 type=102 (BONDS) 130 132 60: 134 type=102 (BONDS) 130 133 60: 135 type=105 (BONDS) 134 135 60: 136 type=106 (BONDS) 134 136 60: 137 type=100 (BONDS) 136 137 60: 138 type=107 (BONDS) 136 138 60: 139 type=102 (BONDS) 138 139 60: 140 type=103 (BONDS) 138 140 60: 141 type=104 (BONDS) 138 144 60: 142 type=102 (BONDS) 140 141 60: 143 type=102 (BONDS) 140 142 60: 144 type=102 (BONDS) 140 143 60: 145 type=105 (BONDS) 144 145 60: 146 type=106 (BONDS) 144 146 60: 147 type=100 (BONDS) 146 147 60: 148 type=107 (BONDS) 146 148 60: 149 type=102 (BONDS) 148 149 60: 150 type=103 (BONDS) 148 150 60: 151 type=104 (BONDS) 148 154 60: 152 type=102 (BONDS) 150 151 60: 153 type=102 (BONDS) 150 152 60: 154 type=102 (BONDS) 150 153 60: 155 type=105 (BONDS) 154 155 60: G96Bond: 60: nr: 0 60: Morse: 60: nr: 0 60: Cubic Bonds: 60: nr: 0 60: Connect Bonds: 60: nr: 0 60: Harmonic Pot.: 60: nr: 0 60: FENE Bonds: 60: nr: 0 60: Tab. Bonds: 60: nr: 0 60: Tab. Bonds NC: 60: nr: 0 60: Restraint Pot.: 60: nr: 0 60: Angle: 60: nr: 1124 60: iatoms: 60: 0 type=116 (ANGLES) 1 0 2 60: 1 type=116 (ANGLES) 1 0 3 60: 2 type=116 (ANGLES) 1 0 4 60: 3 type=116 (ANGLES) 2 0 3 60: 4 type=116 (ANGLES) 2 0 4 60: 5 type=116 (ANGLES) 3 0 4 60: 6 type=116 (ANGLES) 0 4 5 60: 7 type=117 (ANGLES) 0 4 6 60: 8 type=117 (ANGLES) 0 4 22 60: 9 type=118 (ANGLES) 5 4 6 60: 10 type=116 (ANGLES) 5 4 22 60: 11 type=119 (ANGLES) 6 4 22 60: 12 type=118 (ANGLES) 4 6 7 60: 13 type=118 (ANGLES) 4 6 8 60: 14 type=120 (ANGLES) 4 6 9 60: 15 type=121 (ANGLES) 7 6 8 60: 16 type=118 (ANGLES) 7 6 9 60: 17 type=118 (ANGLES) 8 6 9 60: 18 type=118 (ANGLES) 6 9 10 60: 19 type=118 (ANGLES) 6 9 11 60: 20 type=120 (ANGLES) 6 9 12 60: 21 type=121 (ANGLES) 10 9 11 60: 22 type=118 (ANGLES) 10 9 12 60: 23 type=118 (ANGLES) 11 9 12 60: 24 type=118 (ANGLES) 9 12 13 60: 25 type=118 (ANGLES) 9 12 14 60: 26 type=120 (ANGLES) 9 12 15 60: 27 type=121 (ANGLES) 13 12 14 60: 28 type=118 (ANGLES) 13 12 15 60: 29 type=118 (ANGLES) 14 12 15 60: 30 type=118 (ANGLES) 12 15 16 60: 31 type=118 (ANGLES) 12 15 17 60: 32 type=117 (ANGLES) 12 15 18 60: 33 type=121 (ANGLES) 16 15 17 60: 34 type=116 (ANGLES) 16 15 18 60: 35 type=116 (ANGLES) 17 15 18 60: 36 type=116 (ANGLES) 15 18 19 60: 37 type=116 (ANGLES) 15 18 20 60: 38 type=116 (ANGLES) 15 18 21 60: 39 type=116 (ANGLES) 19 18 20 60: 40 type=116 (ANGLES) 19 18 21 60: 41 type=116 (ANGLES) 20 18 21 60: 42 type=122 (ANGLES) 4 22 23 60: 43 type=123 (ANGLES) 4 22 24 60: 44 type=124 (ANGLES) 23 22 24 60: 45 type=125 (ANGLES) 22 24 25 60: 46 type=126 (ANGLES) 22 24 26 60: 47 type=127 (ANGLES) 25 24 26 60: 48 type=116 (ANGLES) 24 26 27 60: 49 type=128 (ANGLES) 24 26 28 60: 50 type=129 (ANGLES) 24 26 38 60: 51 type=118 (ANGLES) 27 26 28 60: 52 type=116 (ANGLES) 27 26 38 60: 53 type=119 (ANGLES) 28 26 38 60: 54 type=118 (ANGLES) 26 28 29 60: 55 type=120 (ANGLES) 26 28 30 60: 56 type=120 (ANGLES) 26 28 34 60: 57 type=118 (ANGLES) 29 28 30 60: 58 type=118 (ANGLES) 29 28 34 60: 59 type=120 (ANGLES) 30 28 34 60: 60 type=118 (ANGLES) 28 30 31 60: 61 type=118 (ANGLES) 28 30 32 60: 62 type=118 (ANGLES) 28 30 33 60: 63 type=121 (ANGLES) 31 30 32 60: 64 type=121 (ANGLES) 31 30 33 60: 65 type=121 (ANGLES) 32 30 33 60: 66 type=118 (ANGLES) 28 34 35 60: 67 type=118 (ANGLES) 28 34 36 60: 68 type=118 (ANGLES) 28 34 37 60: 69 type=121 (ANGLES) 35 34 36 60: 70 type=121 (ANGLES) 35 34 37 60: 71 type=121 (ANGLES) 36 34 37 60: 72 type=122 (ANGLES) 26 38 39 60: 73 type=123 (ANGLES) 26 38 40 60: 74 type=124 (ANGLES) 39 38 40 60: 75 type=125 (ANGLES) 38 40 41 60: 76 type=126 (ANGLES) 38 40 42 60: 77 type=127 (ANGLES) 41 40 42 60: 78 type=116 (ANGLES) 40 42 43 60: 79 type=128 (ANGLES) 40 42 44 60: 80 type=129 (ANGLES) 40 42 58 60: 81 type=118 (ANGLES) 43 42 44 60: 82 type=116 (ANGLES) 43 42 58 60: 83 type=119 (ANGLES) 44 42 58 60: 84 type=118 (ANGLES) 42 44 45 60: 85 type=118 (ANGLES) 42 44 46 60: 86 type=130 (ANGLES) 42 44 47 60: 87 type=121 (ANGLES) 45 44 46 60: 88 type=116 (ANGLES) 45 44 47 60: 89 type=116 (ANGLES) 46 44 47 60: 90 type=131 (ANGLES) 44 47 48 60: 91 type=131 (ANGLES) 44 47 50 60: 92 type=132 (ANGLES) 48 47 50 60: 93 type=133 (ANGLES) 47 48 49 60: 94 type=132 (ANGLES) 47 48 52 60: 95 type=133 (ANGLES) 49 48 52 60: 96 type=133 (ANGLES) 47 50 51 60: 97 type=132 (ANGLES) 47 50 54 60: 98 type=133 (ANGLES) 51 50 54 60: 99 type=133 (ANGLES) 48 52 53 60: 100 type=132 (ANGLES) 48 52 56 60: 101 type=133 (ANGLES) 53 52 56 60: 102 type=133 (ANGLES) 50 54 55 60: 103 type=132 (ANGLES) 50 54 56 60: 104 type=133 (ANGLES) 55 54 56 60: 105 type=132 (ANGLES) 52 56 54 60: 106 type=133 (ANGLES) 52 56 57 60: 107 type=133 (ANGLES) 54 56 57 60: 108 type=122 (ANGLES) 42 58 59 60: 109 type=123 (ANGLES) 42 58 60 60: 110 type=124 (ANGLES) 59 58 60 60: 111 type=125 (ANGLES) 58 60 61 60: 112 type=126 (ANGLES) 58 60 62 60: 113 type=127 (ANGLES) 61 60 62 60: 114 type=116 (ANGLES) 60 62 63 60: 115 type=116 (ANGLES) 60 62 64 60: 116 type=129 (ANGLES) 60 62 65 60: 117 type=121 (ANGLES) 63 62 64 60: 118 type=116 (ANGLES) 63 62 65 60: 119 type=116 (ANGLES) 64 62 65 60: 120 type=122 (ANGLES) 62 65 66 60: 121 type=123 (ANGLES) 62 65 67 60: 122 type=124 (ANGLES) 66 65 67 60: 123 type=125 (ANGLES) 65 67 68 60: 124 type=126 (ANGLES) 65 67 69 60: 125 type=127 (ANGLES) 68 67 69 60: 126 type=116 (ANGLES) 67 69 70 60: 127 type=128 (ANGLES) 67 69 71 60: 128 type=129 (ANGLES) 67 69 89 60: 129 type=118 (ANGLES) 70 69 71 60: 130 type=116 (ANGLES) 70 69 89 60: 131 type=119 (ANGLES) 71 69 89 60: 132 type=118 (ANGLES) 69 71 72 60: 133 type=118 (ANGLES) 69 71 73 60: 134 type=120 (ANGLES) 69 71 74 60: 135 type=121 (ANGLES) 72 71 73 60: 136 type=118 (ANGLES) 72 71 74 60: 137 type=118 (ANGLES) 73 71 74 60: 138 type=118 (ANGLES) 71 74 75 60: 139 type=118 (ANGLES) 71 74 76 60: 140 type=120 (ANGLES) 71 74 77 60: 141 type=121 (ANGLES) 75 74 76 60: 142 type=118 (ANGLES) 75 74 77 60: 143 type=118 (ANGLES) 76 74 77 60: 144 type=118 (ANGLES) 74 77 78 60: 145 type=118 (ANGLES) 74 77 79 60: 146 type=117 (ANGLES) 74 77 80 60: 147 type=121 (ANGLES) 78 77 79 60: 148 type=116 (ANGLES) 78 77 80 60: 149 type=116 (ANGLES) 79 77 80 60: 150 type=134 (ANGLES) 77 80 81 60: 151 type=135 (ANGLES) 77 80 82 60: 152 type=133 (ANGLES) 81 80 82 60: 153 type=131 (ANGLES) 80 82 83 60: 154 type=131 (ANGLES) 80 82 86 60: 155 type=131 (ANGLES) 83 82 86 60: 156 type=133 (ANGLES) 82 83 84 60: 157 type=133 (ANGLES) 82 83 85 60: 158 type=133 (ANGLES) 84 83 85 60: 159 type=133 (ANGLES) 82 86 87 60: 160 type=133 (ANGLES) 82 86 88 60: 161 type=133 (ANGLES) 87 86 88 60: 162 type=122 (ANGLES) 69 89 90 60: 163 type=123 (ANGLES) 69 89 91 60: 164 type=124 (ANGLES) 90 89 91 60: 165 type=125 (ANGLES) 89 91 92 60: 166 type=126 (ANGLES) 89 91 93 60: 167 type=127 (ANGLES) 92 91 93 60: 168 type=116 (ANGLES) 91 93 94 60: 169 type=128 (ANGLES) 91 93 95 60: 170 type=129 (ANGLES) 91 93 100 60: 171 type=118 (ANGLES) 94 93 95 60: 172 type=116 (ANGLES) 94 93 100 60: 173 type=119 (ANGLES) 95 93 100 60: 174 type=118 (ANGLES) 93 95 96 60: 175 type=118 (ANGLES) 93 95 97 60: 176 type=136 (ANGLES) 93 95 98 60: 177 type=121 (ANGLES) 96 95 97 60: 178 type=116 (ANGLES) 96 95 98 60: 179 type=116 (ANGLES) 97 95 98 60: 180 type=137 (ANGLES) 95 98 99 60: 181 type=122 (ANGLES) 93 100 101 60: 182 type=123 (ANGLES) 93 100 102 60: 183 type=124 (ANGLES) 101 100 102 60: 184 type=125 (ANGLES) 100 102 103 60: 185 type=126 (ANGLES) 100 102 104 60: 186 type=127 (ANGLES) 103 102 104 60: 187 type=116 (ANGLES) 102 104 105 60: 188 type=128 (ANGLES) 102 104 106 60: 189 type=129 (ANGLES) 102 104 115 60: 190 type=118 (ANGLES) 105 104 106 60: 191 type=116 (ANGLES) 105 104 115 60: 192 type=119 (ANGLES) 106 104 115 60: 193 type=118 (ANGLES) 104 106 107 60: 194 type=118 (ANGLES) 104 106 108 60: 195 type=120 (ANGLES) 104 106 109 60: 196 type=121 (ANGLES) 107 106 108 60: 197 type=118 (ANGLES) 107 106 109 60: 198 type=118 (ANGLES) 108 106 109 60: 199 type=118 (ANGLES) 106 109 110 60: 200 type=118 (ANGLES) 106 109 111 60: 201 type=119 (ANGLES) 106 109 112 60: 202 type=121 (ANGLES) 110 109 111 60: 203 type=116 (ANGLES) 110 109 112 60: 204 type=116 (ANGLES) 111 109 112 60: 205 type=138 (ANGLES) 109 112 113 60: 206 type=138 (ANGLES) 109 112 114 60: 207 type=139 (ANGLES) 113 112 114 60: 208 type=122 (ANGLES) 104 115 116 60: 209 type=123 (ANGLES) 104 115 117 60: 210 type=124 (ANGLES) 116 115 117 60: 211 type=125 (ANGLES) 115 117 118 60: 212 type=126 (ANGLES) 115 117 119 60: 213 type=127 (ANGLES) 118 117 119 60: 214 type=116 (ANGLES) 117 119 120 60: 215 type=128 (ANGLES) 117 119 121 60: 216 type=129 (ANGLES) 117 119 134 60: 217 type=118 (ANGLES) 120 119 121 60: 218 type=116 (ANGLES) 120 119 134 60: 219 type=119 (ANGLES) 121 119 134 60: 220 type=118 (ANGLES) 119 121 122 60: 221 type=118 (ANGLES) 119 121 123 60: 222 type=120 (ANGLES) 119 121 124 60: 223 type=121 (ANGLES) 122 121 123 60: 224 type=118 (ANGLES) 122 121 124 60: 225 type=118 (ANGLES) 123 121 124 60: 226 type=118 (ANGLES) 121 124 125 60: 227 type=120 (ANGLES) 121 124 126 60: 228 type=120 (ANGLES) 121 124 130 60: 229 type=118 (ANGLES) 125 124 126 60: 230 type=118 (ANGLES) 125 124 130 60: 231 type=120 (ANGLES) 126 124 130 60: 232 type=118 (ANGLES) 124 126 127 60: 233 type=118 (ANGLES) 124 126 128 60: 234 type=118 (ANGLES) 124 126 129 60: 235 type=121 (ANGLES) 127 126 128 60: 236 type=121 (ANGLES) 127 126 129 60: 237 type=121 (ANGLES) 128 126 129 60: 238 type=118 (ANGLES) 124 130 131 60: 239 type=118 (ANGLES) 124 130 132 60: 240 type=118 (ANGLES) 124 130 133 60: 241 type=121 (ANGLES) 131 130 132 60: 242 type=121 (ANGLES) 131 130 133 60: 243 type=121 (ANGLES) 132 130 133 60: 244 type=122 (ANGLES) 119 134 135 60: 245 type=123 (ANGLES) 119 134 136 60: 246 type=124 (ANGLES) 135 134 136 60: 247 type=125 (ANGLES) 134 136 137 60: 248 type=126 (ANGLES) 134 136 138 60: 249 type=127 (ANGLES) 137 136 138 60: 250 type=116 (ANGLES) 136 138 139 60: 251 type=128 (ANGLES) 136 138 140 60: 252 type=129 (ANGLES) 136 138 144 60: 253 type=118 (ANGLES) 139 138 140 60: 254 type=116 (ANGLES) 139 138 144 60: 255 type=119 (ANGLES) 140 138 144 60: 256 type=118 (ANGLES) 138 140 141 60: 257 type=118 (ANGLES) 138 140 142 60: 258 type=118 (ANGLES) 138 140 143 60: 259 type=121 (ANGLES) 141 140 142 60: 260 type=121 (ANGLES) 141 140 143 60: 261 type=121 (ANGLES) 142 140 143 60: 262 type=122 (ANGLES) 138 144 145 60: 263 type=123 (ANGLES) 138 144 146 60: 264 type=124 (ANGLES) 145 144 146 60: 265 type=125 (ANGLES) 144 146 147 60: 266 type=126 (ANGLES) 144 146 148 60: 267 type=127 (ANGLES) 147 146 148 60: 268 type=116 (ANGLES) 146 148 149 60: 269 type=128 (ANGLES) 146 148 150 60: 270 type=129 (ANGLES) 146 148 154 60: 271 type=118 (ANGLES) 149 148 150 60: 272 type=116 (ANGLES) 149 148 154 60: 273 type=119 (ANGLES) 150 148 154 60: 274 type=118 (ANGLES) 148 150 151 60: 275 type=118 (ANGLES) 148 150 152 60: 276 type=118 (ANGLES) 148 150 153 60: 277 type=121 (ANGLES) 151 150 152 60: 278 type=121 (ANGLES) 151 150 153 60: 279 type=121 (ANGLES) 152 150 153 60: 280 type=122 (ANGLES) 148 154 155 60: G96Angle: 60: nr: 0 60: Restr. Angles: 60: nr: 0 60: Lin. Angle: 60: nr: 0 60: Bond-Cross: 60: nr: 0 60: BA-Cross: 60: nr: 0 60: U-B: 60: nr: 0 60: Quartic Angles: 60: nr: 0 60: Tab. Angles: 60: nr: 0 60: Proper Dih.: 60: nr: 145 60: iatoms: 60: 0 type=140 (PDIHS) 4 24 22 23 60: 1 type=141 (PDIHS) 22 26 24 25 60: 2 type=140 (PDIHS) 26 40 38 39 60: 3 type=141 (PDIHS) 38 42 40 41 60: 4 type=140 (PDIHS) 42 60 58 59 60: 5 type=142 (PDIHS) 44 47 50 48 60: 6 type=142 (PDIHS) 47 52 48 49 60: 7 type=142 (PDIHS) 47 54 50 51 60: 8 type=142 (PDIHS) 48 56 52 53 60: 9 type=142 (PDIHS) 50 56 54 55 60: 10 type=142 (PDIHS) 52 54 56 57 60: 11 type=141 (PDIHS) 58 62 60 61 60: 12 type=140 (PDIHS) 62 67 65 66 60: 13 type=141 (PDIHS) 65 69 67 68 60: 14 type=140 (PDIHS) 69 91 89 90 60: 15 type=141 (PDIHS) 77 82 80 81 60: 16 type=140 (PDIHS) 80 83 82 86 60: 17 type=141 (PDIHS) 82 84 83 85 60: 18 type=141 (PDIHS) 82 87 86 88 60: 19 type=141 (PDIHS) 89 93 91 92 60: 20 type=140 (PDIHS) 93 102 100 101 60: 21 type=141 (PDIHS) 100 104 102 103 60: 22 type=140 (PDIHS) 104 117 115 116 60: 23 type=140 (PDIHS) 109 113 112 114 60: 24 type=141 (PDIHS) 115 119 117 118 60: 25 type=140 (PDIHS) 119 136 134 135 60: 26 type=141 (PDIHS) 134 138 136 137 60: 27 type=140 (PDIHS) 138 146 144 145 60: 28 type=141 (PDIHS) 144 148 146 147 60: Ryckaert-Bell.: 60: nr: 1565 60: iatoms: 60: 0 type=143 (RBDIHS) 1 0 4 5 60: 1 type=144 (RBDIHS) 1 0 4 6 60: 2 type=144 (RBDIHS) 1 0 4 22 60: 3 type=143 (RBDIHS) 2 0 4 5 60: 4 type=144 (RBDIHS) 2 0 4 6 60: 5 type=144 (RBDIHS) 2 0 4 22 60: 6 type=143 (RBDIHS) 3 0 4 5 60: 7 type=144 (RBDIHS) 3 0 4 6 60: 8 type=144 (RBDIHS) 3 0 4 22 60: 9 type=145 (RBDIHS) 0 4 6 9 60: 10 type=146 (RBDIHS) 22 4 6 9 60: 11 type=147 (RBDIHS) 0 4 6 7 60: 12 type=147 (RBDIHS) 0 4 6 8 60: 13 type=148 (RBDIHS) 5 4 6 7 60: 14 type=148 (RBDIHS) 5 4 6 8 60: 15 type=148 (RBDIHS) 5 4 6 9 60: 16 type=149 (RBDIHS) 22 4 6 7 60: 17 type=149 (RBDIHS) 22 4 6 8 60: 18 type=150 (RBDIHS) 0 4 22 24 60: 19 type=151 (RBDIHS) 6 4 22 24 60: 20 type=148 (RBDIHS) 4 6 9 10 60: 21 type=148 (RBDIHS) 4 6 9 11 60: 22 type=152 (RBDIHS) 4 6 9 12 60: 23 type=148 (RBDIHS) 7 6 9 10 60: 24 type=148 (RBDIHS) 7 6 9 11 60: 25 type=148 (RBDIHS) 7 6 9 12 60: 26 type=148 (RBDIHS) 8 6 9 10 60: 27 type=148 (RBDIHS) 8 6 9 11 60: 28 type=148 (RBDIHS) 8 6 9 12 60: 29 type=148 (RBDIHS) 6 9 12 13 60: 30 type=148 (RBDIHS) 6 9 12 14 60: 31 type=152 (RBDIHS) 6 9 12 15 60: 32 type=148 (RBDIHS) 10 9 12 13 60: 33 type=148 (RBDIHS) 10 9 12 14 60: 34 type=148 (RBDIHS) 10 9 12 15 60: 35 type=148 (RBDIHS) 11 9 12 13 60: 36 type=148 (RBDIHS) 11 9 12 14 60: 37 type=148 (RBDIHS) 11 9 12 15 60: 38 type=148 (RBDIHS) 9 12 15 16 60: 39 type=148 (RBDIHS) 9 12 15 17 60: 40 type=153 (RBDIHS) 9 12 15 18 60: 41 type=148 (RBDIHS) 13 12 15 16 60: 42 type=148 (RBDIHS) 13 12 15 17 60: 43 type=154 (RBDIHS) 13 12 15 18 60: 44 type=148 (RBDIHS) 14 12 15 16 60: 45 type=148 (RBDIHS) 14 12 15 17 60: 46 type=154 (RBDIHS) 14 12 15 18 60: 47 type=144 (RBDIHS) 12 15 18 19 60: 48 type=144 (RBDIHS) 12 15 18 20 60: 49 type=144 (RBDIHS) 12 15 18 21 60: 50 type=143 (RBDIHS) 16 15 18 19 60: 51 type=143 (RBDIHS) 16 15 18 20 60: 52 type=143 (RBDIHS) 16 15 18 21 60: 53 type=143 (RBDIHS) 17 15 18 19 60: 54 type=143 (RBDIHS) 17 15 18 20 60: 55 type=143 (RBDIHS) 17 15 18 21 60: 56 type=155 (RBDIHS) 4 22 24 25 60: 57 type=156 (RBDIHS) 4 22 24 26 60: 58 type=155 (RBDIHS) 23 22 24 25 60: 59 type=157 (RBDIHS) 23 22 24 26 60: 60 type=158 (RBDIHS) 22 24 26 28 60: 61 type=159 (RBDIHS) 22 24 26 38 60: 62 type=160 (RBDIHS) 24 26 28 30 60: 63 type=160 (RBDIHS) 24 26 28 34 60: 64 type=161 (RBDIHS) 38 26 28 30 60: 65 type=161 (RBDIHS) 38 26 28 34 60: 66 type=147 (RBDIHS) 24 26 28 29 60: 67 type=148 (RBDIHS) 27 26 28 29 60: 68 type=148 (RBDIHS) 27 26 28 30 60: 69 type=148 (RBDIHS) 27 26 28 34 60: 70 type=149 (RBDIHS) 38 26 28 29 60: 71 type=150 (RBDIHS) 24 26 38 40 60: 72 type=151 (RBDIHS) 28 26 38 40 60: 73 type=148 (RBDIHS) 26 28 30 31 60: 74 type=148 (RBDIHS) 26 28 30 32 60: 75 type=148 (RBDIHS) 26 28 30 33 60: 76 type=148 (RBDIHS) 29 28 30 31 60: 77 type=148 (RBDIHS) 29 28 30 32 60: 78 type=148 (RBDIHS) 29 28 30 33 60: 79 type=148 (RBDIHS) 34 28 30 31 60: 80 type=148 (RBDIHS) 34 28 30 32 60: 81 type=148 (RBDIHS) 34 28 30 33 60: 82 type=148 (RBDIHS) 26 28 34 35 60: 83 type=148 (RBDIHS) 26 28 34 36 60: 84 type=148 (RBDIHS) 26 28 34 37 60: 85 type=148 (RBDIHS) 29 28 34 35 60: 86 type=148 (RBDIHS) 29 28 34 36 60: 87 type=148 (RBDIHS) 29 28 34 37 60: 88 type=148 (RBDIHS) 30 28 34 35 60: 89 type=148 (RBDIHS) 30 28 34 36 60: 90 type=148 (RBDIHS) 30 28 34 37 60: 91 type=155 (RBDIHS) 26 38 40 41 60: 92 type=156 (RBDIHS) 26 38 40 42 60: 93 type=155 (RBDIHS) 39 38 40 41 60: 94 type=157 (RBDIHS) 39 38 40 42 60: 95 type=158 (RBDIHS) 38 40 42 44 60: 96 type=159 (RBDIHS) 38 40 42 58 60: 97 type=147 (RBDIHS) 40 42 44 45 60: 98 type=147 (RBDIHS) 40 42 44 46 60: 99 type=162 (RBDIHS) 40 42 44 47 60: 100 type=148 (RBDIHS) 43 42 44 45 60: 101 type=148 (RBDIHS) 43 42 44 46 60: 102 type=163 (RBDIHS) 43 42 44 47 60: 103 type=149 (RBDIHS) 58 42 44 45 60: 104 type=149 (RBDIHS) 58 42 44 46 60: 105 type=164 (RBDIHS) 58 42 44 47 60: 106 type=150 (RBDIHS) 40 42 58 60 60: 107 type=151 (RBDIHS) 44 42 58 60 60: 108 type=165 (RBDIHS) 44 47 48 49 60: 109 type=165 (RBDIHS) 44 47 48 52 60: 110 type=165 (RBDIHS) 50 47 48 49 60: 111 type=165 (RBDIHS) 50 47 48 52 60: 112 type=165 (RBDIHS) 44 47 50 51 60: 113 type=165 (RBDIHS) 44 47 50 54 60: 114 type=165 (RBDIHS) 48 47 50 51 60: 115 type=165 (RBDIHS) 48 47 50 54 60: 116 type=165 (RBDIHS) 47 48 52 53 60: 117 type=165 (RBDIHS) 47 48 52 56 60: 118 type=165 (RBDIHS) 49 48 52 53 60: 119 type=165 (RBDIHS) 49 48 52 56 60: 120 type=165 (RBDIHS) 47 50 54 55 60: 121 type=165 (RBDIHS) 47 50 54 56 60: 122 type=165 (RBDIHS) 51 50 54 55 60: 123 type=165 (RBDIHS) 51 50 54 56 60: 124 type=165 (RBDIHS) 48 52 56 54 60: 125 type=165 (RBDIHS) 48 52 56 57 60: 126 type=165 (RBDIHS) 53 52 56 54 60: 127 type=165 (RBDIHS) 53 52 56 57 60: 128 type=165 (RBDIHS) 50 54 56 52 60: 129 type=165 (RBDIHS) 50 54 56 57 60: 130 type=165 (RBDIHS) 55 54 56 52 60: 131 type=165 (RBDIHS) 55 54 56 57 60: 132 type=155 (RBDIHS) 42 58 60 61 60: 133 type=156 (RBDIHS) 42 58 60 62 60: 134 type=155 (RBDIHS) 59 58 60 61 60: 135 type=157 (RBDIHS) 59 58 60 62 60: 136 type=159 (RBDIHS) 58 60 62 65 60: 137 type=150 (RBDIHS) 60 62 65 67 60: 138 type=155 (RBDIHS) 62 65 67 68 60: 139 type=156 (RBDIHS) 62 65 67 69 60: 140 type=155 (RBDIHS) 66 65 67 68 60: 141 type=157 (RBDIHS) 66 65 67 69 60: 142 type=158 (RBDIHS) 65 67 69 71 60: 143 type=159 (RBDIHS) 65 67 69 89 60: 144 type=166 (RBDIHS) 67 69 71 74 60: 145 type=167 (RBDIHS) 89 69 71 74 60: 146 type=147 (RBDIHS) 67 69 71 72 60: 147 type=147 (RBDIHS) 67 69 71 73 60: 148 type=148 (RBDIHS) 70 69 71 72 60: 149 type=148 (RBDIHS) 70 69 71 73 60: 150 type=148 (RBDIHS) 70 69 71 74 60: 151 type=149 (RBDIHS) 89 69 71 72 60: 152 type=149 (RBDIHS) 89 69 71 73 60: 153 type=150 (RBDIHS) 67 69 89 91 60: 154 type=151 (RBDIHS) 71 69 89 91 60: 155 type=148 (RBDIHS) 69 71 74 75 60: 156 type=148 (RBDIHS) 69 71 74 76 60: 157 type=152 (RBDIHS) 69 71 74 77 60: 158 type=148 (RBDIHS) 72 71 74 75 60: 159 type=148 (RBDIHS) 72 71 74 76 60: 160 type=148 (RBDIHS) 72 71 74 77 60: 161 type=148 (RBDIHS) 73 71 74 75 60: 162 type=148 (RBDIHS) 73 71 74 76 60: 163 type=148 (RBDIHS) 73 71 74 77 60: 164 type=148 (RBDIHS) 71 74 77 78 60: 165 type=148 (RBDIHS) 71 74 77 79 60: 166 type=153 (RBDIHS) 71 74 77 80 60: 167 type=148 (RBDIHS) 75 74 77 78 60: 168 type=148 (RBDIHS) 75 74 77 79 60: 169 type=168 (RBDIHS) 75 74 77 80 60: 170 type=148 (RBDIHS) 76 74 77 78 60: 171 type=148 (RBDIHS) 76 74 77 79 60: 172 type=168 (RBDIHS) 76 74 77 80 60: 173 type=169 (RBDIHS) 74 77 80 81 60: 174 type=170 (RBDIHS) 74 77 80 82 60: 175 type=171 (RBDIHS) 78 77 80 82 60: 176 type=171 (RBDIHS) 79 77 80 82 60: 177 type=172 (RBDIHS) 77 80 82 83 60: 178 type=172 (RBDIHS) 77 80 82 86 60: 179 type=173 (RBDIHS) 81 80 82 83 60: 180 type=173 (RBDIHS) 81 80 82 86 60: 181 type=173 (RBDIHS) 80 82 83 84 60: 182 type=173 (RBDIHS) 80 82 83 85 60: 183 type=173 (RBDIHS) 86 82 83 84 60: 184 type=173 (RBDIHS) 86 82 83 85 60: 185 type=173 (RBDIHS) 80 82 86 87 60: 186 type=173 (RBDIHS) 80 82 86 88 60: 187 type=173 (RBDIHS) 83 82 86 87 60: 188 type=173 (RBDIHS) 83 82 86 88 60: 189 type=155 (RBDIHS) 69 89 91 92 60: 190 type=156 (RBDIHS) 69 89 91 93 60: 191 type=155 (RBDIHS) 90 89 91 92 60: 192 type=157 (RBDIHS) 90 89 91 93 60: 193 type=158 (RBDIHS) 89 91 93 95 60: 194 type=159 (RBDIHS) 89 91 93 100 60: 195 type=174 (RBDIHS) 91 93 95 98 60: 196 type=175 (RBDIHS) 100 93 95 98 60: 197 type=147 (RBDIHS) 91 93 95 96 60: 198 type=147 (RBDIHS) 91 93 95 97 60: 199 type=148 (RBDIHS) 94 93 95 96 60: 200 type=148 (RBDIHS) 94 93 95 97 60: 201 type=176 (RBDIHS) 94 93 95 98 60: 202 type=149 (RBDIHS) 100 93 95 96 60: 203 type=149 (RBDIHS) 100 93 95 97 60: 204 type=150 (RBDIHS) 91 93 100 102 60: 205 type=151 (RBDIHS) 95 93 100 102 60: 206 type=177 (RBDIHS) 93 95 98 99 60: 207 type=178 (RBDIHS) 96 95 98 99 60: 208 type=178 (RBDIHS) 97 95 98 99 60: 209 type=155 (RBDIHS) 93 100 102 103 60: 210 type=156 (RBDIHS) 93 100 102 104 60: 211 type=155 (RBDIHS) 101 100 102 103 60: 212 type=157 (RBDIHS) 101 100 102 104 60: 213 type=158 (RBDIHS) 100 102 104 106 60: 214 type=159 (RBDIHS) 100 102 104 115 60: 215 type=179 (RBDIHS) 102 104 106 109 60: 216 type=180 (RBDIHS) 115 104 106 109 60: 217 type=147 (RBDIHS) 102 104 106 107 60: 218 type=147 (RBDIHS) 102 104 106 108 60: 219 type=148 (RBDIHS) 105 104 106 107 60: 220 type=148 (RBDIHS) 105 104 106 108 60: 221 type=148 (RBDIHS) 105 104 106 109 60: 222 type=149 (RBDIHS) 115 104 106 107 60: 223 type=149 (RBDIHS) 115 104 106 108 60: 224 type=150 (RBDIHS) 102 104 115 117 60: 225 type=151 (RBDIHS) 106 104 115 117 60: 226 type=148 (RBDIHS) 104 106 109 110 60: 227 type=148 (RBDIHS) 104 106 109 111 60: 228 type=181 (RBDIHS) 104 106 109 112 60: 229 type=148 (RBDIHS) 107 106 109 110 60: 230 type=148 (RBDIHS) 107 106 109 111 60: 231 type=182 (RBDIHS) 107 106 109 112 60: 232 type=148 (RBDIHS) 108 106 109 110 60: 233 type=148 (RBDIHS) 108 106 109 111 60: 234 type=182 (RBDIHS) 108 106 109 112 60: 235 type=183 (RBDIHS) 106 109 112 113 60: 236 type=183 (RBDIHS) 106 109 112 114 60: 237 type=155 (RBDIHS) 104 115 117 118 60: 238 type=156 (RBDIHS) 104 115 117 119 60: 239 type=155 (RBDIHS) 116 115 117 118 60: 240 type=157 (RBDIHS) 116 115 117 119 60: 241 type=158 (RBDIHS) 115 117 119 121 60: 242 type=159 (RBDIHS) 115 117 119 134 60: 243 type=184 (RBDIHS) 117 119 121 124 60: 244 type=185 (RBDIHS) 134 119 121 124 60: 245 type=147 (RBDIHS) 117 119 121 122 60: 246 type=147 (RBDIHS) 117 119 121 123 60: 247 type=148 (RBDIHS) 120 119 121 122 60: 248 type=148 (RBDIHS) 120 119 121 123 60: 249 type=148 (RBDIHS) 120 119 121 124 60: 250 type=149 (RBDIHS) 134 119 121 122 60: 251 type=149 (RBDIHS) 134 119 121 123 60: 252 type=150 (RBDIHS) 117 119 134 136 60: 253 type=151 (RBDIHS) 121 119 134 136 60: 254 type=148 (RBDIHS) 119 121 124 125 60: 255 type=152 (RBDIHS) 119 121 124 126 60: 256 type=152 (RBDIHS) 119 121 124 130 60: 257 type=148 (RBDIHS) 122 121 124 125 60: 258 type=148 (RBDIHS) 122 121 124 126 60: 259 type=148 (RBDIHS) 122 121 124 130 60: 260 type=148 (RBDIHS) 123 121 124 125 60: 261 type=148 (RBDIHS) 123 121 124 126 60: 262 type=148 (RBDIHS) 123 121 124 130 60: 263 type=148 (RBDIHS) 121 124 126 127 60: 264 type=148 (RBDIHS) 121 124 126 128 60: 265 type=148 (RBDIHS) 121 124 126 129 60: 266 type=148 (RBDIHS) 125 124 126 127 60: 267 type=148 (RBDIHS) 125 124 126 128 60: 268 type=148 (RBDIHS) 125 124 126 129 60: 269 type=148 (RBDIHS) 130 124 126 127 60: 270 type=148 (RBDIHS) 130 124 126 128 60: 271 type=148 (RBDIHS) 130 124 126 129 60: 272 type=148 (RBDIHS) 121 124 130 131 60: 273 type=148 (RBDIHS) 121 124 130 132 60: 274 type=148 (RBDIHS) 121 124 130 133 60: 275 type=148 (RBDIHS) 125 124 130 131 60: 276 type=148 (RBDIHS) 125 124 130 132 60: 277 type=148 (RBDIHS) 125 124 130 133 60: 278 type=148 (RBDIHS) 126 124 130 131 60: 279 type=148 (RBDIHS) 126 124 130 132 60: 280 type=148 (RBDIHS) 126 124 130 133 60: 281 type=155 (RBDIHS) 119 134 136 137 60: 282 type=156 (RBDIHS) 119 134 136 138 60: 283 type=155 (RBDIHS) 135 134 136 137 60: 284 type=157 (RBDIHS) 135 134 136 138 60: 285 type=158 (RBDIHS) 134 136 138 140 60: 286 type=159 (RBDIHS) 134 136 138 144 60: 287 type=147 (RBDIHS) 136 138 140 141 60: 288 type=147 (RBDIHS) 136 138 140 142 60: 289 type=147 (RBDIHS) 136 138 140 143 60: 290 type=148 (RBDIHS) 139 138 140 141 60: 291 type=148 (RBDIHS) 139 138 140 142 60: 292 type=148 (RBDIHS) 139 138 140 143 60: 293 type=149 (RBDIHS) 144 138 140 141 60: 294 type=149 (RBDIHS) 144 138 140 142 60: 295 type=149 (RBDIHS) 144 138 140 143 60: 296 type=150 (RBDIHS) 136 138 144 146 60: 297 type=151 (RBDIHS) 140 138 144 146 60: 298 type=155 (RBDIHS) 138 144 146 147 60: 299 type=156 (RBDIHS) 138 144 146 148 60: 300 type=155 (RBDIHS) 145 144 146 147 60: 301 type=157 (RBDIHS) 145 144 146 148 60: 302 type=158 (RBDIHS) 144 146 148 150 60: 303 type=159 (RBDIHS) 144 146 148 154 60: 304 type=147 (RBDIHS) 146 148 150 151 60: 305 type=147 (RBDIHS) 146 148 150 152 60: 306 type=147 (RBDIHS) 146 148 150 153 60: 307 type=148 (RBDIHS) 149 148 150 151 60: 308 type=148 (RBDIHS) 149 148 150 152 60: 309 type=148 (RBDIHS) 149 148 150 153 60: 310 type=149 (RBDIHS) 154 148 150 151 60: 311 type=149 (RBDIHS) 154 148 150 152 60: 312 type=149 (RBDIHS) 154 148 150 153 60: Restr. Dih.: 60: nr: 0 60: CBT Dih.: 60: nr: 0 60: Fourier Dih.: 60: nr: 0 60: Improper Dih.: 60: nr: 0 60: Per. Imp. Dih.: 60: nr: 0 60: Tab. Dih.: 60: nr: 0 60: CMAP Dih.: 60: nr: 0 60: GB 1-2 Pol.: 60: nr: 0 60: GB 1-3 Pol.: 60: nr: 0 60: GB 1-4 Pol.: 60: nr: 0 60: GB Polariz.: 60: nr: 0 60: Nonpolar Sol.: 60: nr: 0 60: LJ-14: 60: nr: 1197 60: iatoms: 60: 0 type=186 (LJ14) 0 7 60: 1 type=186 (LJ14) 0 8 60: 2 type=187 (LJ14) 0 9 60: 3 type=188 (LJ14) 0 23 60: 4 type=189 (LJ14) 0 24 60: 5 type=190 (LJ14) 1 5 60: 6 type=190 (LJ14) 1 6 60: 7 type=190 (LJ14) 1 22 60: 8 type=190 (LJ14) 2 5 60: 9 type=190 (LJ14) 2 6 60: 10 type=190 (LJ14) 2 22 60: 11 type=190 (LJ14) 3 5 60: 12 type=190 (LJ14) 3 6 60: 13 type=190 (LJ14) 3 22 60: 14 type=191 (LJ14) 4 10 60: 15 type=191 (LJ14) 4 11 60: 16 type=192 (LJ14) 4 12 60: 17 type=190 (LJ14) 4 25 60: 18 type=192 (LJ14) 4 26 60: 19 type=193 (LJ14) 5 7 60: 20 type=193 (LJ14) 5 8 60: 21 type=191 (LJ14) 5 9 60: 22 type=194 (LJ14) 5 23 60: 23 type=186 (LJ14) 5 24 60: 24 type=191 (LJ14) 6 13 60: 25 type=191 (LJ14) 6 14 60: 26 type=192 (LJ14) 6 15 60: 27 type=195 (LJ14) 6 23 60: 28 type=187 (LJ14) 6 24 60: 29 type=193 (LJ14) 7 10 60: 30 type=193 (LJ14) 7 11 60: 31 type=191 (LJ14) 7 12 60: 32 type=196 (LJ14) 7 22 60: 33 type=193 (LJ14) 8 10 60: 34 type=193 (LJ14) 8 11 60: 35 type=191 (LJ14) 8 12 60: 36 type=196 (LJ14) 8 22 60: 37 type=191 (LJ14) 9 16 60: 38 type=191 (LJ14) 9 17 60: 39 type=187 (LJ14) 9 18 60: 40 type=197 (LJ14) 9 22 60: 41 type=193 (LJ14) 10 13 60: 42 type=193 (LJ14) 10 14 60: 43 type=191 (LJ14) 10 15 60: 44 type=193 (LJ14) 11 13 60: 45 type=193 (LJ14) 11 14 60: 46 type=191 (LJ14) 11 15 60: 47 type=190 (LJ14) 12 19 60: 48 type=190 (LJ14) 12 20 60: 49 type=190 (LJ14) 12 21 60: 50 type=193 (LJ14) 13 16 60: 51 type=193 (LJ14) 13 17 60: 52 type=186 (LJ14) 13 18 60: 53 type=193 (LJ14) 14 16 60: 54 type=193 (LJ14) 14 17 60: 55 type=186 (LJ14) 14 18 60: 56 type=190 (LJ14) 16 19 60: 57 type=190 (LJ14) 16 20 60: 58 type=190 (LJ14) 16 21 60: 59 type=190 (LJ14) 17 19 60: 60 type=190 (LJ14) 17 20 60: 61 type=190 (LJ14) 17 21 60: 62 type=196 (LJ14) 22 27 60: 63 type=197 (LJ14) 22 28 60: 64 type=198 (LJ14) 22 38 60: 65 type=190 (LJ14) 23 25 60: 66 type=195 (LJ14) 23 26 60: 67 type=186 (LJ14) 24 29 60: 68 type=187 (LJ14) 24 30 60: 69 type=187 (LJ14) 24 34 60: 70 type=188 (LJ14) 24 39 60: 71 type=189 (LJ14) 24 40 60: 72 type=190 (LJ14) 25 27 60: 73 type=190 (LJ14) 25 28 60: 74 type=190 (LJ14) 25 38 60: 75 type=191 (LJ14) 26 31 60: 76 type=191 (LJ14) 26 32 60: 77 type=191 (LJ14) 26 33 60: 78 type=191 (LJ14) 26 35 60: 79 type=191 (LJ14) 26 36 60: 80 type=191 (LJ14) 26 37 60: 81 type=190 (LJ14) 26 41 60: 82 type=192 (LJ14) 26 42 60: 83 type=193 (LJ14) 27 29 60: 84 type=191 (LJ14) 27 30 60: 85 type=191 (LJ14) 27 34 60: 86 type=194 (LJ14) 27 39 60: 87 type=186 (LJ14) 27 40 60: 88 type=195 (LJ14) 28 39 60: 89 type=187 (LJ14) 28 40 60: 90 type=193 (LJ14) 29 31 60: 91 type=193 (LJ14) 29 32 60: 92 type=193 (LJ14) 29 33 60: 93 type=193 (LJ14) 29 35 60: 94 type=193 (LJ14) 29 36 60: 95 type=193 (LJ14) 29 37 60: 96 type=196 (LJ14) 29 38 60: 97 type=191 (LJ14) 30 35 60: 98 type=191 (LJ14) 30 36 60: 99 type=191 (LJ14) 30 37 60: 100 type=197 (LJ14) 30 38 60: 101 type=191 (LJ14) 31 34 60: 102 type=191 (LJ14) 32 34 60: 103 type=191 (LJ14) 33 34 60: 104 type=197 (LJ14) 34 38 60: 105 type=196 (LJ14) 38 43 60: 106 type=197 (LJ14) 38 44 60: 107 type=198 (LJ14) 38 58 60: 108 type=190 (LJ14) 39 41 60: 109 type=195 (LJ14) 39 42 60: 110 type=186 (LJ14) 40 45 60: 111 type=186 (LJ14) 40 46 60: 112 type=199 (LJ14) 40 47 60: 113 type=188 (LJ14) 40 59 60: 114 type=189 (LJ14) 40 60 60: 115 type=190 (LJ14) 41 43 60: 116 type=190 (LJ14) 41 44 60: 117 type=190 (LJ14) 41 58 60: 118 type=200 (LJ14) 42 48 60: 119 type=200 (LJ14) 42 50 60: 120 type=190 (LJ14) 42 61 60: 121 type=192 (LJ14) 42 62 60: 122 type=193 (LJ14) 43 45 60: 123 type=193 (LJ14) 43 46 60: 124 type=201 (LJ14) 43 47 60: 125 type=194 (LJ14) 43 59 60: 126 type=186 (LJ14) 43 60 60: 127 type=202 (LJ14) 44 49 60: 128 type=202 (LJ14) 44 51 60: 129 type=200 (LJ14) 44 52 60: 130 type=200 (LJ14) 44 54 60: 131 type=195 (LJ14) 44 59 60: 132 type=187 (LJ14) 44 60 60: 133 type=201 (LJ14) 45 48 60: 134 type=201 (LJ14) 45 50 60: 135 type=196 (LJ14) 45 58 60: 136 type=201 (LJ14) 46 48 60: 137 type=201 (LJ14) 46 50 60: 138 type=196 (LJ14) 46 58 60: 139 type=203 (LJ14) 47 53 60: 140 type=203 (LJ14) 47 55 60: 141 type=204 (LJ14) 47 56 60: 142 type=205 (LJ14) 47 58 60: 143 type=203 (LJ14) 48 51 60: 144 type=204 (LJ14) 48 54 60: 145 type=203 (LJ14) 48 57 60: 146 type=203 (LJ14) 49 50 60: 147 type=206 (LJ14) 49 53 60: 148 type=203 (LJ14) 49 56 60: 149 type=204 (LJ14) 50 52 60: 150 type=203 (LJ14) 50 57 60: 151 type=206 (LJ14) 51 55 60: 152 type=203 (LJ14) 51 56 60: 153 type=203 (LJ14) 52 55 60: 154 type=203 (LJ14) 53 54 60: 155 type=206 (LJ14) 53 57 60: 156 type=206 (LJ14) 55 57 60: 157 type=196 (LJ14) 58 63 60: 158 type=196 (LJ14) 58 64 60: 159 type=198 (LJ14) 58 65 60: 160 type=190 (LJ14) 59 61 60: 161 type=195 (LJ14) 59 62 60: 162 type=188 (LJ14) 60 66 60: 163 type=189 (LJ14) 60 67 60: 164 type=190 (LJ14) 61 63 60: 165 type=190 (LJ14) 61 64 60: 166 type=190 (LJ14) 61 65 60: 167 type=190 (LJ14) 62 68 60: 168 type=192 (LJ14) 62 69 60: 169 type=194 (LJ14) 63 66 60: 170 type=186 (LJ14) 63 67 60: 171 type=194 (LJ14) 64 66 60: 172 type=186 (LJ14) 64 67 60: 173 type=196 (LJ14) 65 70 60: 174 type=197 (LJ14) 65 71 60: 175 type=198 (LJ14) 65 89 60: 176 type=190 (LJ14) 66 68 60: 177 type=195 (LJ14) 66 69 60: 178 type=186 (LJ14) 67 72 60: 179 type=186 (LJ14) 67 73 60: 180 type=187 (LJ14) 67 74 60: 181 type=188 (LJ14) 67 90 60: 182 type=189 (LJ14) 67 91 60: 183 type=190 (LJ14) 68 70 60: 184 type=190 (LJ14) 68 71 60: 185 type=190 (LJ14) 68 89 60: 186 type=191 (LJ14) 69 75 60: 187 type=191 (LJ14) 69 76 60: 188 type=192 (LJ14) 69 77 60: 189 type=190 (LJ14) 69 92 60: 190 type=192 (LJ14) 69 93 60: 191 type=193 (LJ14) 70 72 60: 192 type=193 (LJ14) 70 73 60: 193 type=191 (LJ14) 70 74 60: 194 type=194 (LJ14) 70 90 60: 195 type=186 (LJ14) 70 91 60: 196 type=191 (LJ14) 71 78 60: 197 type=191 (LJ14) 71 79 60: 198 type=187 (LJ14) 71 80 60: 199 type=195 (LJ14) 71 90 60: 200 type=187 (LJ14) 71 91 60: 201 type=193 (LJ14) 72 75 60: 202 type=193 (LJ14) 72 76 60: 203 type=191 (LJ14) 72 77 60: 204 type=196 (LJ14) 72 89 60: 205 type=193 (LJ14) 73 75 60: 206 type=193 (LJ14) 73 76 60: 207 type=191 (LJ14) 73 77 60: 208 type=196 (LJ14) 73 89 60: 209 type=190 (LJ14) 74 81 60: 210 type=207 (LJ14) 74 82 60: 211 type=197 (LJ14) 74 89 60: 212 type=193 (LJ14) 75 78 60: 213 type=193 (LJ14) 75 79 60: 214 type=186 (LJ14) 75 80 60: 215 type=193 (LJ14) 76 78 60: 216 type=193 (LJ14) 76 79 60: 217 type=186 (LJ14) 76 80 60: 218 type=187 (LJ14) 77 83 60: 219 type=187 (LJ14) 77 86 60: 220 type=190 (LJ14) 78 81 60: 221 type=208 (LJ14) 78 82 60: 222 type=190 (LJ14) 79 81 60: 223 type=208 (LJ14) 79 82 60: 224 type=190 (LJ14) 80 84 60: 225 type=190 (LJ14) 80 85 60: 226 type=190 (LJ14) 80 87 60: 227 type=190 (LJ14) 80 88 60: 228 type=190 (LJ14) 81 83 60: 229 type=190 (LJ14) 81 86 60: 230 type=190 (LJ14) 83 87 60: 231 type=190 (LJ14) 83 88 60: 232 type=190 (LJ14) 84 86 60: 233 type=190 (LJ14) 85 86 60: 234 type=196 (LJ14) 89 94 60: 235 type=197 (LJ14) 89 95 60: 236 type=198 (LJ14) 89 100 60: 237 type=190 (LJ14) 90 92 60: 238 type=195 (LJ14) 90 93 60: 239 type=186 (LJ14) 91 96 60: 240 type=186 (LJ14) 91 97 60: 241 type=209 (LJ14) 91 98 60: 242 type=188 (LJ14) 91 101 60: 243 type=189 (LJ14) 91 102 60: 244 type=190 (LJ14) 92 94 60: 245 type=190 (LJ14) 92 95 60: 246 type=190 (LJ14) 92 100 60: 247 type=190 (LJ14) 93 99 60: 248 type=190 (LJ14) 93 103 60: 249 type=192 (LJ14) 93 104 60: 250 type=193 (LJ14) 94 96 60: 251 type=193 (LJ14) 94 97 60: 252 type=210 (LJ14) 94 98 60: 253 type=194 (LJ14) 94 101 60: 254 type=186 (LJ14) 94 102 60: 255 type=195 (LJ14) 95 101 60: 256 type=187 (LJ14) 95 102 60: 257 type=190 (LJ14) 96 99 60: 258 type=196 (LJ14) 96 100 60: 259 type=190 (LJ14) 97 99 60: 260 type=196 (LJ14) 97 100 60: 261 type=211 (LJ14) 98 100 60: 262 type=196 (LJ14) 100 105 60: 263 type=197 (LJ14) 100 106 60: 264 type=198 (LJ14) 100 115 60: 265 type=190 (LJ14) 101 103 60: 266 type=195 (LJ14) 101 104 60: 267 type=186 (LJ14) 102 107 60: 268 type=186 (LJ14) 102 108 60: 269 type=187 (LJ14) 102 109 60: 270 type=188 (LJ14) 102 116 60: 271 type=189 (LJ14) 102 117 60: 272 type=190 (LJ14) 103 105 60: 273 type=190 (LJ14) 103 106 60: 274 type=190 (LJ14) 103 115 60: 275 type=191 (LJ14) 104 110 60: 276 type=191 (LJ14) 104 111 60: 277 type=197 (LJ14) 104 112 60: 278 type=190 (LJ14) 104 118 60: 279 type=192 (LJ14) 104 119 60: 280 type=193 (LJ14) 105 107 60: 281 type=193 (LJ14) 105 108 60: 282 type=191 (LJ14) 105 109 60: 283 type=194 (LJ14) 105 116 60: 284 type=186 (LJ14) 105 117 60: 285 type=195 (LJ14) 106 113 60: 286 type=195 (LJ14) 106 114 60: 287 type=195 (LJ14) 106 116 60: 288 type=187 (LJ14) 106 117 60: 289 type=193 (LJ14) 107 110 60: 290 type=193 (LJ14) 107 111 60: 291 type=196 (LJ14) 107 112 60: 292 type=196 (LJ14) 107 115 60: 293 type=193 (LJ14) 108 110 60: 294 type=193 (LJ14) 108 111 60: 295 type=196 (LJ14) 108 112 60: 296 type=196 (LJ14) 108 115 60: 297 type=197 (LJ14) 109 115 60: 298 type=194 (LJ14) 110 113 60: 299 type=194 (LJ14) 110 114 60: 300 type=194 (LJ14) 111 113 60: 301 type=194 (LJ14) 111 114 60: 302 type=196 (LJ14) 115 120 60: 303 type=197 (LJ14) 115 121 60: 304 type=198 (LJ14) 115 134 60: 305 type=190 (LJ14) 116 118 60: 306 type=195 (LJ14) 116 119 60: 307 type=186 (LJ14) 117 122 60: 308 type=186 (LJ14) 117 123 60: 309 type=187 (LJ14) 117 124 60: 310 type=188 (LJ14) 117 135 60: 311 type=189 (LJ14) 117 136 60: 312 type=190 (LJ14) 118 120 60: 313 type=190 (LJ14) 118 121 60: 314 type=190 (LJ14) 118 134 60: 315 type=191 (LJ14) 119 125 60: 316 type=192 (LJ14) 119 126 60: 317 type=192 (LJ14) 119 130 60: 318 type=190 (LJ14) 119 137 60: 319 type=192 (LJ14) 119 138 60: 320 type=193 (LJ14) 120 122 60: 321 type=193 (LJ14) 120 123 60: 322 type=191 (LJ14) 120 124 60: 323 type=194 (LJ14) 120 135 60: 324 type=186 (LJ14) 120 136 60: 325 type=191 (LJ14) 121 127 60: 326 type=191 (LJ14) 121 128 60: 327 type=191 (LJ14) 121 129 60: 328 type=191 (LJ14) 121 131 60: 329 type=191 (LJ14) 121 132 60: 330 type=191 (LJ14) 121 133 60: 331 type=195 (LJ14) 121 135 60: 332 type=187 (LJ14) 121 136 60: 333 type=193 (LJ14) 122 125 60: 334 type=191 (LJ14) 122 126 60: 335 type=191 (LJ14) 122 130 60: 336 type=196 (LJ14) 122 134 60: 337 type=193 (LJ14) 123 125 60: 338 type=191 (LJ14) 123 126 60: 339 type=191 (LJ14) 123 130 60: 340 type=196 (LJ14) 123 134 60: 341 type=197 (LJ14) 124 134 60: 342 type=193 (LJ14) 125 127 60: 343 type=193 (LJ14) 125 128 60: 344 type=193 (LJ14) 125 129 60: 345 type=193 (LJ14) 125 131 60: 346 type=193 (LJ14) 125 132 60: 347 type=193 (LJ14) 125 133 60: 348 type=191 (LJ14) 126 131 60: 349 type=191 (LJ14) 126 132 60: 350 type=191 (LJ14) 126 133 60: 351 type=191 (LJ14) 127 130 60: 352 type=191 (LJ14) 128 130 60: 353 type=191 (LJ14) 129 130 60: 354 type=196 (LJ14) 134 139 60: 355 type=197 (LJ14) 134 140 60: 356 type=198 (LJ14) 134 144 60: 357 type=190 (LJ14) 135 137 60: 358 type=195 (LJ14) 135 138 60: 359 type=186 (LJ14) 136 141 60: 360 type=186 (LJ14) 136 142 60: 361 type=186 (LJ14) 136 143 60: 362 type=188 (LJ14) 136 145 60: 363 type=189 (LJ14) 136 146 60: 364 type=190 (LJ14) 137 139 60: 365 type=190 (LJ14) 137 140 60: 366 type=190 (LJ14) 137 144 60: 367 type=190 (LJ14) 138 147 60: 368 type=192 (LJ14) 138 148 60: 369 type=193 (LJ14) 139 141 60: 370 type=193 (LJ14) 139 142 60: 371 type=193 (LJ14) 139 143 60: 372 type=194 (LJ14) 139 145 60: 373 type=186 (LJ14) 139 146 60: 374 type=195 (LJ14) 140 145 60: 375 type=187 (LJ14) 140 146 60: 376 type=196 (LJ14) 141 144 60: 377 type=196 (LJ14) 142 144 60: 378 type=196 (LJ14) 143 144 60: 379 type=196 (LJ14) 144 149 60: 380 type=197 (LJ14) 144 150 60: 381 type=198 (LJ14) 144 154 60: 382 type=190 (LJ14) 145 147 60: 383 type=195 (LJ14) 145 148 60: 384 type=186 (LJ14) 146 151 60: 385 type=186 (LJ14) 146 152 60: 386 type=186 (LJ14) 146 153 60: 387 type=188 (LJ14) 146 155 60: 388 type=190 (LJ14) 147 149 60: 389 type=190 (LJ14) 147 150 60: 390 type=190 (LJ14) 147 154 60: 391 type=193 (LJ14) 149 151 60: 392 type=193 (LJ14) 149 152 60: 393 type=193 (LJ14) 149 153 60: 394 type=194 (LJ14) 149 155 60: 395 type=195 (LJ14) 150 155 60: 396 type=196 (LJ14) 151 154 60: 397 type=196 (LJ14) 152 154 60: 398 type=196 (LJ14) 153 154 60: Coulomb-14: 60: nr: 0 60: LJC-14 q: 60: nr: 0 60: LJC Pairs NB: 60: nr: 0 60: LJ (SR): 60: nr: 0 60: Buck.ham (SR): 60: nr: 0 60: LJ: 60: nr: 0 60: B.ham: 60: nr: 0 60: Disper. corr.: 60: nr: 0 60: Coulomb (SR): 60: nr: 0 60: Coul: 60: nr: 0 60: RF excl.: 60: nr: 0 60: Coul. recip.: 60: nr: 0 60: LJ recip.: 60: nr: 0 60: DPD: 60: nr: 0 60: Polarization: 60: nr: 0 60: Water Pol.: 60: nr: 0 60: Thole Pol.: 60: nr: 0 60: Anharm. Pol.: 60: nr: 0 60: Position Rest.: 60: nr: 0 60: Flat-b. P-R.: 60: nr: 0 60: Dis. Rest.: 60: nr: 0 60: D.R.Viol. (nm): 60: nr: 0 60: Orient. Rest.: 60: nr: 0 60: Ori. R. RMSD: 60: nr: 0 60: Angle Rest.: 60: nr: 0 60: Angle Rest. Z: 60: nr: 0 60: Dih. Rest.: 60: nr: 0 60: Dih. Rest. Vi.: 60: nr: 0 60: Constraint: 60: nr: 0 60: Constr. No Co.: 60: nr: 0 60: Settle: 60: nr: 0 60: Virtual site 1: 60: nr: 0 60: Virtual site 2: 60: nr: 0 60: Virt. site 2fd: 60: nr: 0 60: Virtual site 3: 60: nr: 0 60: Virt. site 3fd: 60: nr: 0 60: Vir. site 3fad: 60: nr: 0 60: Vir. site 3out: 60: nr: 0 60: Virt. site 4fd: 60: nr: 0 60: Vir. site 4fdn: 60: nr: 0 60: Virtual site N: 60: nr: 0 60: COM Pull En.: 60: nr: 0 60: Dens. fitting: 60: nr: 0 60: Quantum En.: 60: nr: 0 60: NN Potential: 60: nr: 0 60: Potential: 60: nr: 0 60: Kinetic En.: 60: nr: 0 60: Total Energy: 60: nr: 0 60: Conserved En.: 60: nr: 0 60: Temperature: 60: nr: 0 60: Vir. Temp.: 60: nr: 0 60: Pres. DC: 60: nr: 0 60: Pressure: 60: nr: 0 60: dH/dl constr.: 60: nr: 0 60: dVremain/dl: 60: nr: 0 60: dEkin/dl: 60: nr: 0 60: dVcoul/dl: 60: nr: 0 60: dVvdw/dl: 60: nr: 0 60: dVbonded/dl: 60: nr: 0 60: dVrestraint/dl: 60: nr: 0 60: dVtemp/dl: 60: nr: 0 60: grp[T-Coupling ] nr=1, name=[ rest] 60: grp[Energy Mon. ] nr=1, name=[ rest] 60: grp[Acc. not used] nr=1, name=[ rest] 60: grp[Freeze ] nr=1, name=[ rest] 60: grp[User1 ] nr=1, name=[ rest] 60: grp[User2 ] nr=1, name=[ rest] 60: grp[VCM ] nr=1, name=[ rest] 60: grp[Compressed X] nr=1, name=[ rest] 60: grp[Or. Res. Fit] nr=1, name=[ rest] 60: grp[QMMM ] nr=1, name=[ rest] 60: grpname (11): 60: grpname[0]={name="System"} 60: grpname[1]={name="Protein"} 60: grpname[2]={name="Protein-H"} 60: grpname[3]={name="C-alpha"} 60: grpname[4]={name="Backbone"} 60: grpname[5]={name="MainChain"} 60: grpname[6]={name="MainChain+Cb"} 60: grpname[7]={name="MainChain+H"} 60: grpname[8]={name="SideChain"} 60: grpname[9]={name="SideChain-H"} 60: grpname[10]={name="rest"} 60: groups T-Cou Energ Acc. Freez User1 User2 VCM Compr Or. R QMMM 60: allocated 0 0 0 0 0 0 0 0 0 0 60: groupnr[ *] = 0 0 0 0 0 0 0 0 0 0 60: box (3x3): 60: box[ 0]={ 5.90620e+00, 0.00000e+00, 0.00000e+00} 60: box[ 1]={ 0.00000e+00, 6.84510e+00, 0.00000e+00} 60: box[ 2]={ 0.00000e+00, 0.00000e+00, 3.05170e+00} 60: box_rel (3x3): 60: box_rel[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: box_rel[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: box_rel[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: boxv (3x3): 60: boxv[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: boxv[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: boxv[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: pres_prev (3x3): 60: pres_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: pres_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: pres_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: svir_prev (3x3): 60: svir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: svir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: svir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: fvir_prev (3x3): 60: fvir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: fvir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: fvir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: nosehoover_xi: not available 60: x (156x3): 60: x[ 0]={ 3.53600e+00, 2.23400e+00, -1.19800e+00} 60: x[ 1]={ 3.61200e+00, 2.28800e+00, -1.23600e+00} 60: x[ 2]={ 3.47000e+00, 2.21400e+00, -1.27000e+00} 60: x[ 3]={ 3.49200e+00, 2.28600e+00, -1.12500e+00} 60: x[ 4]={ 3.58900e+00, 2.10700e+00, -1.14300e+00} 60: x[ 5]={ 3.63300e+00, 2.05500e+00, -1.21600e+00} 60: x[ 6]={ 3.68700e+00, 2.14400e+00, -1.03100e+00} 60: x[ 7]={ 3.76300e+00, 2.19500e+00, -1.07000e+00} 60: x[ 8]={ 3.63900e+00, 2.20100e+00, -9.64000e-01} 60: x[ 9]={ 3.74500e+00, 2.02500e+00, -9.56000e-01} 60: x[ 10]={ 3.67600e+00, 1.98900e+00, -8.94000e-01} 60: x[ 11]={ 3.77000e+00, 1.95400e+00, -1.02300e+00} 60: x[ 12]={ 3.86900e+00, 2.06500e+00, -8.77000e-01} 60: x[ 13]={ 3.94500e+00, 2.08300e+00, -9.40000e-01} 60: x[ 14]={ 3.84900e+00, 2.14700e+00, -8.24000e-01} 60: x[ 15]={ 3.90600e+00, 1.95100e+00, -7.84000e-01} 60: x[ 16]={ 3.84100e+00, 1.94600e+00, -7.08000e-01} 60: x[ 17]={ 3.90600e+00, 1.86400e+00, -8.33000e-01} 60: x[ 18]={ 4.04200e+00, 1.97700e+00, -7.30000e-01} 60: x[ 19]={ 4.06900e+00, 1.90300e+00, -6.68000e-01} 60: x[ 20]={ 4.10800e+00, 1.98200e+00, -8.06000e-01} 60: x[ 21]={ 4.04200e+00, 2.06400e+00, -6.80000e-01} 60: x[ 22]={ 3.47400e+00, 2.02600e+00, -1.08400e+00} 60: x[ 23]={ 3.39500e+00, 2.08100e+00, -1.00800e+00} 60: x[ 24]={ 3.47400e+00, 1.89600e+00, -1.10400e+00} 60: x[ 25]={ 3.53600e+00, 1.86000e+00, -1.17400e+00} 60: x[ 26]={ 3.39000e+00, 1.80000e+00, -1.03300e+00} 60: x[ 27]={ 3.31700e+00, 1.85200e+00, -9.90000e-01} 60: x[ 28]={ 3.31400e+00, 1.70300e+00, -1.12300e+00} 60: x[ 29]={ 3.38600e+00, 1.65200e+00, -1.17000e+00} 60: x[ 30]={ 3.22500e+00, 1.60800e+00, -1.04300e+00} 60: x[ 31]={ 3.17700e+00, 1.54700e+00, -1.10600e+00} 60: x[ 32]={ 3.28200e+00, 1.55500e+00, -9.81000e-01} 60: x[ 33]={ 3.15800e+00, 1.66100e+00, -9.91000e-01} 60: x[ 34]={ 3.22900e+00, 1.77100e+00, -1.22900e+00} 60: x[ 35]={ 3.18300e+00, 1.70200e+00, -1.28400e+00} 60: x[ 36]={ 3.16200e+00, 1.83000e+00, -1.18500e+00} 60: x[ 37]={ 3.28800e+00, 1.82700e+00, -1.28800e+00} 60: x[ 38]={ 3.48000e+00, 1.73100e+00, -9.29000e-01} 60: x[ 39]={ 3.57600e+00, 1.66100e+00, -9.66000e-01} 60: x[ 40]={ 3.44900e+00, 1.75500e+00, -8.04000e-01} 60: x[ 41]={ 3.37500e+00, 1.81900e+00, -7.84000e-01} 60: x[ 42]={ 3.51900e+00, 1.69000e+00, -6.92000e-01} 60: x[ 43]={ 3.61500e+00, 1.69700e+00, -7.17000e-01} 60: x[ 44]={ 3.49700e+00, 1.76300e+00, -5.59000e-01} 60: x[ 45]={ 3.40500e+00, 1.80200e+00, -5.58000e-01} 60: x[ 46]={ 3.50600e+00, 1.69800e+00, -4.84000e-01} 60: x[ 47]={ 3.59400e+00, 1.87400e+00, -5.38000e-01} 60: x[ 48]={ 3.56700e+00, 2.00500e+00, -5.80000e-01} 60: x[ 49]={ 3.48100e+00, 2.02500e+00, -6.27000e-01} 60: x[ 50]={ 3.70000e+00, 1.85600e+00, -4.47000e-01} 60: x[ 51]={ 3.71300e+00, 1.76600e+00, -4.05000e-01} 60: x[ 52]={ 3.65800e+00, 2.10800e+00, -5.57000e-01} 60: x[ 53]={ 3.64800e+00, 2.19500e+00, -6.04000e-01} 60: x[ 54]={ 3.78700e+00, 1.95900e+00, -4.16000e-01} 60: x[ 55]={ 3.86600e+00, 1.94200e+00, -3.57000e-01} 60: x[ 56]={ 3.76400e+00, 2.08700e+00, -4.67000e-01} 60: x[ 57]={ 3.82200e+00, 2.16400e+00, -4.39000e-01} 60: x[ 58]={ 3.47400e+00, 1.54400e+00, -6.77000e-01} 60: x[ 59]={ 3.35200e+00, 1.51600e+00, -6.86000e-01} 60: x[ 60]={ 3.57200e+00, 1.46400e+00, -6.33000e-01} 60: x[ 61]={ 3.66700e+00, 1.49500e+00, -6.32000e-01} 60: x[ 62]={ 3.53700e+00, 1.32800e+00, -5.87000e-01} 60: x[ 63]={ 3.46200e+00, 1.29200e+00, -6.43000e-01} 60: x[ 64]={ 3.61600e+00, 1.26800e+00, -5.94000e-01} 60: x[ 65]={ 3.49200e+00, 1.34200e+00, -4.42000e-01} 60: x[ 66]={ 3.53000e+00, 1.44000e+00, -3.78000e-01} 60: x[ 67]={ 3.40500e+00, 1.25400e+00, -3.97000e-01} 60: x[ 68]={ 3.37100e+00, 1.18400e+00, -4.60000e-01} 60: x[ 69]={ 3.35600e+00, 1.25400e+00, -2.59000e-01} 60: x[ 70]={ 3.29800e+00, 1.33400e+00, -2.52000e-01} 60: x[ 71]={ 3.27600e+00, 1.12600e+00, -2.33000e-01} 60: x[ 72]={ 3.20000e+00, 1.12200e+00, -2.97000e-01} 60: x[ 73]={ 3.33600e+00, 1.04700e+00, -2.47000e-01} 60: x[ 74]={ 3.22100e+00, 1.12000e+00, -9.20000e-02} 60: x[ 75]={ 3.29700e+00, 1.11700e+00, -2.70000e-02} 60: x[ 76]={ 3.16500e+00, 1.20100e+00, -7.50000e-02} 60: x[ 77]={ 3.13800e+00, 1.00000e+00, -7.20000e-02} 60: x[ 78]={ 3.10400e+00, 9.99000e-01, 2.20000e-02} 60: x[ 79]={ 3.06000e+00, 1.00500e+00, -1.35000e-01} 60: x[ 80]={ 3.20600e+00, 8.75000e-01, -9.60000e-02} 60: x[ 81]={ 3.20200e+00, 8.40000e-01, -1.89000e-01} 60: x[ 82]={ 3.27300e+00, 8.01000e-01, -1.00000e-02} 60: x[ 83]={ 3.28400e+00, 8.33000e-01, 1.19000e-01} 60: x[ 84]={ 3.23900e+00, 9.16000e-01, 1.53000e-01} 60: x[ 85]={ 3.33600e+00, 7.75000e-01, 1.81000e-01} 60: x[ 86]={ 3.32500e+00, 6.84000e-01, -5.30000e-02} 60: x[ 87]={ 3.31100e+00, 6.55000e-01, -1.47000e-01} 60: x[ 88]={ 3.37600e+00, 6.26000e-01, 1.00000e-02} 60: x[ 89]={ 3.46700e+00, 1.27300e+00, -1.56000e-01} 60: x[ 90]={ 3.46700e+00, 1.36500e+00, -7.00000e-02} 60: x[ 91]={ 3.56700e+00, 1.18500e+00, -1.61000e-01} 60: x[ 92]={ 3.56700e+00, 1.11600e+00, -2.33000e-01} 60: x[ 93]={ 3.67800e+00, 1.18700e+00, -6.50000e-02} 60: x[ 94]={ 3.63100e+00, 1.20200e+00, 2.20000e-02} 60: x[ 95]={ 3.74900e+00, 1.05300e+00, -6.20000e-02} 60: x[ 96]={ 3.77000e+00, 1.03400e+00, -1.58000e-01} 60: x[ 97]={ 3.83400e+00, 1.07200e+00, -1.30000e-02} 60: x[ 98]={ 3.65400e+00, 9.20000e-01, 1.40000e-02} 60: x[ 99]={ 3.70750e+00, 8.35500e-01, 1.20000e-02} 60: x[ 100]={ 3.77500e+00, 1.30500e+00, -7.80000e-02} 60: x[ 101]={ 3.81500e+00, 1.36100e+00, 2.60000e-02} 60: x[ 102]={ 3.78600e+00, 1.34800e+00, -2.02000e-01} 60: x[ 103]={ 3.74000e+00, 1.30000e+00, -2.76000e-01} 60: x[ 104]={ 3.86800e+00, 1.46900e+00, -2.31000e-01} 60: x[ 105]={ 3.96000e+00, 1.45500e+00, -1.93000e-01} 60: x[ 106]={ 3.87800e+00, 1.48500e+00, -3.82000e-01} 60: x[ 107]={ 3.92300e+00, 1.40200e+00, -4.17000e-01} 60: x[ 108]={ 3.78500e+00, 1.48900e+00, -4.17000e-01} 60: x[ 109]={ 3.95400e+00, 1.60500e+00, -4.38000e-01} 60: x[ 110]={ 3.91300e+00, 1.68700e+00, -3.99000e-01} 60: x[ 111]={ 4.04900e+00, 1.59800e+00, -4.07000e-01} 60: x[ 112]={ 3.95800e+00, 1.62400e+00, -5.87000e-01} 60: x[ 113]={ 3.86700e+00, 1.56400e+00, -6.49000e-01} 60: x[ 114]={ 4.04200e+00, 1.69500e+00, -6.38000e-01} 60: x[ 115]={ 3.80500e+00, 1.59300e+00, -1.66000e-01} 60: x[ 116]={ 3.87400e+00, 1.67300e+00, -1.01000e-01} 60: x[ 117]={ 3.67400e+00, 1.60500e+00, -1.82000e-01} 60: x[ 118]={ 3.62600e+00, 1.53500e+00, -2.35000e-01} 60: x[ 119]={ 3.59600e+00, 1.71600e+00, -1.25000e-01} 60: x[ 120]={ 3.64000e+00, 1.80100e+00, -1.56000e-01} 60: x[ 121]={ 3.45300e+00, 1.71700e+00, -1.81000e-01} 60: x[ 122]={ 3.45700e+00, 1.72200e+00, -2.81000e-01} 60: x[ 123]={ 3.40600e+00, 1.63300e+00, -1.53000e-01} 60: x[ 124]={ 3.37200e+00, 1.83500e+00, -1.31000e-01} 60: x[ 125]={ 3.37800e+00, 1.84200e+00, -3.10000e-02} 60: x[ 126]={ 3.43000e+00, 1.96600e+00, -1.84000e-01} 60: x[ 127]={ 3.37600e+00, 2.04300e+00, -1.50000e-01} 60: x[ 128]={ 3.52400e+00, 1.97500e+00, -1.53000e-01} 60: x[ 129]={ 3.42700e+00, 1.96500e+00, -2.84000e-01} 60: x[ 130]={ 3.22500e+00, 1.81400e+00, -1.60000e-01} 60: x[ 131]={ 3.17200e+00, 1.89300e+00, -1.26000e-01} 60: x[ 132]={ 3.21100e+00, 1.80500e+00, -2.58000e-01} 60: x[ 133]={ 3.19300e+00, 1.73100e+00, -1.14000e-01} 60: x[ 134]={ 3.60500e+00, 1.71300e+00, 2.70000e-02} 60: x[ 135]={ 3.61600e+00, 1.81700e+00, 9.20000e-02} 60: x[ 136]={ 3.57500e+00, 1.59800e+00, 8.30000e-02} 60: x[ 137]={ 3.54600e+00, 1.52200e+00, 2.40000e-02} 60: x[ 138]={ 3.58400e+00, 1.57600e+00, 2.28000e-01} 60: x[ 139]={ 3.50800e+00, 1.62600e+00, 2.69000e-01} 60: x[ 140]={ 3.56600e+00, 1.42900e+00, 2.62000e-01} 60: x[ 141]={ 3.57200e+00, 1.41600e+00, 3.61000e-01} 60: x[ 142]={ 3.47600e+00, 1.39800e+00, 2.30000e-01} 60: x[ 143]={ 3.63700e+00, 1.37500e+00, 2.18000e-01} 60: x[ 144]={ 3.71400e+00, 1.63100e+00, 2.84000e-01} 60: x[ 145]={ 3.71500e+00, 1.69800e+00, 3.90000e-01} 60: x[ 146]={ 3.82700e+00, 1.59800e+00, 2.20000e-01} 60: x[ 147]={ 3.82000e+00, 1.53900e+00, 1.40000e-01} 60: x[ 148]={ 3.96100e+00, 1.64300e+00, 2.62000e-01} 60: x[ 149]={ 3.96900e+00, 1.61900e+00, 3.58000e-01} 60: x[ 150]={ 4.07100e+00, 1.57100e+00, 1.84000e-01} 60: x[ 151]={ 4.16000e+00, 1.60300e+00, 2.15000e-01} 60: x[ 152]={ 4.06400e+00, 1.47200e+00, 2.01000e-01} 60: x[ 153]={ 4.06000e+00, 1.58900e+00, 8.60000e-02} 60: x[ 154]={ 3.97400e+00, 1.79400e+00, 2.46000e-01} 60: x[ 155]={ 4.01900e+00, 1.85000e+00, 3.47000e-01} 60: v (156x3): 60: v[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 3]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 4]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 5]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 6]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 7]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 8]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 9]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 10]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 11]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 12]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 13]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 14]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 15]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 16]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 17]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 18]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 19]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 20]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 21]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 22]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 23]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 24]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 25]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 26]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 27]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 28]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 29]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 30]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 31]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 32]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 33]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 34]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 35]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 36]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 37]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 38]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 39]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 40]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 41]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 42]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 43]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 44]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 45]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 46]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 47]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 48]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 49]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 50]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 51]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 52]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 53]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 54]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 55]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 56]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 57]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 58]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 59]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 60]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 61]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 62]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 63]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 64]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 65]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 66]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 67]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 68]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 69]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 70]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 71]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 72]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 73]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 74]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 75]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 76]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 77]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 78]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 79]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 80]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 81]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 82]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 83]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 84]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 85]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 86]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 87]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 88]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 89]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 90]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 91]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 92]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 93]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 94]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 95]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 96]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 97]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 98]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 99]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 100]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 101]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 102]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 103]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 104]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 105]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 106]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 107]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 108]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 109]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 110]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 111]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 112]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 113]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 114]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 115]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 116]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 117]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 118]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 119]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 120]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 121]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 122]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 123]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 124]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 125]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 126]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 127]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 128]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 129]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 130]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 131]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 132]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 133]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 134]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 135]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 136]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 137]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 138]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 139]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 140]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 141]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 142]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 143]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 144]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 145]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 146]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 147]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 148]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 149]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 150]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 151]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 152]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 153]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 154]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 155]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: Group statistics 60: T-Coupling : 156 (total 156 atoms) 60: Energy Mon. : 156 (total 156 atoms) 60: Acc. not used: 156 (total 156 atoms) 60: Freeze : 156 (total 156 atoms) 60: User1 : 156 (total 156 atoms) 60: User2 : 156 (total 156 atoms) 60: VCM : 156 (total 156 atoms) 60: Compressed X: 156 (total 156 atoms) 60: Or. Res. Fit: 156 (total 156 atoms) 60: QMMM : 156 (total 156 atoms) 60: [ OK ] DumpTest.WorksWithTpr (21 ms) 60: [ RUN ] DumpTest.WorksWithTprAndMdpWriting 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: [ OK ] DumpTest.WorksWithTprAndMdpWriting (1 ms) 60: [----------] 2 tests from DumpTest (23 ms total) 60: 60: [----------] 3 tests from HelpwritingTest 60: [ RUN ] HelpwritingTest.ConvertTprWritesHelp 60: [ OK ] HelpwritingTest.ConvertTprWritesHelp (0 ms) 60: [ RUN ] HelpwritingTest.DumpWritesHelp 60: [ OK ] HelpwritingTest.DumpWritesHelp (0 ms) 60: [ RUN ] HelpwritingTest.ReportMethodsWritesHelp 60: [ OK ] HelpwritingTest.ReportMethodsWritesHelp (0 ms) 60: [----------] 3 tests from HelpwritingTest (0 ms total) 60: 60: [----------] 7 tests from GmxMakeNdx 60: [ RUN ] GmxMakeNdx.WritesDefaultProteinIndexGroups 60: 60: Reading structure file 60: Going to read 0 old index file(s) 60: Analysing residue names: 60: There are: 16 Protein residues 60: Analysing Protein... 60: 60: 0 System : 256 atoms 60: 1 Protein : 256 atoms 60: 2 Protein-H : 139 atoms 60: 3 C-alpha : 16 atoms 60: 4 Backbone : 48 atoms 60: 5 MainChain : 63 atoms 60: 6 MainChain+Cb : 78 atoms 60: 7 MainChain+H : 81 atoms 60: 8 SideChain : 175 atoms 60: 9 SideChain-H : 76 atoms 60: 60: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 60: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 60: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 60: 'r': residue 'res' nr 'chain' char 60: "name": group 'case': case sensitive 'q': save and quit 60: 'ri': residue index 60: 60: > 60: [ OK ] GmxMakeNdx.WritesDefaultProteinIndexGroups (3 ms) 60: [ RUN ] GmxMakeNdx.HandlesNoStructureInput 60: Going to read 1 old index file(s) 60: Deducing 22 atoms in the system from indices in the index file 60: 60: 0 System : 22 atoms 60: 1 Protein : 22 atoms 60: 2 Protein-H : 10 atoms 60: 3 C-alpha : 1 atoms 60: 4 Backbone : 5 atoms 60: 5 MainChain : 7 atoms 60: 6 MainChain+Cb : 8 atoms 60: 7 MainChain+H : 9 atoms 60: 8 SideChain : 13 atoms 60: 9 SideChain-H : 3 atoms 60: 10 CA : 1 atoms 60: 11 C_&_r_1 : 1 atoms 60: 12 C_&_r_2 : 1 atoms 60: 13 N_&_r_2 : 1 atoms 60: 14 N_&_r_3 : 1 atoms 60: 60: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 60: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 60: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 60: 'r': residue 'res' nr 'chain' char 60: "name": group 'case': case sensitive 'q': save and quit 60: 'ri': residue index 60: 60: > 60: Copied index group 1 'Protein' 60: Copied index group 2 'Protein-H' 60: Merged two groups with OR: 22 10 -> 22 60: 60: > 60: [ OK ] GmxMakeNdx.HandlesNoStructureInput (0 ms) 60: [ RUN ] GmxMakeNdx.HandlesNotProtein 60: Going to read 1 old index file(s) 60: Deducing 6 atoms in the system from indices in the index file 60: 60: 0 System : 6 atoms 60: 60: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 60: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 60: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 60: 'r': residue 'res' nr 'chain' char 60: "name": group 'case': case sensitive 'q': save and quit 60: 'ri': residue index 60: 60: > 60: [ OK ] GmxMakeNdx.HandlesNotProtein (0 ms) 60: [ RUN ] GmxMakeNdx.HandlesEmptyIndexResult 60: Going to read 1 old index file(s) 60: Deducing 22 atoms in the system from indices in the index file 60: 60: 0 System : 22 atoms 60: 1 Protein : 22 atoms 60: 2 Protein-H : 10 atoms 60: 3 C-alpha : 1 atoms 60: 4 Backbone : 5 atoms 60: 5 MainChain : 7 atoms 60: 6 MainChain+Cb : 8 atoms 60: 7 MainChain+H : 9 atoms 60: 8 SideChain : 13 atoms 60: 9 SideChain-H : 3 atoms 60: 10 CA : 1 atoms 60: 11 C_&_r_1 : 1 atoms 60: 12 C_&_r_2 : 1 atoms 60: 13 N_&_r_2 : 1 atoms 60: 14 N_&_r_3 : 1 atoms 60: 60: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 60: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 60: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 60: 'r': residue 'res' nr 'chain' char 60: "name": group 'case': case sensitive 'q': save and quit 60: 'ri': residue index 60: 60: > 60: Copied index group 4 'Backbone' 60: Copied index group 8 'SideChain' 60: Merged two groups with AND: 5 13 -> 0 60: Group is empty 60: 60: > 60: [ OK ] GmxMakeNdx.HandlesEmptyIndexResult (0 ms) 60: [ RUN ] GmxMakeNdx.HandlesEmptyIndexFile 60: Going to read 1 old index file(s) 60: Deducing 6 atoms in the system from indices in the index file 60: 60: 0 System : 6 atoms 60: 60: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 60: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 60: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 60: 'r': residue 'res' nr 'chain' char 60: "name": group 'case': case sensitive 'q': save and quit 60: 'ri': residue index 60: 60: > 60: Removed group 0 'System' 60: 60: > 60: [ OK ] GmxMakeNdx.HandlesEmptyIndexFile (0 ms) 60: [ RUN ] GmxMakeNdx.Splitres 60: 60: Reading structure file 60: Going to read 0 old index file(s) 60: Analysing residue names: 60: There are: 2 Water residues 60: 60: 0 System : 6 atoms 60: 1 Water : 6 atoms 60: 2 SOL : 6 atoms 60: 60: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 60: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 60: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 60: 'r': residue 'res' nr 'chain' char 60: "name": group 'case': case sensitive 'q': save and quit 60: 'ri': residue index 60: 60: > 60: Splitting group 1 'Water' into residues 60: 60: > 60: [ OK ] GmxMakeNdx.Splitres (1 ms) 60: [ RUN ] GmxMakeNdx.Splitat 60: 60: Reading structure file 60: Going to read 0 old index file(s) 60: Analysing residue names: 60: There are: 2 Water residues 60: 60: 0 System : 6 atoms 60: 1 Water : 6 atoms 60: 2 SOL : 6 atoms 60: 60: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 60: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 60: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 60: 'r': residue 'res' nr 'chain' char 60: "name": group 'case': case sensitive 'q': save and quit 60: 'ri': residue index 60: 60: > 60: Splitting group 1 'Water' into atoms 60: 60: > 60: [ OK ] GmxMakeNdx.Splitat (0 ms) 60: [----------] 7 tests from GmxMakeNdx (8 ms total) 60: 60: [----------] 4 tests from ReportMethodsTest 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file lysozyme.top, line 1465]: 60: System has non-zero total charge: 2.000000 60: Total charge should normally be an integer. See 60: https://manual.gromacs.org/current/user-guide/floating-point.html 60: for discussion on how close it should be to an integer. 60: 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 465.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 60: NVE simulation with an initial temperature of zero: will use a Verlet 60: buffer of 10%. Check your energy drift! 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 NOTEs 60: Setting the LD random seed to 1606442483 60: 60: Generated 330891 of the 330891 non-bonded parameter combinations 60: 60: Generated 330891 of the 330891 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 60: Analysing residue names: 60: There are: 10 Protein residues 60: Analysing Protein... 60: 60: This run will generate roughly 0 Mb of data 60: [ RUN ] ReportMethodsTest.WritesCorrectHeadersFormated 60: [ OK ] ReportMethodsTest.WritesCorrectHeadersFormated (0 ms) 60: [ RUN ] ReportMethodsTest.WritesCorrectHeadersUnformatted 60: [ OK ] ReportMethodsTest.WritesCorrectHeadersUnformatted (0 ms) 60: [ RUN ] ReportMethodsTest.WritesCorrectInformation 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: [ OK ] ReportMethodsTest.WritesCorrectInformation (0 ms) 60: [ RUN ] ReportMethodsTest.ToolEndToEndTest 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: section: Methods 60: subsection: Simulation system 60: A system of 1 molecules (156 atoms) was simulated. 60: 60: subsection: Simulation settings 60: A total of 0 ns were simulated with a time step of 1 fs. 60: Neighbor searching was performed every 10 steps. 60: The Cut-off algorithm was used for electrostatic interactions. 60: with a cut-off of 1 nm. 60: A single cut-off of 1.1 nm was used for Van der Waals interactions. 60: [ OK ] ReportMethodsTest.ToolEndToEndTest (0 ms) 60: [----------] 4 tests from ReportMethodsTest (1 ms total) 60: 60: [----------] 4 tests from ConvertTprTest 60: [ RUN ] ConvertTprTest.ExtendRuntimeExtensionTest 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file lysozyme.top, line 1465]: 60: System has non-zero total charge: 2.000000 60: Total charge should normally be an integer. See 60: https://manual.gromacs.org/current/user-guide/floating-point.html 60: for discussion on how close it should be to an integer. 60: 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 465.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 60: NVE simulation with an initial temperature of zero: will use a Verlet 60: buffer of 10%. Check your energy drift! 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended_again.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Setting the LD random seed to 2103443427 60: 60: Generated 330891 of the 330891 non-bonded parameter combinations 60: 60: Generated 330891 of the 330891 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 60: Analysing residue names: 60: There are: 10 Protein residues 60: Analysing Protein... 60: 60: This run will generate roughly 0 Mb of data 60: Input file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 0 60: Runtime for the run 0 ps 60: Run end step 0 60: Run end time 0 ps 60: 60: Extending remaining runtime by 100 ps 60: 60: Output file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 100000 60: Runtime for the run 100 ps 60: Run end step 100000 60: Run end time 100 ps 60: 60: Input file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 100000 60: Runtime for the run 100 ps 60: Run end step 100000 60: Run end time 100 ps 60: 60: Extending remaining runtime by 100 ps 60: 60: Output file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 200000 60: Runtime for the run 200 ps 60: Run end step 200000 60: Run end time 200 ps 60: 60: [ OK ] ConvertTprTest.ExtendRuntimeExtensionTest (537 ms) 60: [ RUN ] ConvertTprTest.UntilRuntimeExtensionTest 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file lysozyme.top, line 1465]: 60: System has non-zero total charge: 2.000000 60: Total charge should normally be an integer. See 60: https://manual.gromacs.org/current/user-guide/floating-point.html 60: for discussion on how close it should be to an integer. 60: 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 465.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 60: NVE simulation with an initial temperature of zero: will use a Verlet 60: buffer of 10%. Check your energy drift! 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_extended.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Setting the LD random seed to 2097080686 60: 60: Generated 330891 of the 330891 non-bonded parameter combinations 60: 60: Generated 330891 of the 330891 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 60: Analysing residue names: 60: There are: 10 Protein residues 60: Analysing Protein... 60: 60: This run will generate roughly 0 Mb of data 60: Input file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 0 60: Runtime for the run 0 ps 60: Run end step 0 60: Run end time 0 ps 60: 60: Extending remaining runtime to 100 ps 60: 60: Output file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 100000 60: Runtime for the run 100 ps 60: Run end step 100000 60: Run end time 100 ps 60: 60: [ OK ] ConvertTprTest.UntilRuntimeExtensionTest (525 ms) 60: [ RUN ] ConvertTprTest.nstepRuntimeExtensionTest 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file lysozyme.top, line 1465]: 60: System has non-zero total charge: 2.000000 60: Total charge should normally be an integer. See 60: https://manual.gromacs.org/current/user-guide/floating-point.html 60: for discussion on how close it should be to an integer. 60: 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 465.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 60: NVE simulation with an initial temperature of zero: will use a Verlet 60: buffer of 10%. Check your energy drift! 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Setting nsteps to 102 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_extended.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Setting the LD random seed to -1073750162 60: 60: Generated 330891 of the 330891 non-bonded parameter combinations 60: 60: Generated 330891 of the 330891 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 60: Analysing residue names: 60: There are: 10 Protein residues 60: Analysing Protein... 60: 60: This run will generate roughly 0 Mb of data 60: Input file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 0 60: Runtime for the run 0 ps 60: Run end step 0 60: Run end time 0 ps 60: 60: 60: Output file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 102 60: Runtime for the run 0.102 ps 60: Run end step 102 60: Run end time 0.102 ps 60: 60: [ OK ] ConvertTprTest.nstepRuntimeExtensionTest (514 ms) 60: [ RUN ] ConvertTprTest.generateVelocitiesTest 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file lysozyme.top, line 1465]: 60: System has non-zero total charge: 2.000000 60: Total charge should normally be an integer. See 60: https://manual.gromacs.org/current/user-guide/floating-point.html 60: for discussion on how close it should be to an integer. 60: 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 465.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 60: NVE simulation with an initial temperature of zero: will use a Verlet 60: buffer of 10%. Check your energy drift! 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_new_velocities.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Setting the LD random seed to -1654808713 60: 60: Generated 330891 of the 330891 non-bonded parameter combinations 60: 60: Generated 330891 of the 330891 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 60: Analysing residue names: 60: There are: 10 Protein residues 60: Analysing Protein... 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] ConvertTprTest.generateVelocitiesTest (546 ms) 60: [----------] 4 tests from ConvertTprTest (2125 ms total) 60: 60: [----------] 1 test from ConvertTprNoVelocityTest 60: [ RUN ] ConvertTprNoVelocityTest.refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest_lysozyme.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file lysozyme.top, line 1465]: 60: System has non-zero total charge: 2.000000 60: Total charge should normally be an integer. See 60: https://manual.gromacs.org/current/user-guide/floating-point.html 60: for discussion on how close it should be to an integer. 60: 60: 60: 60: 60: NOTE 3 [file lysozyme.top, line 1465]: 60: Zero-step energy minimization will alter the coordinates before 60: calculating the energy. If you just want the energy of a single point, 60: try zero-step MD (with unconstrained_start = yes). To do multiple 60: single-point energy evaluations of different configurations of the same 60: topology, use mdrun -rerun. 60: 60: Number of degrees of freedom in T-Coupling group rest is 465.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest_lysozyme.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Setting the LD random seed to 1608473462 60: 60: Generated 330891 of the 330891 non-bonded parameter combinations 60: 60: Generated 330891 of the 330891 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 60: Analysing residue names: 60: There are: 10 Protein residues 60: Analysing Protein... 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] ConvertTprNoVelocityTest.refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest (551 ms) 60: [----------] 1 test from ConvertTprNoVelocityTest (551 ms total) 60: 60: [----------] 12 tests from Works/TrjconvWithDifferentInputFormats 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_trr 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: trr version: GMX_trn_file (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_trr (1 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_tng 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 60: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_tng (1 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_xtc 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_xtc (0 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_gro 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 60: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_gro (2 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_pdb 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 60: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 60: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_pdb (0 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_g96 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_g96 (1 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_trr 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_trr (0 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_tng 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 60: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_tng (1 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_xtc 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_xtc (0 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_gro 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 60: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_gro (0 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_pdb 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 60: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 60: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_pdb (0 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_g96 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_g96 (1 ms) 60: [----------] 12 tests from Works/TrjconvWithDifferentInputFormats (15 ms total) 60: 60: [----------] 30 tests from Works/TrjconvDumpTest 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time__1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time__1_00 (7 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_30 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_30 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_1_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_999999_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_999999_00 (1 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time__1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 60: Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time__1_00 (2 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 60: Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_00 (1 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_30 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 60: Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_30 (1 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 60: Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_1_00 (2 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_999999_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 60: Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_999999_00 (1 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time__1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time__1_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_00 (1 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_30 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_30 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_1_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_999999_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_999999_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time__1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 60: Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time__1_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 60: Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_30 60: Will write trr: Trajectory in portable xdr format 60: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 60: Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_30 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 60: Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_1_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_999999_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 60: Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_999999_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time__1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 60: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 60: Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time__1_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 60: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 60: Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_30 60: Will write trr: Trajectory in portable xdr format 60: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 60: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 60: Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_30 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 60: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 60: Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_1_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_999999_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 60: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 60: Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_999999_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time__1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time__1_00 (1 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_30 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_30 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_1_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_999999_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_999999_00 (1 ms) 60: [----------] 30 tests from Works/TrjconvDumpTest (33 ms total) 60: 60: [----------] Global test environment tear-down 60: [==========] 63 tests from 8 test suites ran. (3955 ms total) 60: [ PASSED ] 63 tests. 60/90 Test #60: ToolUnitTests ............................. Passed 3.98 sec test 61 Start 61: ToolWithLeaksUnitTests 61: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/tool-test-with-leaks "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/ToolWithLeaksUnitTests.xml" 61: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests 61: Test timeout computed to be: 1920 61: [==========] Running 2 tests from 2 test suites. 61: [----------] Global test environment set-up. 61: [----------] 1 test from ConvertTprTest 61: [ RUN ] ConvertTprTest.selectIndexTest 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.mdp]: 61: For a correct single-point energy evaluation with nsteps = 0, use 61: continuation = yes to avoid constraining the input coordinates. 61: 61: Generating 1-4 interactions: fudge = 0.5 61: 61: NOTE 2 [file lysozyme.top, line 1465]: 61: System has non-zero total charge: 2.000000 61: Total charge should normally be an integer. See 61: https://manual.gromacs.org/current/user-guide/floating-point.html 61: for discussion on how close it should be to an integer. 61: 61: 61: 61: Number of degrees of freedom in T-Coupling group rest is 465.00 61: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 61: 61: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.mdp]: 61: NVE simulation with an initial temperature of zero: will use a Verlet 61: buffer of 10%. Check your energy drift! 61: 61: 61: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There were 4 NOTEs 61: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 61: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 61: Group 0 ( System) has 156 elements 61: Group 1 ( Protein) has 156 elements 61: Group 2 ( Protein-H) has 75 elements 61: Group 3 ( C-alpha) has 10 elements 61: Group 4 ( Backbone) has 30 elements 61: Group 5 ( MainChain) has 40 elements 61: Group 6 ( MainChain+Cb) has 49 elements 61: Group 7 ( MainChain+H) has 52 elements 61: Group 8 ( SideChain) has 104 elements 61: Group 9 ( SideChain-H) has 35 elements 61: Select a group: Will write subset Protein-H of original tpx containing 75 atoms 61: Reduced ilist BONDS from 156 to 75 entries 61: Reduced ilist ANGLES from 281 to 98 entries 61: Reduced ilist PDIHS from 29 to 12 entries 61: Reduced ilist RBDIHS from 313 to 89 entries 61: Reduced ilist LJ14 from 399 to 107 entries 61: Reduced block excls from 156 to 75 index-, 1828 to 635 a-entries 61: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_extended.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 61: Setting the LD random seed to -1075531779 61: 61: Generated 330891 of the 330891 non-bonded parameter combinations 61: 61: Generated 330891 of the 330891 1-4 parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 61: 61: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 61: Analysing residue names: 61: There are: 10 Protein residues 61: Analysing Protein... 61: 61: This run will generate roughly 0 Mb of data 61: Selected 2: 'Protein-H' 61: [ OK ] ConvertTprTest.selectIndexTest (662 ms) 61: [----------] 1 test from ConvertTprTest (662 ms total) 61: 61: [----------] 1 test from ConvertTprNoVelocityTest 61: [ RUN ] ConvertTprNoVelocityTest.selectIndexTestWithoutVelocity 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.mdp]: 61: For a correct single-point energy evaluation with nsteps = 0, use 61: continuation = yes to avoid constraining the input coordinates. 61: 61: Generating 1-4 interactions: fudge = 0.5 61: 61: NOTE 2 [file lysozyme.top, line 1465]: 61: System has non-zero total charge: 2.000000 61: Total charge should normally be an integer. See 61: https://manual.gromacs.org/current/user-guide/floating-point.html 61: for discussion on how close it should be to an integer. 61: 61: 61: 61: 61: NOTE 3 [file lysozyme.top, line 1465]: 61: Zero-step energy minimization will alter the coordinates before 61: calculating the energy. If you just want the energy of a single point, 61: try zero-step MD (with unconstrained_start = yes). To do multiple 61: single-point energy evaluations of different configurations of the same 61: topology, use mdrun -rerun. 61: 61: Number of degrees of freedom in T-Coupling group rest is 465.00 61: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 61: 61: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There were 4 NOTEs 61: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 61: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 61: Group 0 ( System) has 156 elements 61: Group 1 ( Protein) has 156 elements 61: Group 2 ( Protein-H) has 75 elements 61: Group 3 ( C-alpha) has 10 elements 61: Group 4 ( Backbone) has 30 elements 61: Group 5 ( MainChain) has 40 elements 61: Group 6 ( MainChain+Cb) has 49 elements 61: Group 7 ( MainChain+H) has 52 elements 61: Group 8 ( SideChain) has 104 elements 61: Group 9 ( SideChain-H) has 35 elements 61: Select a group: Will write subset Protein-H of original tpx containing 75 atoms 61: Reduced ilist BONDS from 156 to 75 entries 61: Reduced ilist ANGLES from 281 to 98 entries 61: Reduced ilist PDIHS from 29 to 12 entries 61: Reduced ilist RBDIHS from 313 to 89 entries 61: Reduced ilist LJ14 from 399 to 107 entries 61: Reduced block excls from 156 to 75 index-, 1828 to 635 a-entries 61: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_extended.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 61: Setting the LD random seed to -6422937 61: 61: Generated 330891 of the 330891 non-bonded parameter combinations 61: 61: Generated 330891 of the 330891 1-4 parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 61: Analysing residue names: 61: There are: 10 Protein residues 61: Analysing Protein... 61: 61: This run will generate roughly 0 Mb of data 61: Selected 2: 'Protein-H' 61: [ OK ] ConvertTprNoVelocityTest.selectIndexTestWithoutVelocity (589 ms) 61: [----------] 1 test from ConvertTprNoVelocityTest (589 ms total) 61: 61: [----------] Global test environment tear-down 61: [==========] 2 tests from 2 test suites ran. (1251 ms total) 61: [ PASSED ] 2 tests. 61/90 Test #61: ToolWithLeaksUnitTests .................... Passed 1.27 sec test 62 Start 62: FileIOTests 62: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/fileio-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/FileIOTests.xml" 62: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/fileio/tests 62: Test timeout computed to be: 30 62: [==========] Running 421 tests from 17 test suites. 62: [----------] Global test environment set-up. 62: [----------] 4 tests from Checkpoint 62: [ RUN ] Checkpoint.ReadingThrowsWhenValueNotPresent 62: [ OK ] Checkpoint.ReadingThrowsWhenValueNotPresent (0 ms) 62: [ RUN ] Checkpoint.ReadingDoesNotThrowWhenValuePresent 62: [ OK ] Checkpoint.ReadingDoesNotThrowWhenValuePresent (0 ms) 62: [ RUN ] Checkpoint.KvtRoundTripInt64 62: [ OK ] Checkpoint.KvtRoundTripInt64 (0 ms) 62: [ RUN ] Checkpoint.KvtRoundTripReal 62: [ OK ] Checkpoint.KvtRoundTripReal (0 ms) 62: [----------] 4 tests from Checkpoint (0 ms total) 62: 62: [----------] 1 test from StructureIOTest 62: [ RUN ] StructureIOTest.ReadTpsConfRetainsChainids 62: [ OK ] StructureIOTest.ReadTpsConfRetainsChainids (0 ms) 62: [----------] 1 test from StructureIOTest (0 ms total) 62: 62: [----------] 2 tests from FileMD5Test 62: [ RUN ] FileMD5Test.CanComputeMD5 62: [ OK ] FileMD5Test.CanComputeMD5 (2 ms) 62: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong 62: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (0 ms) 62: [----------] 2 tests from FileMD5Test (2 ms total) 62: 62: [----------] 4 tests from FileTypeTest 62: [ RUN ] FileTypeTest.CorrectValueForEmptyString 62: [ OK ] FileTypeTest.CorrectValueForEmptyString (0 ms) 62: [ RUN ] FileTypeTest.CorrectValueForNoExtension 62: [ OK ] FileTypeTest.CorrectValueForNoExtension (0 ms) 62: [ RUN ] FileTypeTest.CorrectValueForEmptyExtension 62: [ OK ] FileTypeTest.CorrectValueForEmptyExtension (0 ms) 62: [ RUN ] FileTypeTest.CorrectValueForLongExtensionWithStrangeCharacters 62: [ OK ] FileTypeTest.CorrectValueForLongExtensionWithStrangeCharacters (0 ms) 62: [----------] 4 tests from FileTypeTest (0 ms total) 62: 62: [----------] 4 tests from ColorMapTest 62: [ RUN ] ColorMapTest.CanReadFromFile 62: [ OK ] ColorMapTest.CanReadFromFile (0 ms) 62: [ RUN ] ColorMapTest.CanWriteToFile 62: [ OK ] ColorMapTest.CanWriteToFile (0 ms) 62: [ RUN ] ColorMapTest.RoundTrip 62: [ OK ] ColorMapTest.RoundTrip (0 ms) 62: [ RUN ] ColorMapTest.SearchWorks 62: [ OK ] ColorMapTest.SearchWorks (0 ms) 62: [----------] 4 tests from ColorMapTest (0 ms total) 62: 62: [----------] 4 tests from MatioTest 62: [ RUN ] MatioTest.CanWriteToFile 62: 33% 66%100%[ OK ] MatioTest.CanWriteToFile (0 ms) 62: [ RUN ] MatioTest.CanConvertToExistingRealMatrix 62: Converted a 4x3 matrix with 4 levels to reals 62: [ OK ] MatioTest.CanConvertToExistingRealMatrix (0 ms) 62: [ RUN ] MatioTest.CanConvertToNewRealMatrix 62: Converted a 4x3 matrix with 4 levels to reals 62: [ OK ] MatioTest.CanConvertToNewRealMatrix (0 ms) 62: [ RUN ] MatioTest.CanReadSingleMatrixAfterWriting 62: 33% 66%100% 33% 66%100%[ OK ] MatioTest.CanReadSingleMatrixAfterWriting (3 ms) 62: [----------] 4 tests from MatioTest (3 ms total) 62: 62: [----------] 3 tests from MrcSerializer 62: [ RUN ] MrcSerializer.DefaultHeaderValuesAreSet 62: [ OK ] MrcSerializer.DefaultHeaderValuesAreSet (0 ms) 62: [ RUN ] MrcSerializer.DefaultHeaderHasRightSerialSize 62: [ OK ] MrcSerializer.DefaultHeaderHasRightSerialSize (0 ms) 62: [ RUN ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip 62: [ OK ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip (0 ms) 62: [----------] 3 tests from MrcSerializer (0 ms total) 62: 62: [----------] 4 tests from MrcDensityMap 62: [ RUN ] MrcDensityMap.RoundTripIsIdempotent 62: [ OK ] MrcDensityMap.RoundTripIsIdempotent (0 ms) 62: [ RUN ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent 62: [ OK ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent (0 ms) 62: [ RUN ] MrcDensityMap.ReadsCoordinateTransformationFromFile 62: [ OK ] MrcDensityMap.ReadsCoordinateTransformationFromFile (0 ms) 62: [ RUN ] MrcDensityMap.ReadsDensityDataFromFile 62: [ OK ] MrcDensityMap.ReadsDensityDataFromFile (1 ms) 62: [----------] 4 tests from MrcDensityMap (1 ms total) 62: 62: [----------] 8 tests from MrcDensityMapHeaderTest 62: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader 62: [ OK ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader (0 ms) 62: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsCorrect 62: [ OK ] MrcDensityMapHeaderTest.DataSizeIsCorrect (0 ms) 62: [ RUN ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid 62: [ OK ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid (0 ms) 62: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven 62: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven (0 ms) 62: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined 62: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined (0 ms) 62: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues 62: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues (0 ms) 62: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectExtents 62: [ OK ] MrcDensityMapHeaderTest.GetsCorrectExtents (0 ms) 62: [ RUN ] MrcDensityMapHeaderTest.IsSane 62: [ OK ] MrcDensityMapHeaderTest.IsSane (0 ms) 62: [----------] 8 tests from MrcDensityMapHeaderTest (0 ms total) 62: 62: [----------] 10 tests from ReadTest 62: [ RUN ] ReadTest.get_eint_ReadsInteger 62: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms) 62: [ RUN ] ReadTest.get_eint_WarnsAboutFloat 62: 62: ERROR 1 [file unknown]: 62: Right hand side '0.8' for parameter 'test' in parameter file is not an 62: integer value 62: 62: 62: [ OK ] ReadTest.get_eint_WarnsAboutFloat (0 ms) 62: [ RUN ] ReadTest.get_eint_WarnsAboutString 62: 62: ERROR 1 [file unknown]: 62: Right hand side 'hello' for parameter 'test' in parameter file is not an 62: integer value 62: 62: 62: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms) 62: [ RUN ] ReadTest.get_eint64_ReadsInteger 62: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms) 62: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat 62: 62: ERROR 1 [file unknown]: 62: Right hand side '0.8' for parameter 'test' in parameter file is not an 62: integer value 62: 62: 62: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (0 ms) 62: [ RUN ] ReadTest.get_eint64_WarnsAboutString 62: 62: ERROR 1 [file unknown]: 62: Right hand side 'hello' for parameter 'test' in parameter file is not an 62: integer value 62: 62: 62: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms) 62: [ RUN ] ReadTest.get_ereal_ReadsInteger 62: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms) 62: [ RUN ] ReadTest.get_ereal_ReadsFloat 62: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms) 62: [ RUN ] ReadTest.get_ereal_WarnsAboutString 62: 62: ERROR 1 [file unknown]: 62: Right hand side 'hello' for parameter 'test' in parameter file is not a 62: real value 62: 62: 62: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms) 62: [ RUN ] ReadTest.setStringEntry_ReturnsCorrectString 62: [ OK ] ReadTest.setStringEntry_ReturnsCorrectString (0 ms) 62: [----------] 10 tests from ReadTest (0 ms total) 62: 62: [----------] 3 tests from TimeControlTest 62: [ RUN ] TimeControlTest.UnSetHasNoValue 62: [ OK ] TimeControlTest.UnSetHasNoValue (0 ms) 62: [ RUN ] TimeControlTest.CanSetValue 62: [ OK ] TimeControlTest.CanSetValue (0 ms) 62: [ RUN ] TimeControlTest.CanUnsetValueAgain 62: [ OK ] TimeControlTest.CanUnsetValueAgain (0 ms) 62: [----------] 3 tests from TimeControlTest (0 ms total) 62: 62: [----------] 1 test from FileIOXdrSerializerTest 62: [ RUN ] FileIOXdrSerializerTest.SizeIsCorrect 62: [ OK ] FileIOXdrSerializerTest.SizeIsCorrect (1 ms) 62: [----------] 1 test from FileIOXdrSerializerTest (1 ms total) 62: 62: [----------] 1 test from TngTest 62: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal 62: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms) 62: [----------] 1 test from TngTest (0 ms total) 62: 62: [----------] 4 tests from XvgioTest 62: [ RUN ] XvgioTest.readXvgIntWorks 62: [ OK ] XvgioTest.readXvgIntWorks (0 ms) 62: [ RUN ] XvgioTest.readXvgRealWorks 62: [ OK ] XvgioTest.readXvgRealWorks (0 ms) 62: [ RUN ] XvgioTest.readXvgIgnoreCommentLineWorks 62: [ OK ] XvgioTest.readXvgIgnoreCommentLineWorks (0 ms) 62: [ RUN ] XvgioTest.readXvgDeprecatedWorks 62: [ OK ] XvgioTest.readXvgDeprecatedWorks (0 ms) 62: [----------] 4 tests from XvgioTest (0 ms total) 62: 62: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest 62: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 62: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (0 ms) 62: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 62: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (3 ms) 62: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 62: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (0 ms) 62: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 62: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (0 ms) 62: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (5 ms total) 62: 62: [----------] 360 tests from FileTypeMatch/FileTypeTest 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/0 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/0 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/1 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/1 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/2 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/2 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/3 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/3 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/4 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/4 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/5 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/5 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/6 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/6 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/7 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/7 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/8 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/8 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/9 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/9 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/10 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/10 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/11 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/11 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/12 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/12 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/13 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/13 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/14 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/14 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/15 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/15 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/16 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/16 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/17 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/17 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/18 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/18 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/19 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/19 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/20 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/20 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/21 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/21 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/22 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/22 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/23 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/23 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/24 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/24 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/25 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/25 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/26 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/26 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/27 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/27 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/28 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/28 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/29 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/29 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/30 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/30 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/31 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/31 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/32 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/32 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/33 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/33 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/34 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/34 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/35 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/35 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/36 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/36 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/37 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/37 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/38 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/38 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/39 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/39 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/40 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/40 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/41 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/41 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/42 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/42 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/43 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/43 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/44 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/44 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/45 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/45 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/46 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/46 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/47 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/47 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/48 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/48 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/49 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/49 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/50 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/50 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/51 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/51 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/52 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/52 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/53 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/53 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/54 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/54 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/55 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/55 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/56 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/56 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/57 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/57 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/58 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/58 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/59 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/59 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/60 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/60 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/61 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/61 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/62 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/62 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/63 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/63 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/64 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/64 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/65 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/65 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/66 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/66 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/67 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/67 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/68 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/68 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/69 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/69 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/70 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/70 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/71 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/71 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/72 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/72 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/73 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/73 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/74 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/74 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/75 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/75 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/76 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/76 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/77 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/77 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/78 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/78 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/79 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/79 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/80 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/80 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/81 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/81 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/82 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/82 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/83 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/83 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/84 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/84 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/85 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/85 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/86 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/86 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/87 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/87 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/88 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/88 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/89 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/89 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/90 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/90 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/91 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/91 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/92 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/92 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/93 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/93 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/94 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/94 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/95 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/95 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/96 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/96 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/97 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/97 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/98 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/98 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/99 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/99 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/100 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/100 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/101 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/101 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/102 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/102 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/103 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/103 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/104 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/104 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/105 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/105 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/106 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/106 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/107 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/107 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/108 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/108 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/109 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/109 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/110 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/110 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/111 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/111 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/112 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/112 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/113 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/113 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/114 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/114 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/115 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/115 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/116 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/116 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/117 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/117 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/118 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/118 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/119 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/119 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/120 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/120 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/121 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/121 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/122 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/122 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/123 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/123 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/124 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/124 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/125 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/125 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/126 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/126 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/127 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/127 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/128 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/128 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/129 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/129 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/130 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/130 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/131 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/131 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/132 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/132 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/133 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/133 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/134 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/134 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/135 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/135 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/136 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/136 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/137 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/137 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/138 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/138 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/139 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/139 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/140 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/140 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/141 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/141 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/142 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/142 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/143 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/143 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/144 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/144 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/145 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/145 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/146 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/146 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/147 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/147 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/148 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/148 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/149 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/149 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/150 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/150 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/151 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/151 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/152 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/152 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/153 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/153 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/154 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/154 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/155 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/155 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/156 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/156 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/157 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/157 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/158 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/158 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/159 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/159 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/160 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/160 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/161 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/161 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/162 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/162 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/163 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/163 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/164 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/164 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/165 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/165 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/166 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/166 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/167 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/167 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/168 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/168 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/169 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/169 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/170 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/170 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/171 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/171 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/172 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/172 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/173 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/173 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/174 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/174 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/175 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/175 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/176 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/176 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/177 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/177 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/178 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/178 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/179 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/179 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/0 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/0 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/1 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/1 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/2 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/2 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/3 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/3 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/4 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/4 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/5 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/5 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/6 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/6 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/7 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/7 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/8 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/8 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/9 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/9 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/10 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/10 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/11 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/11 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/12 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/12 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/13 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/13 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/14 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/14 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/15 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/15 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/16 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/16 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/17 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/17 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/18 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/18 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/19 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/19 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/20 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/20 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/21 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/21 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/22 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/22 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/23 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/23 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/24 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/24 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/25 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/25 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/26 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/26 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/27 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/27 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/28 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/28 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/29 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/29 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/30 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/30 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/31 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/31 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/32 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/32 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/33 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/33 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/34 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/34 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/35 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/35 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/36 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/36 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/37 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/37 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/38 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/38 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/39 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/39 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/40 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/40 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/41 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/41 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/42 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/42 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/43 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/43 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/44 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/44 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/45 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/45 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/46 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/46 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/47 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/47 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/48 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/48 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/49 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/49 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/50 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/50 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/51 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/51 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/52 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/52 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/53 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/53 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/54 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/54 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/55 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/55 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/56 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/56 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/57 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/57 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/58 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/58 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/59 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/59 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/60 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/60 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/61 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/61 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/62 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/62 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/63 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/63 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/64 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/64 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/65 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/65 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/66 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/66 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/67 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/67 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/68 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/68 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/69 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/69 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/70 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/70 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/71 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/71 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/72 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/72 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/73 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/73 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/74 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/74 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/75 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/75 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/76 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/76 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/77 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/77 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/78 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/78 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/79 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/79 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/80 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/80 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/81 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/81 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/82 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/82 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/83 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/83 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/84 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/84 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/85 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/85 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/86 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/86 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/87 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/87 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/88 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/88 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/89 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/89 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/90 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/90 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/91 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/91 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/92 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/92 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/93 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/93 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/94 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/94 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/95 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/95 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/96 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/96 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/97 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/97 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/98 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/98 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/99 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/99 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/100 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/100 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/101 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/101 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/102 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/102 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/103 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/103 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/104 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/104 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/105 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/105 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/106 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/106 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/107 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/107 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/108 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/108 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/109 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/109 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/110 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/110 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/111 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/111 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/112 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/112 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/113 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/113 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/114 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/114 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/115 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/115 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/116 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/116 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/117 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/117 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/118 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/118 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/119 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/119 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/120 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/120 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/121 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/121 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/122 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/122 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/123 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/123 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/124 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/124 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/125 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/125 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/126 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/126 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/127 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/127 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/128 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/128 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/129 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/129 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/130 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/130 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/131 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/131 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/132 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/132 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/133 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/133 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/134 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/134 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/135 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/135 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/136 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/136 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/137 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/137 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/138 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/138 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/139 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/139 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/140 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/140 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/141 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/141 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/142 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/142 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/143 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/143 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/144 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/144 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/145 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/145 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/146 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/146 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/147 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/147 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/148 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/148 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/149 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/149 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/150 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/150 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/151 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/151 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/152 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/152 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/153 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/153 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/154 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/154 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/155 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/155 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/156 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/156 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/157 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/157 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/158 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/158 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/159 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/159 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/160 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/160 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/161 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/161 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/162 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/162 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/163 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/163 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/164 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/164 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/165 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/165 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/166 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/166 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/167 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/167 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/168 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/168 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/169 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/169 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/170 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/170 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/171 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/171 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/172 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/172 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/173 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/173 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/174 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/174 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/175 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/175 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/176 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/176 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/177 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/177 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/178 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/178 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/179 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/179 (0 ms) 62: [----------] 360 tests from FileTypeMatch/FileTypeTest (2 ms total) 62: 62: [----------] 4 tests from XvgReadTimeSeries/XvgioTest 62: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/0 62: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/0 (1 ms) 62: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/1 62: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/1 (0 ms) 62: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/2 62: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/2 (0 ms) 62: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/3 62: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/3 (0 ms) 62: [----------] 4 tests from XvgReadTimeSeries/XvgioTest (2 ms total) 62: 62: [----------] Global test environment tear-down 62: [==========] 421 tests from 17 test suites ran. (23 ms total) 62: [ PASSED ] 421 tests. 62/90 Test #62: FileIOTests ............................... Passed 0.06 sec test 63 Start 63: SelectionUnitTests 63: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/selection-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/SelectionUnitTests.xml" 63: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/selection/tests 63: Test timeout computed to be: 30 63: [==========] Running 201 tests from 11 test suites. 63: [----------] Global test environment set-up. 63: [----------] 1 test from IndexGroupTest 63: [ RUN ] IndexGroupTest.RemovesDuplicates 63: [ OK ] IndexGroupTest.RemovesDuplicates (0 ms) 63: [----------] 1 test from IndexGroupTest (0 ms total) 63: 63: [----------] 15 tests from IndexBlockTest 63: [ RUN ] IndexBlockTest.CreatesUnknownBlock 63: [ OK ] IndexBlockTest.CreatesUnknownBlock (0 ms) 63: [ RUN ] IndexBlockTest.CreatesAtomBlock 63: [ OK ] IndexBlockTest.CreatesAtomBlock (0 ms) 63: [ RUN ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology 63: [ OK ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology (0 ms) 63: [ RUN ] IndexBlockTest.CreatesResidueBlocksForComplexTopology 63: [ OK ] IndexBlockTest.CreatesResidueBlocksForComplexTopology (1 ms) 63: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology 63: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology (0 ms) 63: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology 63: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology (0 ms) 63: [ RUN ] IndexBlockTest.CreatesSingleBlock 63: [ OK ] IndexBlockTest.CreatesSingleBlock (0 ms) 63: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksPositive 63: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksPositive (0 ms) 63: [ RUN ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive 63: [ OK ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive (0 ms) 63: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksNegative 63: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksNegative (0 ms) 63: [ RUN ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial 63: [ OK ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial (0 ms) 63: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive 63: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive (0 ms) 63: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative 63: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative (0 ms) 63: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive 63: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive (0 ms) 63: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative 63: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative (0 ms) 63: [----------] 15 tests from IndexBlockTest (3 ms total) 63: 63: [----------] 11 tests from IndexMapTest 63: [ RUN ] IndexMapTest.InitializesAtomBlock 63: [ OK ] IndexMapTest.InitializesAtomBlock (1 ms) 63: [ RUN ] IndexMapTest.InitializesOrgIdGroupAtom 63: [ OK ] IndexMapTest.InitializesOrgIdGroupAtom (0 ms) 63: [ RUN ] IndexMapTest.InitializesOrgIdGroupSingle 63: [ OK ] IndexMapTest.InitializesOrgIdGroupSingle (0 ms) 63: [ RUN ] IndexMapTest.InitializesOrgIdGroupResidue 63: [ OK ] IndexMapTest.InitializesOrgIdGroupResidue (0 ms) 63: [ RUN ] IndexMapTest.InitializesOrgIdGroupMolecule 63: [ OK ] IndexMapTest.InitializesOrgIdGroupMolecule (0 ms) 63: [ RUN ] IndexMapTest.InitializesOrgIdGroupAll 63: [ OK ] IndexMapTest.InitializesOrgIdGroupAll (0 ms) 63: [ RUN ] IndexMapTest.InitializesMoleculeBlock 63: [ OK ] IndexMapTest.InitializesMoleculeBlock (0 ms) 63: [ RUN ] IndexMapTest.MapsSingleBlock 63: [ OK ] IndexMapTest.MapsSingleBlock (0 ms) 63: [ RUN ] IndexMapTest.MapsResidueBlocks 63: [ OK ] IndexMapTest.MapsResidueBlocks (1 ms) 63: [ RUN ] IndexMapTest.MapsResidueBlocksWithMask 63: [ OK ] IndexMapTest.MapsResidueBlocksWithMask (0 ms) 63: [ RUN ] IndexMapTest.HandlesMultipleRequests 63: [ OK ] IndexMapTest.HandlesMultipleRequests (0 ms) 63: [----------] 11 tests from IndexMapTest (4 ms total) 63: 63: [----------] 3 tests from IndexGroupsAndNamesTest 63: [ RUN ] IndexGroupsAndNamesTest.containsNames 63: [ OK ] IndexGroupsAndNamesTest.containsNames (0 ms) 63: [ RUN ] IndexGroupsAndNamesTest.throwsWhenNameMissing 63: [ OK ] IndexGroupsAndNamesTest.throwsWhenNameMissing (0 ms) 63: [ RUN ] IndexGroupsAndNamesTest.groupIndicesCorrect 63: [ OK ] IndexGroupsAndNamesTest.groupIndicesCorrect (0 ms) 63: [----------] 3 tests from IndexGroupsAndNamesTest (0 ms total) 63: 63: [----------] 15 tests from NeighborhoodSearchTest 63: [ RUN ] NeighborhoodSearchTest.SimpleSearch 63: [ OK ] NeighborhoodSearchTest.SimpleSearch (17 ms) 63: [ RUN ] NeighborhoodSearchTest.SimpleSearchXY 63: [ OK ] NeighborhoodSearchTest.SimpleSearchXY (17 ms) 63: [ RUN ] NeighborhoodSearchTest.GridSearchBox 63: [ OK ] NeighborhoodSearchTest.GridSearchBox (2 ms) 63: [ RUN ] NeighborhoodSearchTest.GridSearchTriclinic 63: [ OK ] NeighborhoodSearchTest.GridSearchTriclinic (9 ms) 63: [ RUN ] NeighborhoodSearchTest.GridSearch2DPBC 63: [ OK ] NeighborhoodSearchTest.GridSearch2DPBC (4 ms) 63: [ RUN ] NeighborhoodSearchTest.GridSearchNoPBC 63: [ OK ] NeighborhoodSearchTest.GridSearchNoPBC (1 ms) 63: [ RUN ] NeighborhoodSearchTest.GridSearchXYBox 63: [ OK ] NeighborhoodSearchTest.GridSearchXYBox (2 ms) 63: [ RUN ] NeighborhoodSearchTest.SimpleSelfPairsSearch 63: [ OK ] NeighborhoodSearchTest.SimpleSelfPairsSearch (0 ms) 63: [ RUN ] NeighborhoodSearchTest.GridSelfPairsSearch 63: [ OK ] NeighborhoodSearchTest.GridSelfPairsSearch (48 ms) 63: [ RUN ] NeighborhoodSearchTest.HandlesConcurrentSearches 63: [ OK ] NeighborhoodSearchTest.HandlesConcurrentSearches (0 ms) 63: [ RUN ] NeighborhoodSearchTest.HandlesNoPBC 63: [ OK ] NeighborhoodSearchTest.HandlesNoPBC (0 ms) 63: [ RUN ] NeighborhoodSearchTest.HandlesNullPBC 63: [ OK ] NeighborhoodSearchTest.HandlesNullPBC (0 ms) 63: [ RUN ] NeighborhoodSearchTest.HandlesSkippingPairs 63: [ OK ] NeighborhoodSearchTest.HandlesSkippingPairs (0 ms) 63: [ RUN ] NeighborhoodSearchTest.SimpleSearchExclusions 63: [ OK ] NeighborhoodSearchTest.SimpleSearchExclusions (3 ms) 63: [ RUN ] NeighborhoodSearchTest.GridSearchExclusions 63: [ OK ] NeighborhoodSearchTest.GridSearchExclusions (0 ms) 63: [----------] 15 tests from NeighborhoodSearchTest (109 ms total) 63: 63: [----------] 13 tests from PositionCalculationTest 63: [ RUN ] PositionCalculationTest.ComputesAtomPositions 63: [ OK ] PositionCalculationTest.ComputesAtomPositions (0 ms) 63: [ RUN ] PositionCalculationTest.ComputesAtomPositionsWithRepeatedIndex 63: [ OK ] PositionCalculationTest.ComputesAtomPositionsWithRepeatedIndex (0 ms) 63: [ RUN ] PositionCalculationTest.ComputesResidueCOGPositions 63: [ OK ] PositionCalculationTest.ComputesResidueCOGPositions (0 ms) 63: [ RUN ] PositionCalculationTest.ComputesResidueCOMPositions 63: [ OK ] PositionCalculationTest.ComputesResidueCOMPositions (0 ms) 63: [ RUN ] PositionCalculationTest.ComputesGroupCOGPositions 63: [ OK ] PositionCalculationTest.ComputesGroupCOGPositions (0 ms) 63: [ RUN ] PositionCalculationTest.ComputesGroupCOMPositions 63: [ OK ] PositionCalculationTest.ComputesGroupCOMPositions (0 ms) 63: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteWhole 63: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteWhole (0 ms) 63: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteMax 63: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteMax (0 ms) 63: [ RUN ] PositionCalculationTest.ComputesPositionMask 63: [ OK ] PositionCalculationTest.ComputesPositionMask (0 ms) 63: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms 63: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms (0 ms) 63: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms2 63: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms2 (0 ms) 63: [ RUN ] PositionCalculationTest.HandlesIdenticalStaticCalculations 63: [ OK ] PositionCalculationTest.HandlesIdenticalStaticCalculations (0 ms) 63: [ RUN ] PositionCalculationTest.HandlesOverlappingStaticCalculations 63: [ OK ] PositionCalculationTest.HandlesOverlappingStaticCalculations (1 ms) 63: [----------] 13 tests from PositionCalculationTest (4 ms total) 63: 63: [----------] 33 tests from SelectionCollectionTest 63: [ RUN ] SelectionCollectionTest.HandlesNoSelections 63: [ OK ] SelectionCollectionTest.HandlesNoSelections (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType 63: [ OK ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesVelocityAndForceRequests 63: [ OK ] SelectionCollectionTest.HandlesVelocityAndForceRequests (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry 63: [ OK ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry (0 ms) 63: [ RUN ] SelectionCollectionTest.ParsesSelectionsFromFile 63: [ OK ] SelectionCollectionTest.ParsesSelectionsFromFile (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesAtypicalWhitespace 63: [ OK ] SelectionCollectionTest.HandlesAtypicalWhitespace (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesInvalidRegularExpressions 63: [ OK ] SelectionCollectionTest.HandlesInvalidRegularExpressions (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue 63: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue2 63: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue2 (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue3 63: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue3 (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 63: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 63: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 63: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 63: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReference 63: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReference (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed 63: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup 63: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed 63: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 63: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 (0 ms) 63: [ RUN ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo 63: [ OK ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo (0 ms) 63: [ RUN ] SelectionCollectionTest.RecoversFromMissingAtomTypes 63: [ OK ] SelectionCollectionTest.RecoversFromMissingAtomTypes (0 ms) 63: [ RUN ] SelectionCollectionTest.RecoversFromMissingPDBInfo 63: [ OK ] SelectionCollectionTest.RecoversFromMissingPDBInfo (0 ms) 63: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation 63: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation (0 ms) 63: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation2 63: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation2 (0 ms) 63: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation3 63: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation3 (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets 63: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 63: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 63: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 63: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 (0 ms) 63: [ RUN ] SelectionCollectionTest.RetrieveValidSelection 63: [ OK ] SelectionCollectionTest.RetrieveValidSelection (0 ms) 63: [ RUN ] SelectionCollectionTest.RetrieveInvalidSelection 63: [ OK ] SelectionCollectionTest.RetrieveInvalidSelection (0 ms) 63: [ RUN ] SelectionCollectionTest.CanCopyEmptyCollection 63: [ OK ] SelectionCollectionTest.CanCopyEmptyCollection (0 ms) 63: [ RUN ] SelectionCollectionTest.CopiedSelectionListsAreHandledSeparately 63: [ OK ] SelectionCollectionTest.CopiedSelectionListsAreHandledSeparately (0 ms) 63: [----------] 33 tests from SelectionCollectionTest (10 ms total) 63: 63: [----------] 14 tests from SelectionCollectionInteractiveTest 63: [ RUN ] SelectionCollectionInteractiveTest.HandlesBasicInput 63: [ OK ] SelectionCollectionInteractiveTest.HandlesBasicInput (0 ms) 63: [ RUN ] SelectionCollectionInteractiveTest.HandlesContinuation 63: [ OK ] SelectionCollectionInteractiveTest.HandlesContinuation (0 ms) 63: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput 63: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput (0 ms) 63: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput 63: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput (0 ms) 63: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups 63: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups (0 ms) 63: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections 63: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections (0 ms) 63: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus 63: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus (0 ms) 63: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus 63: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus (0 ms) 63: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus 63: [ OK ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus (1 ms) 63: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline 63: [ OK ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline (0 ms) 63: [ RUN ] SelectionCollectionInteractiveTest.HandlesEmptySelections 63: [ OK ] SelectionCollectionInteractiveTest.HandlesEmptySelections (0 ms) 63: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine 63: [ OK ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine (0 ms) 63: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput 63: [ OK ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput (0 ms) 63: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively 63: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively (0 ms) 63: [----------] 14 tests from SelectionCollectionInteractiveTest (5 ms total) 63: 63: [----------] 70 tests from SelectionCollectionDataTest 63: [ RUN ] SelectionCollectionDataTest.HandlesAllNone 63: [ OK ] SelectionCollectionDataTest.HandlesAllNone (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesAtomnr 63: [ OK ] SelectionCollectionDataTest.HandlesAtomnr (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesResnr 63: [ OK ] SelectionCollectionDataTest.HandlesResnr (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesResIndex 63: [ OK ] SelectionCollectionDataTest.HandlesResIndex (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesMolIndex 63: [ OK ] SelectionCollectionDataTest.HandlesMolIndex (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesAtomname 63: [ OK ] SelectionCollectionDataTest.HandlesAtomname (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesPdbAtomname 63: [ OK ] SelectionCollectionDataTest.HandlesPdbAtomname (2 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesAtomtype 63: [ OK ] SelectionCollectionDataTest.HandlesAtomtype (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesChain 63: [ OK ] SelectionCollectionDataTest.HandlesChain (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesMass 63: [ OK ] SelectionCollectionDataTest.HandlesMass (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesCharge 63: [ OK ] SelectionCollectionDataTest.HandlesCharge (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesAltLoc 63: [ OK ] SelectionCollectionDataTest.HandlesAltLoc (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesInsertCode 63: [ OK ] SelectionCollectionDataTest.HandlesInsertCode (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesOccupancy 63: [ OK ] SelectionCollectionDataTest.HandlesOccupancy (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesBeta 63: [ OK ] SelectionCollectionDataTest.HandlesBeta (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesResname 63: [ OK ] SelectionCollectionDataTest.HandlesResname (1 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesCoordinateKeywords 63: [ OK ] SelectionCollectionDataTest.HandlesCoordinateKeywords (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesSameResidue 63: [ OK ] SelectionCollectionDataTest.HandlesSameResidue (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesSameResidueName 63: [ OK ] SelectionCollectionDataTest.HandlesSameResidueName (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesPositionKeywords 63: [ OK ] SelectionCollectionDataTest.HandlesPositionKeywords (1 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesDistanceKeyword 63: [ OK ] SelectionCollectionDataTest.HandlesDistanceKeyword (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesMinDistanceKeyword 63: [ OK ] SelectionCollectionDataTest.HandlesMinDistanceKeyword (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesWithinKeyword 63: [ OK ] SelectionCollectionDataTest.HandlesWithinKeyword (2 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword 63: [ OK ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword (2 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesPermuteModifier 63: [ OK ] SelectionCollectionDataTest.HandlesPermuteModifier (1 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesPlusModifier 63: [ OK ] SelectionCollectionDataTest.HandlesPlusModifier (1 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesMergeModifier 63: [ OK ] SelectionCollectionDataTest.HandlesMergeModifier (1 ms) 63: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndCharges 63: [ OK ] SelectionCollectionDataTest.ComputesMassesAndCharges (1 ms) 63: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology 63: [ OK ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets 63: [ OK ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesSelectionNames 63: [ OK ] SelectionCollectionDataTest.HandlesSelectionNames (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections 63: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed 63: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed (1 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections 63: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections (1 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed 63: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositions 63: [ OK ] SelectionCollectionDataTest.HandlesConstantPositions (1 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers 63: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesWithinConstantPositions 63: [ OK ] SelectionCollectionDataTest.HandlesWithinConstantPositions (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges 63: [ OK ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingRealRanges 63: [ OK ] SelectionCollectionDataTest.HandlesOverlappingRealRanges (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode 63: [ OK ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesWildcardMatching 63: [ OK ] SelectionCollectionDataTest.HandlesWildcardMatching (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesRegexMatching 63: [ OK ] SelectionCollectionDataTest.HandlesRegexMatching (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesBasicBoolean 63: [ OK ] SelectionCollectionDataTest.HandlesBasicBoolean (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters 63: [ OK ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions 63: [ OK ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame 63: [ OK ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords 63: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods 63: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositions 63: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositions (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic 63: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesNumericComparisons 63: [ OK ] SelectionCollectionDataTest.HandlesNumericComparisons (1 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesArithmeticExpressions 63: [ OK ] SelectionCollectionDataTest.HandlesArithmeticExpressions (1 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesNumericVariables 63: [ OK ] SelectionCollectionDataTest.HandlesNumericVariables (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesComplexNumericVariables 63: [ OK ] SelectionCollectionDataTest.HandlesComplexNumericVariables (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariables 63: [ OK ] SelectionCollectionDataTest.HandlesPositionVariables (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariableInModifier 63: [ OK ] SelectionCollectionDataTest.HandlesPositionVariableInModifier (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionInVariable 63: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionInVariable (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables 63: [ OK ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables (2 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis 63: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables 63: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables 63: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesUnusedVariables 63: [ OK ] SelectionCollectionDataTest.HandlesUnusedVariables (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups 63: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups 63: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 63: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 (0 ms) 63: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWorksPreCompilation 63: [ OK ] SelectionCollectionDataTest.CopiedSelectionWorksPreCompilation (1 ms) 63: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation 63: [ OK ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation (1 ms) 63: [ RUN ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent 63: [ OK ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent (2 ms) 63: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation 63: [ OK ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation (1 ms) 63: [----------] 70 tests from SelectionCollectionDataTest (62 ms total) 63: 63: [----------] 17 tests from SelectionOptionTest 63: [ RUN ] SelectionOptionTest.ParsesSimpleSelection 63: [ OK ] SelectionOptionTest.ParsesSimpleSelection (0 ms) 63: [ RUN ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired 63: [ OK ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired (0 ms) 63: [ RUN ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired 63: [ OK ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired (0 ms) 63: [ RUN ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired 63: [ OK ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired (0 ms) 63: [ RUN ] SelectionOptionTest.ChecksEmptySelections 63: [ OK ] SelectionOptionTest.ChecksEmptySelections (0 ms) 63: [ RUN ] SelectionOptionTest.ChecksEmptyDelayedSelections 63: [ OK ] SelectionOptionTest.ChecksEmptyDelayedSelections (0 ms) 63: [ RUN ] SelectionOptionTest.HandlesTooManySelections 63: [ OK ] SelectionOptionTest.HandlesTooManySelections (0 ms) 63: [ RUN ] SelectionOptionTest.HandlesTooFewSelections 63: [ OK ] SelectionOptionTest.HandlesTooFewSelections (0 ms) 63: [ RUN ] SelectionOptionTest.HandlesDefaultSelectionText 63: [ OK ] SelectionOptionTest.HandlesDefaultSelectionText (0 ms) 63: [ RUN ] SelectionOptionTest.HandlesAdjuster 63: [ OK ] SelectionOptionTest.HandlesAdjuster (0 ms) 63: [ RUN ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster 63: [ OK ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster (0 ms) 63: [ RUN ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster 63: [ OK ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster (0 ms) 63: [ RUN ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster 63: [ OK ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster (0 ms) 63: [ RUN ] SelectionOptionTest.HandlesDelayedRequiredSelection 63: [ OK ] SelectionOptionTest.HandlesDelayedRequiredSelection (0 ms) 63: [ RUN ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections 63: [ OK ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections (0 ms) 63: [ RUN ] SelectionOptionTest.HandlesDelayedOptionalSelection 63: [ OK ] SelectionOptionTest.HandlesDelayedOptionalSelection (0 ms) 63: [ RUN ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster 63: [ OK ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster (0 ms) 63: [----------] 17 tests from SelectionOptionTest (4 ms total) 63: 63: [----------] 9 tests from SelectionFileOptionTest 63: [ RUN ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile 63: [ OK ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile (0 ms) 63: [ RUN ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions 63: [ OK ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions (0 ms) 63: [ RUN ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile 63: [ OK ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile (0 ms) 63: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFile 63: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFile (0 ms) 63: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet 63: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet (0 ms) 63: [ RUN ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile 63: [ OK ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile (0 ms) 63: [ RUN ] SelectionFileOptionTest.GivesErrorWithNoFile 63: [ OK ] SelectionFileOptionTest.GivesErrorWithNoFile (0 ms) 63: [ RUN ] SelectionFileOptionTest.GivesErrorWithNonExistentFile 63: [ OK ] SelectionFileOptionTest.GivesErrorWithNonExistentFile (0 ms) 63: [ RUN ] SelectionFileOptionTest.GivesErrorWithMultipleFiles 63: [ OK ] SelectionFileOptionTest.GivesErrorWithMultipleFiles (0 ms) 63: [----------] 9 tests from SelectionFileOptionTest (2 ms total) 63: 63: [----------] Global test environment tear-down 63: [==========] 201 tests from 11 test suites ran. (209 ms total) 63: [ PASSED ] 201 tests. 63/90 Test #63: SelectionUnitTests ........................ Passed 0.24 sec test 64 Start 64: MdrunOutputTests 64: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/mdrun-output-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/MdrunOutputTests.xml" 64: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests 64: Test timeout computed to be: 600 64: [==========] Running 12 tests from 5 test suites. 64: [----------] Global test environment set-up. 64: [----------] 1 test from MdrunTest 64: [ RUN ] MdrunTest.WritesHelp 64: [ OK ] MdrunTest.WritesHelp (123 ms) 64: [----------] 1 test from MdrunTest (123 ms total) 64: 64: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput 64: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group rest is 9.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 64: NVE simulation: will use the initial temperature of 2573.591 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 2 NOTEs 64: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc2' 64: 1 steps, 0.0 ps. 64: Setting the LD random seed to -139080225 64: 64: Generated 3 of the 3 non-bonded parameter combinations 64: 64: Generated 3 of the 3 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 64: 64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 64: 64: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.044 0.022 199.1 64: (ns/day) (hour/ns) 64: Performance: 7.874 3.048 64: Reading frame 0 time 0.000 64: # Atoms 6 64: Reading frame 1 time 0.001 Last frame 1 time 0.001 64: 64: 64: Item #frames Timestep (ps) 64: Step 2 0.001 64: Time 2 0.001 64: Lambda 0 64: Coords 2 0.001 64: Velocities 0 64: Forces 0 64: Box 2 0.001 64: Checking file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.xtc 64: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 (41 ms) 64: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group rest is 9.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 64: NVE simulation: will use the initial temperature of 2573.591 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 2 NOTEs 64: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc2' 64: 1 steps, 0.0 ps. 64: Setting the LD random seed to -374343691 64: 64: Generated 3 of the 3 non-bonded parameter combinations 64: 64: Generated 3 of the 3 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 64: 64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 64: 64: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.029 0.014 198.8 64: (ns/day) (hour/ns) 64: Performance: 12.021 1.996 64: Reading frame 0 time 0.000 64: # Atoms 6 64: Reading frame 1 time 0.001 Last frame 1 time 0.001 64: 64: 64: Item #frames Timestep (ps) 64: Step 2 0.001 64: Time 2 0.001 64: Lambda 0 64: Coords 2 0.001 64: Velocities 0 64: Forces 0 64: Box 2 0.001 64: Checking file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.xtc 64: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 (30 ms) 64: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group rest is 9.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 64: NVE simulation: will use the initial temperature of 2573.591 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 2 NOTEs 64: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc2' 64: 1 steps, 0.0 ps. 64: Setting the LD random seed to -69109779 64: 64: Generated 3 of the 3 non-bonded parameter combinations 64: 64: Generated 3 of the 3 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 64: 64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 64: 64: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.038 0.019 199.0 64: (ns/day) (hour/ns) 64: Performance: 8.939 2.685 64: Reading frame 0 time 0.000 64: # Atoms 3 64: Reading frame 1 time 0.001 Last frame 1 time 0.001 64: 64: 64: Item #frames Timestep (ps) 64: Step 2 0.001 64: Time 2 0.001 64: Lambda 0 64: Coords 2 0.001 64: Velocities 0 64: Forces 0 64: Box 2 0.001 64: Checking file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.xtc 64: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 (30 ms) 64: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput (103 ms total) 64: 64: [----------] 2 tests from Argon12/OutputFiles 64: [ RUN ] Argon12/OutputFiles.FilesArePresent/0 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Number of degrees of freedom in T-Coupling group System is 33.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 64: NVE simulation: will use the initial temperature of 68.810 K for 64: determining the Verlet buffer size 64: 64: 64: There were 3 NOTEs 64: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Argon' 64: 16 steps, 0.0 ps. 64: Generated 1 of the 1 non-bonded parameter combinations 64: 64: Excluding 1 bonded neighbours molecule type 'Argon' 64: 64: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.055 0.028 199.1 64: (ns/day) (hour/ns) 64: Performance: 52.709 0.455 64: [ OK ] Argon12/OutputFiles.FilesArePresent/0 (38 ms) 64: [ RUN ] Argon12/OutputFiles.FilesArePresent/1 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Number of degrees of freedom in T-Coupling group System is 33.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 64: NVE simulation: will use the initial temperature of 68.810 K for 64: determining the Verlet buffer size 64: 64: 64: There were 3 NOTEs 64: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Argon' 64: 16 steps, 0.0 ps. 64: Generated 1 of the 1 non-bonded parameter combinations 64: 64: Excluding 1 bonded neighbours molecule type 'Argon' 64: 64: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.030 0.015 199.0 64: (ns/day) (hour/ns) 64: Performance: 97.604 0.246 64: [ OK ] Argon12/OutputFiles.FilesArePresent/1 (27 ms) 64: [----------] 2 tests from Argon12/OutputFiles (65 ms total) 64: 64: [----------] 3 tests from MdrunCanWrite/Trajectories 64: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 64: Number of degrees of freedom in T-Coupling group System is 12.00 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There was 1 NOTE 64: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 64: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc-and-methanol' 64: 6 steps, 0.0 ps. 64: Setting the LD random seed to -8454145 64: 64: Generated 8 of the 10 non-bonded parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'Methanol' 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 64: 64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.061 0.031 199.4 64: (ns/day) (hour/ns) 64: Performance: 19.613 1.224 64: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 (49 ms) 64: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 64: Number of degrees of freedom in T-Coupling group System is 12.00 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There was 1 NOTE 64: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 64: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc-and-methanol' 64: 6 steps, 0.0 ps. 64: Setting the LD random seed to -1677852689 64: 64: Generated 8 of the 10 non-bonded parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'Methanol' 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 64: 64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.039 0.020 199.0 64: (ns/day) (hour/ns) 64: Performance: 30.770 0.780 64: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 (35 ms) 64: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 64: Number of degrees of freedom in T-Coupling group System is 12.00 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There was 1 NOTE 64: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 64: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc-and-methanol' 64: 6 steps, 0.0 ps. 64: Setting the LD random seed to -92292104 64: 64: Generated 8 of the 10 non-bonded parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'Methanol' 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 64: 64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.035 0.018 198.8 64: (ns/day) (hour/ns) 64: Performance: 33.978 0.706 64: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 (33 ms) 64: [----------] 3 tests from MdrunCanWrite/Trajectories (118 ms total) 64: 64: [----------] 3 tests from MdrunCanWrite/NptTrajectories 64: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 64: Number of degrees of freedom in T-Coupling group System is 12.00 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There was 1 NOTE 64: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 64: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc-and-methanol' 64: 2 steps, 0.0 ps. 64: Setting the LD random seed to -434110845 64: 64: Generated 8 of the 10 non-bonded parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'Methanol' 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 64: 64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.032 0.016 196.2 64: (ns/day) (hour/ns) 64: Performance: 15.988 1.501 64: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 (29 ms) 64: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 64: 64: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: 64: The Berendsen barostat does not generate any strictly correct ensemble, 64: and should not be used for new production simulations (in our opinion). 64: We recommend using the C-rescale barostat instead. 64: 64: Number of degrees of freedom in T-Coupling group System is 12.00 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There was 1 NOTE 64: 64: There was 1 WARNING 64: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 64: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc-and-methanol' 64: 2 steps, 0.0 ps. 64: Setting the LD random seed to -71443123 64: 64: Generated 8 of the 10 non-bonded parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'Methanol' 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 64: 64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.020 0.010 198.2 64: (ns/day) (hour/ns) 64: Performance: 25.192 0.953 64: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 (27 ms) 64: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 64: Number of degrees of freedom in T-Coupling group System is 12.00 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There was 1 NOTE 64: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 64: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc-and-methanol' 64: 2 steps, 0.0 ps. 64: Setting the LD random seed to -76105481 64: 64: Generated 8 of the 10 non-bonded parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'Methanol' 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 64: 64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.021 0.011 198.3 64: (ns/day) (hour/ns) 64: Performance: 24.635 0.974 64: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 (26 ms) 64: [----------] 3 tests from MdrunCanWrite/NptTrajectories (84 ms total) 64: 64: [----------] Global test environment tear-down 64: [==========] 12 tests from 5 test suites ran. (974 ms total) 64: [ PASSED ] 12 tests. 64/90 Test #64: MdrunOutputTests .......................... Passed 1.00 sec test 65 Start 65: MdrunModulesTests 65: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/mdrun-modules-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/MdrunModulesTests.xml" 65: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests 65: Test timeout computed to be: 600 65: [==========] Running 15 tests from 3 test suites. 65: [----------] Global test environment set-up. 65: [----------] 9 tests from DensityFittingTest 65: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct 65: Number of degrees of freedom in T-Coupling group rest is 33.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 65: Using 1 MPI thread 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: 65: Steepest Descents: 65: Tolerance (Fmax) = 1.00000e+01 65: Number of steps = 2 65: 65: Energy minimization reached the maximum number of steps before the forces 65: reached the requested precision Fmax < 10. 65: 65: writing lowest energy coordinates. 65: 65: Steepest Descents did not converge to Fmax < 10 in 3 steps. 65: Potential Energy = -3.8565254e+03 65: Maximum force = 4.5099883e+03 on atom 3 65: Norm of force = 1.6816849e+03 65: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -35360801 65: 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct (22 ms) 65: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation 65: Number of degrees of freedom in T-Coupling group rest is 33.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 65: Using 1 MPI thread 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: 65: Steepest Descents: 65: Tolerance (Fmax) = 1.00000e+01 65: Number of steps = 2 65: 65: Energy minimization reached the maximum number of steps before the forces 65: reached the requested precision Fmax < 10. 65: 65: writing lowest energy coordinates. 65: 65: Steepest Descents did not converge to Fmax < 10 in 3 steps. 65: Potential Energy = -9.8207725e+03 65: Maximum force = 7.3954834e+03 on atom 2 65: Norm of force = 2.7825089e+03 65: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to 1341125599 65: 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation (9 ms) 65: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff 65: 65: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1108:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/main/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. 65: [ OK ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff (12 ms) 65: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix 65: Number of degrees of freedom in T-Coupling group rest is 33.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 65: Overriding nsteps with value passed on the command line: 4 steps 65: 65: Using 1 MPI thread 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: 65: Steepest Descents: 65: Tolerance (Fmax) = 1.00000e+01 65: Number of steps = 4 65: 65: Energy minimization reached the maximum number of steps before the forces 65: reached the requested precision Fmax < 10. 65: 65: writing lowest energy coordinates. 65: 65: Steepest Descents did not converge to Fmax < 10 in 5 steps. 65: Potential Energy = -1.0954993e+04 65: Maximum force = 7.4724790e+03 on atom 2 65: Norm of force = 2.7758003e+03 65: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Setting the LD random seed to 936836963 65: 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix (8 ms) 65: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff 65: 65: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1108:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/main/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. 65: [ OK ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff (27 ms) 65: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix 65: Number of degrees of freedom in T-Coupling group rest is 33.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 65: Using 1 MPI thread 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: 65: Steepest Descents: 65: Tolerance (Fmax) = 1.00000e+01 65: Number of steps = 2 65: 65: Energy minimization reached the maximum number of steps before the forces 65: reached the requested precision Fmax < 10. 65: 65: writing lowest energy coordinates. 65: 65: Steepest Descents did not converge to Fmax < 10 in 3 steps. 65: Potential Energy = -3.8565254e+03 65: Maximum force = 4.5099883e+03 on atom 3 65: Norm of force = 1.6816849e+03 65: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -8956033 65: 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix (13 ms) 65: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy 65: Number of degrees of freedom in T-Coupling group rest is 33.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 65: Using 1 MPI thread 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: 65: Steepest Descents: 65: Tolerance (Fmax) = 1.00000e+01 65: Number of steps = 2 65: 65: Energy minimization reached the maximum number of steps before the forces 65: reached the requested precision Fmax < 10. 65: 65: writing lowest energy coordinates. 65: 65: Steepest Descents did not converge to Fmax < 10 in 3 steps. 65: Potential Energy = -2.7138664e+04 65: Maximum force = 6.7827656e+03 on atom 2 65: Norm of force = 1.9608866e+03 65: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to 1149093481 65: 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy (8 ms) 65: [ RUN ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch 65: 65: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1108:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/main/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. 65: Setting the LD random seed to -68232211 65: 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 65: [ OK ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch (9 ms) 65: [ RUN ] DensityFittingTest.CheckpointWorks 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (2) 65: 65: Number of degrees of freedom in T-Coupling group rest is 33.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: 65: NVE simulation: will use the initial temperature of 68.810 K for 65: determining the Verlet buffer size 65: 65: 65: There were 2 NOTEs 65: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI thread 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 2 steps, 0.0 ps. 65: Setting the LD random seed to -23612689 65: 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 65: 65: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 68.8096 K 65: 65: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.110 0.055 199.6 65: (ns/day) (hour/ns) 65: Performance: 4.700 5.107 65: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 65: Overriding nsteps with value passed on the command line: 4 steps, 0.004 ps 65: Can not increase nstlist because an NVE ensemble is used 65: 65: Using 1 MPI thread 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 6 steps, 0.0 ps (continuing from step 2, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.025 0.013 198.6 65: (ns/day) (hour/ns) 65: Performance: 34.368 0.698 65: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Last energy frame read 1 time 0.002 [ OK ] DensityFittingTest.CheckpointWorks (81 ms) 65: [----------] 9 tests from DensityFittingTest (192 ms total) 65: 65: [----------] 4 tests from MimicTest 65: [ RUN ] MimicTest.OneQuantumMol 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 65: For a correct single-point energy evaluation with nsteps = 0, use 65: continuation = yes to avoid constraining the input coordinates. 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group rest is 21.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 65: NVE simulation with an initial temperature of zero: will use a Verlet 65: buffer of 10%. Check your energy drift! 65: 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 3 NOTEs 65: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI thread 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro' 65: 65: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 65: Reading frame 0 time 0.000 Last frame 0 time 0.000 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.023 0.011 198.8 65: (ns/day) (hour/ns) 65: Performance: 7.540 3.183 65: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -1140850723 65: 65: Generated 10 of the 10 non-bonded parameter combinations 65: 65: Generated 10 of the 10 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] MimicTest.OneQuantumMol (28 ms) 65: [ RUN ] MimicTest.AllQuantumMol 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 65: For a correct single-point energy evaluation with nsteps = 0, use 65: continuation = yes to avoid constraining the input coordinates. 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group rest is 21.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 65: NVE simulation with an initial temperature of zero: will use a Verlet 65: buffer of 10%. Check your energy drift! 65: 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 3 NOTEs 65: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI thread 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro' 65: 65: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 65: Reading frame 0 time 0.000 Last frame 0 time 0.000 65: 65: NOTE: 34 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.001 0.000 189.3 65: (ns/day) (hour/ns) 65: Performance: 257.378 0.093 65: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -1347571999 65: 65: Generated 10 of the 10 non-bonded parameter combinations 65: 65: Generated 10 of the 10 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] MimicTest.AllQuantumMol (6 ms) 65: [ RUN ] MimicTest.TwoQuantumMol 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 65: For a correct single-point energy evaluation with nsteps = 0, use 65: continuation = yes to avoid constraining the input coordinates. 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group rest is 21.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 65: NVE simulation with an initial temperature of zero: will use a Verlet 65: buffer of 10%. Check your energy drift! 65: 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 3 NOTEs 65: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI thread 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro' 65: 65: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 65: Reading frame 0 time 0.000 Last frame 0 time 0.000 65: 65: NOTE: 25 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.001 0.000 187.0 65: (ns/day) (hour/ns) 65: Performance: 225.086 0.107 65: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 1874852317 65: 65: Generated 10 of the 10 non-bonded parameter combinations 65: 65: Generated 10 of the 10 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] MimicTest.TwoQuantumMol (21 ms) 65: [ RUN ] MimicTest.BondCuts 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 65: For a correct single-point energy evaluation with nsteps = 0, use 65: continuation = yes to avoid constraining the input coordinates. 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group rest is 66.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 65: NVE simulation: will use the initial temperature of 300.368 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 3 NOTEs 65: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI thread 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 65: 65: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 65: Reading frame 0 time 0.000 Last frame 0 time 0.000 65: 65: NOTE: 24 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.001 0.001 188.8 65: (ns/day) (hour/ns) 65: Performance: 136.596 0.176 65: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 1841295327 65: 65: Generated 2211 of the 2211 non-bonded parameter combinations 65: 65: Generated 2211 of the 2211 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 65: 65: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 65: 65: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 65: 65: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] MimicTest.BondCuts (43 ms) 65: [----------] 4 tests from MimicTest (101 ms total) 65: 65: [----------] 2 tests from WithIntegrator/ImdTest 65: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/0 65: Generating 1-4 interactions: fudge = 1 65: 65: NOTE 1 [file glycine_vacuo.top, line 12]: 65: The bond in molecule-type Glycine between atoms 1 N and 2 H1 has an 65: estimated oscillational period of 1.0e-02 ps, which is less than 10 times 65: the time step of 2.0e-03 ps. 65: Maybe you forgot to change the constraints mdp option. 65: 65: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). 65: Number of degrees of freedom in T-Coupling group System is 27.00 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 2 NOTEs 65: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 65: Changing nstlist from 10 to 25, rlist from 1.071 to 1.232 65: 65: Using 1 MPI thread 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: 65: IMD: Enabled. This simulation will accept incoming IMD connections. 65: IMD: Pulling from IMD remote is enabled (-imdpull). 65: IMD: Setting port for connection requests to 0. 65: IMD: Setting up incoming socket. 65: IMD: Listening for IMD connection on port 33805. 65: IMD: -imdwait not set, starting simulation. 65: starting mdrun 'Glycine' 65: 2 steps, 0.0 ps. 65: Setting the LD random seed to 2126169073 65: 65: Generated 20503 of the 20503 non-bonded parameter combinations 65: 65: Generated 17396 of the 20503 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Glycine' 65: 65: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/glycine_vacuo.gro', all velocities are zero 65: 65: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 65: 65: Calculated rlist for 1x1 atom pair-list as 1.093 nm, buffer size 0.093 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 1.071 nm, buffer size 0.071 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.075 0.038 199.3 65: (ns/day) (hour/ns) 65: Performance: 13.717 1.750 65: [ OK ] WithIntegrator/ImdTest.ImdCanRun/0 (216 ms) 65: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/1 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: 65: Setting tcoupl from 'V-rescale' to 'no'. Temperature coupling does not 65: apply to steep. 65: 65: Generating 1-4 interactions: fudge = 1 65: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). 65: Number of degrees of freedom in T-Coupling group System is 27.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 2 NOTEs 65: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 65: Using 1 MPI thread 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: 65: IMD: Enabled. This simulation will accept incoming IMD connections. 65: IMD: Pulling from IMD remote is enabled (-imdpull). 65: IMD: Setting port for connection requests to 0. 65: IMD: Setting up incoming socket. 65: IMD: Listening for IMD connection on port 58175. 65: IMD: -imdwait not set, starting simulation. 65: 65: Steepest Descents: 65: Tolerance (Fmax) = 1.00000e+01 65: Number of steps = 2 65: 65: Energy minimization reached the maximum number of steps before the forces 65: reached the requested precision Fmax < 10. 65: 65: writing lowest energy coordinates. 65: 65: Steepest Descents did not converge to Fmax < 10 in 3 steps. 65: Potential Energy = 1.1977064e+03 65: Maximum force = 1.7794877e+04 on atom 9 65: Norm of force = 7.8732901e+03 65: Setting the LD random seed to -1144406019 65: 65: Generated 20503 of the 20503 non-bonded parameter combinations 65: 65: Generated 17396 of the 20503 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Glycine' 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] WithIntegrator/ImdTest.ImdCanRun/1 (213 ms) 65: [----------] 2 tests from WithIntegrator/ImdTest (430 ms total) 65: 65: [----------] Global test environment tear-down 65: [==========] 15 tests from 3 test suites ran. (1255 ms total) 65: [ PASSED ] 15 tests. 65/90 Test #65: MdrunModulesTests ......................... Passed 1.28 sec test 66 Start 66: MdrunIOTests 66: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/mdrun-io-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/MdrunIOTests.xml" 66: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests 66: Test timeout computed to be: 600 66: [==========] Running 76 tests from 13 test suites. 66: [----------] Global test environment set-up. 66: [----------] 9 tests from GromppTest 66: [ RUN ] GromppTest.EmptyMdpFileWorks 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 66: For a correct single-point energy evaluation with nsteps = 0, use 66: continuation = yes to avoid constraining the input coordinates. 66: 66: Number of degrees of freedom in T-Coupling group rest is 12.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 66: NVE simulation: will use the initial temperature of 1046.791 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: Setting the LD random seed to -12256491 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: [ OK ] GromppTest.EmptyMdpFileWorks (9 ms) 66: [ RUN ] GromppTest.SimulatedAnnealingWorks 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 66: For a correct single-point energy evaluation with nsteps = 0, use 66: continuation = yes to avoid constraining the input coordinates. 66: 66: Simulated annealing for group rest: Periodic, 4 timepoints 66: Time (ps) Temperature (K) 66: 0.0 298.0 66: 2.0 320.0 66: 4.0 320.0 66: 6.0 298.0 66: Number of degrees of freedom in T-Coupling group rest is 12.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 66: NVE simulation: will use the initial temperature of 1046.791 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: Setting the LD random seed to 737537407 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: [ OK ] GromppTest.SimulatedAnnealingWorks (19 ms) 66: [ RUN ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 66: For a correct single-point energy evaluation with nsteps = 0, use 66: continuation = yes to avoid constraining the input coordinates. 66: 66: Simulated annealing for group Methanol: Single, 3 timepoints 66: Time (ps) Temperature (K) 66: 0.0 298.0 66: 3.0 280.0 66: 6.0- 270.0 66: Simulated annealing for group SOL: Periodic, 4 timepoints 66: Time (ps) Temperature (K) 66: 0.0 298.0 66: 2.0 320.0 66: 4.0 320.0 66: 6.0 298.0 66: Number of degrees of freedom in T-Coupling group Methanol is 7.20 66: Number of degrees of freedom in T-Coupling group SOL is 4.80 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 66: NVE simulation: will use the initial temperature of 1046.791 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: Setting the LD random seed to -305156635 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: [ OK ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups (6 ms) 66: [ RUN ] GromppTest.DeathTestHandlesNoMaxwarnError 66: Setting the LD random seed to 1941176270 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: [ OK ] GromppTest.DeathTestHandlesNoMaxwarnError (28 ms) 66: [ RUN ] GromppTest.HandlesMaxwarn 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 66: For a correct single-point energy evaluation with nsteps = 0, use 66: continuation = yes to avoid constraining the input coordinates. 66: 66: 66: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 66: The Berendsen thermostat does not generate the correct kinetic energy 66: distribution, and should not be used for new production simulations (in 66: our opinion). We would recommend the V-rescale thermostat. 66: 66: Number of degrees of freedom in T-Coupling group System is 12.00 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 2 NOTEs 66: 66: There was 1 WARNING 66: Setting the LD random seed to -29909003 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: [ OK ] GromppTest.HandlesMaxwarn (7 ms) 66: [ RUN ] GromppTest.MaxwarnShouldBePositive 66: [ OK ] GromppTest.MaxwarnShouldBePositive (6 ms) 66: [ RUN ] GromppTest.ValidTransformationCoord 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 66: For a correct single-point energy evaluation with nsteps = 0, use 66: continuation = yes to avoid constraining the input coordinates. 66: 66: Pull group 1 'SOL' has 3 atoms 66: Pull group 2 'Methanol' has 3 atoms 66: Number of degrees of freedom in T-Coupling group rest is 12.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 66: NVE simulation: will use the initial temperature of 1046.791 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: Pull group natoms pbc atom distance at start reference at t=0 66: 1 3 5 66: 2 3 2 0.613 nm 0.000 nm 66: 1 3 5 66: 2 3 2 0.613 nm 0.000 nm 66: 66: There were 3 NOTEs 66: Setting the LD random seed to -43053 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: [ OK ] GromppTest.ValidTransformationCoord (15 ms) 66: [ RUN ] GromppTest.InvalidTransformationCoord 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 66: For a correct single-point energy evaluation with nsteps = 0, use 66: continuation = yes to avoid constraining the input coordinates. 66: 66: Pull group 1 'SOL' has 3 atoms 66: Pull group 2 'Methanol' has 3 atoms 66: Number of degrees of freedom in T-Coupling group rest is 12.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 66: NVE simulation: will use the initial temperature of 1046.791 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: Pull group natoms pbc atom distance at start reference at t=0 66: 1 3 5 66: 2 3 2 0.613 nm 0.000 nm 66: 1 3 5 66: 2 3 2 Setting the LD random seed to -805838935 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: [ OK ] GromppTest.InvalidTransformationCoord (7 ms) 66: [ RUN ] GromppTest.RejectCRescaleAndAnisotropic 66: Setting the LD random seed to 2147450853 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: [ OK ] GromppTest.RejectCRescaleAndAnisotropic (16 ms) 66: [----------] 9 tests from GromppTest (117 ms total) 66: 66: [----------] 6 tests from MdrunTerminationTest 66: [ RUN ] MdrunTerminationTest.CheckpointRestartAppendsByDefault 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There was 1 NOTE 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 2 steps, 0.0 ps. 66: Setting the LD random seed to -1082264380 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.025 0.013 198.8 66: (ns/day) (hour/ns) 66: Performance: 20.598 1.165 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Setting nsteps to 4 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 66: Input file: 66: Run start step 0 66: Run start time 0 ps 66: Step to be made during run 2 66: Runtime for the run 0.002 ps 66: Run end step 2 66: Run end time 0.002 ps 66: 66: 66: Output file: 66: Run start step 0 66: Run start time 0 ps 66: Step to be made during run 4 66: Runtime for the run 0.004 ps 66: Run end step 4 66: Run end time 0.004 ps 66: 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.015 0.007 197.0 66: (ns/day) (hour/ns) 66: Performance: 34.895 0.688 66: [ OK ] MdrunTerminationTest.CheckpointRestartAppendsByDefault (38 ms) 66: [ RUN ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There was 1 NOTE 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 10 to 1, rlist from 1.032 to 1 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 100 steps, 0.1 ps. 66: 66: Step 3: Run time exceeded 0.000 hours, will terminate the run within 200 steps 66: Setting the LD random seed to -1086336003 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: NOTE: 44 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.050 0.025 199.4 66: (ns/day) (hour/ns) 66: Performance: 347.441 0.069 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Setting nsteps to 102 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 102 steps, 0.1 ps (continuing from step 100, 0.1 ps). 66: Input file: 66: Run start step 0 66: Run start time 0 ps 66: Step to be made during run 100 66: Runtime for the run 0.1 ps 66: Run end step 100 66: Run end time 0.1 ps 66: 66: 66: Output file: 66: Run start step 0 66: Run start time 0 ps 66: Step to be made during run 102 66: Runtime for the run 0.102 ps 66: Run end step 102 66: Run end time 0.102 ps 66: 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.010 0.005 197.3 66: (ns/day) (hour/ns) 66: Performance: 53.690 0.447 66: [ OK ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (46 ms) 66: [ RUN ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There was 1 NOTE 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 2 steps, 0.0 ps. 66: Setting the LD random seed to 1610448764 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.019 0.010 198.7 66: (ns/day) (hour/ns) 66: Performance: 26.454 0.907 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Setting nsteps to 4 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 66: Input file: 66: Run start step 0 66: Run start time 0 ps 66: Step to be made during run 2 66: Runtime for the run 0.002 ps 66: Run end step 2 66: Run end time 0.002 ps 66: 66: 66: Output file: 66: Run start step 0 66: Run start time 0 ps 66: Step to be made during run 4 66: Runtime for the run 0.004 ps 66: Run end step 4 66: Run end time 0.004 ps 66: 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.019 0.010 198.8 66: (ns/day) (hour/ns) 66: Performance: 26.474 0.907 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Setting nsteps to 6 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 6 steps, 0.0 ps (continuing from step 4, 0.0 ps). 66: Input file: 66: Run start step 0 66: Run start time 0 ps 66: Step to be made during run 4 66: Runtime for the run 0.004 ps 66: Run end step 4 66: Run end time 0.004 ps 66: 66: 66: Output file: 66: Run start step 0 66: Run start time 0 ps 66: Step to be made during run 6 66: Runtime for the run 0.006 ps 66: Run end step 6 66: Run end time 0.006 ps 66: 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.028 0.014 199.1 66: (ns/day) (hour/ns) 66: Performance: 18.148 1.322 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Setting nsteps to 8 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 8 steps, 0.0 ps (continuing from step 6, 0.0 ps). 66: Input file: 66: Run start step 0 66: Run start time 0 ps 66: Step to be made during run 6 66: Runtime for the run 0.006 ps 66: Run end step 6 66: Run end time 0.006 ps 66: 66: 66: Output file: 66: Run start step 0 66: Run start time 0 ps 66: Step to be made during run 8 66: Runtime for the run 0.008 ps 66: Run end step 8 66: Run end time 0.008 ps 66: 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.030 0.015 199.2 66: (ns/day) (hour/ns) 66: Performance: 17.388 1.380 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 8 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: NOTE: 29 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.000 0.000 181.6 66: (ns/day) (hour/ns) 66: Performance: 354.934 0.068 66: [ OK ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend (78 ms) 66: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There was 1 NOTE 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 2 steps, 0.0 ps. 66: Setting the LD random seed to -49286276 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.016 0.008 198.1 66: (ns/day) (hour/ns) 66: Performance: 32.778 0.732 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Setting nsteps to 4 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 4 steps, 0.0 ps. 66: Input file: 66: Run start step 0 66: Run start time 0 ps 66: Step to be made during run 2 66: Runtime for the run 0.002 ps 66: Run end step 2 66: Run end time 0.002 ps 66: 66: 66: Output file: 66: Run start step 0 66: Run start time 0 ps 66: Step to be made during run 4 66: Runtime for the run 0.004 ps 66: Run end step 4 66: Run end time 0.004 ps 66: 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.024 0.012 198.4 66: (ns/day) (hour/ns) 66: Performance: 36.043 0.666 66: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile (35 ms) 66: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There was 1 NOTE 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 2 steps, 0.0 ps. 66: Setting the LD random seed to 2074033646 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.021 0.010 198.2 66: (ns/day) (hour/ns) 66: Performance: 25.010 0.960 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Setting nsteps to 4 66: Input file: 66: Run start step 0 66: Run start time 0 ps 66: Step to be made during run 2 66: Runtime for the run 0.002 ps 66: Run end step 2 66: Run end time 0.002 ps 66: 66: 66: Output file: 66: Run start step 0 66: Run start time 0 ps 66: Step to be made during run 4 66: Runtime for the run 0.004 ps 66: Run end step 4 66: Run end time 0.004 ps 66: 66: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile (23 ms) 66: [ RUN ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There was 1 NOTE 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 2 steps, 0.0 ps. 66: Setting the LD random seed to -8781865 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.016 0.008 197.9 66: (ns/day) (hour/ns) 66: Performance: 32.307 0.743 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Setting nsteps to 4 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 66: Input file: 66: Run start step 0 66: Run start time 0 ps 66: Step to be made during run 2 66: Runtime for the run 0.002 ps 66: Run end step 2 66: Run end time 0.002 ps 66: 66: 66: Output file: 66: Run start step 0 66: Run start time 0 ps 66: Step to be made during run 4 66: Runtime for the run 0.004 ps 66: Run end step 4 66: Run end time 0.004 ps 66: 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.015 0.008 198.0 66: (ns/day) (hour/ns) 66: Performance: 34.546 0.695 66: [ OK ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles (31 ms) 66: [----------] 6 tests from MdrunTerminationTest (254 ms total) 66: 66: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks 66: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps. 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.045 0.023 199.0 66: (ns/day) (hour/ns) 66: Performance: 64.496 0.372 66: trr version: GMX_trn_file (single precision) 66: 66: 66: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 (32 ms) 66: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps. 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.027 0.013 198.6 66: (ns/day) (hour/ns) 66: Performance: 109.085 0.220 66: 66: 66: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 (25 ms) 66: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks (58 ms total) 66: 66: [----------] 24 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: NVE simulation: will use the initial temperature of 68.810 K for 66: determining the Verlet buffer size 66: 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: NVE simulation: will use the initial temperature of 68.810 K for 66: determining the Verlet buffer size 66: 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.062 0.031 199.3 66: (ns/day) (hour/ns) 66: Performance: 47.164 0.509 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.039 0.020 199.2 66: (ns/day) (hour/ns) 66: Performance: 39.793 0.603 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.028 0.014 199.0 66: (ns/day) (hour/ns) 66: Performance: 54.319 0.442 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (89 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: NVE simulation: will use the initial temperature of 68.810 K for 66: determining the Verlet buffer size 66: 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: NVE simulation: will use the initial temperature of 68.810 K for 66: determining the Verlet buffer size 66: 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.029 0.014 199.1 66: (ns/day) (hour/ns) 66: Performance: 101.831 0.236 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.028 0.014 199.0 66: (ns/day) (hour/ns) 66: Performance: 55.353 0.434 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.029 0.015 198.9 66: (ns/day) (hour/ns) 66: Performance: 53.369 0.450 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (58 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: NVE simulation: will use the initial temperature of 68.810 K for 66: determining the Verlet buffer size 66: 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: NVE simulation: will use the initial temperature of 68.810 K for 66: determining the Verlet buffer size 66: 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.028 0.014 199.2 66: (ns/day) (hour/ns) 66: Performance: 103.193 0.233 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.028 0.014 199.2 66: (ns/day) (hour/ns) 66: Performance: 55.701 0.431 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.046 0.023 199.1 66: (ns/day) (hour/ns) 66: Performance: 33.569 0.715 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (72 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: NVE simulation: will use the initial temperature of 68.810 K for 66: determining the Verlet buffer size 66: 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: NVE simulation: will use the initial temperature of 68.810 K for 66: determining the Verlet buffer size 66: 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.033 0.016 199.2 66: (ns/day) (hour/ns) 66: Performance: 89.975 0.267 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.052 0.026 199.6 66: (ns/day) (hour/ns) 66: Performance: 30.105 0.797 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.041 0.021 198.8 66: (ns/day) (hour/ns) 66: Performance: 37.783 0.635 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (85 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.054 0.027 199.4 66: (ns/day) (hour/ns) 66: Performance: 54.511 0.440 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.079 0.040 199.4 66: (ns/day) (hour/ns) 66: Performance: 19.599 1.225 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.070 0.035 199.5 66: (ns/day) (hour/ns) 66: Performance: 22.132 1.084 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (155 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 100, rlist from 0.709 to 0.733 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.711 nm, buffer size 0.011 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.711 nm, buffer size 0.011 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.079 0.039 199.6 66: (ns/day) (hour/ns) 66: Performance: 37.330 0.643 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 100, rlist from 0.709 to 0.733 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.106 0.053 199.7 66: (ns/day) (hour/ns) 66: Performance: 14.665 1.637 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 100, rlist from 0.709 to 0.733 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.372 0.186 199.9 66: (ns/day) (hour/ns) 66: Performance: 4.183 5.738 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (324 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.097 0.049 199.6 66: (ns/day) (hour/ns) 66: Performance: 30.128 0.797 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.076 0.038 199.6 66: (ns/day) (hour/ns) 66: Performance: 20.463 1.173 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.096 0.048 199.7 66: (ns/day) (hour/ns) 66: Performance: 16.099 1.491 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (215 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.052 0.026 199.4 66: (ns/day) (hour/ns) 66: Performance: 56.438 0.425 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.078 0.039 199.3 66: (ns/day) (hour/ns) 66: Performance: 19.944 1.203 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.110 0.055 199.7 66: (ns/day) (hour/ns) 66: Performance: 14.076 1.705 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (180 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps. 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.079 0.040 199.5 66: (ns/day) (hour/ns) 66: Performance: 37.080 0.647 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.074 0.037 199.5 66: (ns/day) (hour/ns) 66: Performance: 20.944 1.146 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.032 0.016 199.0 66: (ns/day) (hour/ns) 66: Performance: 48.256 0.497 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (167 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps. 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.189 0.095 199.7 66: (ns/day) (hour/ns) 66: Performance: 15.539 1.545 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.146 0.073 199.8 66: (ns/day) (hour/ns) 66: Performance: 10.614 2.261 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.065 0.033 199.3 66: (ns/day) (hour/ns) 66: Performance: 23.683 1.013 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (232 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps. 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.046 0.023 199.5 66: (ns/day) (hour/ns) 66: Performance: 63.962 0.375 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.038 0.019 198.4 66: (ns/day) (hour/ns) 66: Performance: 41.013 0.585 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.039 0.020 199.1 66: (ns/day) (hour/ns) 66: Performance: 39.383 0.609 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_secondpart.part0002.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (86 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps. 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.057 0.028 199.5 66: (ns/day) (hour/ns) 66: Performance: 51.601 0.465 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.052 0.026 199.5 66: (ns/day) (hour/ns) 66: Performance: 29.805 0.805 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.085 0.042 199.6 66: (ns/day) (hour/ns) 66: Performance: 18.347 1.308 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_secondpart.part0002.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (118 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/12 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps. 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.107 0.054 199.7 66: (ns/day) (hour/ns) 66: Performance: 27.435 0.875 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.088 0.044 199.6 66: (ns/day) (hour/ns) 66: Performance: 17.618 1.362 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.056 0.028 199.0 66: (ns/day) (hour/ns) 66: Performance: 27.417 0.875 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_secondpart.part0002.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/12 (170 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/13 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 100, rlist from 0.73 to 0.811 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps. 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.037 0.019 199.3 66: (ns/day) (hour/ns) 66: Performance: 78.093 0.307 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 100, rlist from 0.73 to 0.811 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.106 0.053 199.7 66: (ns/day) (hour/ns) 66: Performance: 14.594 1.644 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 100, rlist from 0.73 to 0.811 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.038 0.019 199.2 66: (ns/day) (hour/ns) 66: Performance: 40.963 0.586 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_secondpart.part0002.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/13 (132 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/14 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps. 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.760 nm, buffer size 0.060 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.760 nm, buffer size 0.060 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.039 0.020 199.1 66: (ns/day) (hour/ns) 66: Performance: 74.368 0.323 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.061 0.030 199.5 66: (ns/day) (hour/ns) 66: Performance: 25.618 0.937 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.047 0.024 199.1 66: (ns/day) (hour/ns) 66: Performance: 33.020 0.727 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_secondpart.part0002.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/14 (117 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/15 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 25, rlist from 0.752 to 0.89 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps. 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.757 nm, buffer size 0.057 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.752 nm, buffer size 0.052 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.757 nm, buffer size 0.057 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.752 nm, buffer size 0.052 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.047 0.024 199.4 66: (ns/day) (hour/ns) 66: Performance: 61.923 0.388 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 25, rlist from 0.752 to 0.89 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.030 0.015 199.0 66: (ns/day) (hour/ns) 66: Performance: 51.207 0.469 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 25, rlist from 0.752 to 0.89 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.054 0.027 199.3 66: (ns/day) (hour/ns) 66: Performance: 28.576 0.840 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_secondpart.part0002.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/15 (104 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/16 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 66: NVE simulation: will use the initial temperature of 456.887 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 6 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 66: NVE simulation: will use the initial temperature of 456.887 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 6 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 16 steps, 0.0 ps. 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.071 0.036 199.5 66: (ns/day) (hour/ns) 66: Performance: 41.010 0.585 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.040 0.020 197.4 66: (ns/day) (hour/ns) 66: Performance: 38.510 0.623 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.037 0.019 195.3 66: (ns/day) (hour/ns) 66: Performance: 40.891 0.587 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_secondpart.part0002.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/16 (229 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/17 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 66: NVE simulation: will use the initial temperature of 456.887 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 6 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 66: NVE simulation: will use the initial temperature of 456.887 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 6 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 16 steps, 0.0 ps. 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.048 0.024 199.1 66: (ns/day) (hour/ns) 66: Performance: 60.623 0.396 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.088 0.044 199.5 66: (ns/day) (hour/ns) 66: Performance: 17.537 1.369 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.042 0.021 196.9 66: (ns/day) (hour/ns) 66: Performance: 36.886 0.651 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_secondpart.part0002.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/17 (165 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/18 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 66: NVE simulation: will use the initial temperature of 456.887 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 6 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 66: NVE simulation: will use the initial temperature of 456.887 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 6 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 16 steps, 0.0 ps. 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.080 0.040 199.5 66: (ns/day) (hour/ns) 66: Performance: 36.739 0.653 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.079 0.040 199.4 66: (ns/day) (hour/ns) 66: Performance: 19.576 1.226 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.073 0.036 199.0 66: (ns/day) (hour/ns) 66: Performance: 21.328 1.125 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_secondpart.part0002.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/18 (188 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/19 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 66: NVE simulation: will use the initial temperature of 456.887 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 6 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 66: NVE simulation: will use the initial temperature of 456.887 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 6 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 16 steps, 0.0 ps. 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.101 0.051 199.5 66: (ns/day) (hour/ns) 66: Performance: 28.975 0.828 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.067 0.034 199.2 66: (ns/day) (hour/ns) 66: Performance: 23.134 1.037 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.066 0.033 199.3 66: (ns/day) (hour/ns) 66: Performance: 23.568 1.018 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_secondpart.part0002.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/19 (181 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/20 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 5 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 5 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 16 steps, 0.0 ps. 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.152 0.076 199.7 66: (ns/day) (hour/ns) 66: Performance: 19.244 1.247 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.048 0.024 199.3 66: (ns/day) (hour/ns) 66: Performance: 32.020 0.750 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.070 0.035 199.5 66: (ns/day) (hour/ns) 66: Performance: 22.314 1.076 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_secondpart.part0002.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/20 (289 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/21 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 5 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 5 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 80, rlist from 0.741 to 0.841 66: 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 16 steps, 0.0 ps. 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.747 nm, buffer size 0.047 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.747 nm, buffer size 0.047 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.048 0.024 199.3 66: (ns/day) (hour/ns) 66: Performance: 61.108 0.393 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 80, rlist from 0.741 to 0.841 66: 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: NOTE: 12 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.056 0.028 198.6 66: (ns/day) (hour/ns) 66: Performance: 27.810 0.863 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 80, rlist from 0.741 to 0.841 66: 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.027 0.013 198.4 66: (ns/day) (hour/ns) 66: Performance: 57.857 0.415 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_secondpart.part0002.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/21 (388 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/22 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 5 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 5 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 16 steps, 0.0 ps. 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.034 0.017 198.8 66: (ns/day) (hour/ns) 66: Performance: 86.274 0.278 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.031 0.015 198.7 66: (ns/day) (hour/ns) 66: Performance: 50.470 0.476 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.078 0.039 199.5 66: (ns/day) (hour/ns) 66: Performance: 19.935 1.204 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_secondpart.part0002.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/22 (180 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/23 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 5 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 5 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 25, rlist from 0.724 to 0.793 66: 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 16 steps, 0.0 ps. 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.728 nm, buffer size 0.028 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.724 nm, buffer size 0.024 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.728 nm, buffer size 0.028 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.724 nm, buffer size 0.024 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.051 0.025 199.2 66: (ns/day) (hour/ns) 66: Performance: 57.778 0.415 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 25, rlist from 0.724 to 0.793 66: 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.045 0.025 178.3 66: (ns/day) (hour/ns) 66: Performance: 30.772 0.780 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 25, rlist from 0.724 to 0.793 66: 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.039 0.020 198.5 66: (ns/day) (hour/ns) 66: Performance: 39.299 0.611 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_secondpart.part0002.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/23 (213 ms) 66: [----------] 24 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact (4149 ms total) 66: 66: [----------] 8 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact 66: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: NVE simulation: will use the initial temperature of 294.908 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: NVE simulation: will use the initial temperature of 294.908 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps. 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.215 0.107 199.7 66: (ns/day) (hour/ns) 66: Performance: 13.663 1.757 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.048 0.024 198.1 66: (ns/day) (hour/ns) 66: Performance: 32.360 0.742 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.082 0.041 199.5 66: (ns/day) (hour/ns) 66: Performance: 18.911 1.269 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (233 ms) 66: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: NVE simulation: will use the initial temperature of 294.908 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: NVE simulation: will use the initial temperature of 294.908 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps. 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.045 0.023 199.1 66: (ns/day) (hour/ns) 66: Performance: 65.156 0.368 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.038 0.019 198.2 66: (ns/day) (hour/ns) 66: Performance: 40.794 0.588 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.046 0.023 198.9 66: (ns/day) (hour/ns) 66: Performance: 33.463 0.717 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (116 ms) 66: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: NVE simulation: will use the initial temperature of 294.908 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: NVE simulation: will use the initial temperature of 294.908 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps. 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.043 0.022 199.3 66: (ns/day) (hour/ns) 66: Performance: 67.363 0.356 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.061 0.031 199.5 66: (ns/day) (hour/ns) 66: Performance: 25.273 0.950 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.057 0.029 199.1 66: (ns/day) (hour/ns) 66: Performance: 26.987 0.889 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (136 ms) 66: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: NVE simulation: will use the initial temperature of 294.908 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: NVE simulation: will use the initial temperature of 294.908 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps. 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.059 0.030 199.5 66: (ns/day) (hour/ns) 66: Performance: 49.778 0.482 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.063 0.032 198.9 66: (ns/day) (hour/ns) 66: Performance: 24.674 0.973 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.042 0.021 198.7 66: (ns/day) (hour/ns) 66: Performance: 36.761 0.653 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (150 ms) 66: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/4 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps. 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.732 nm, buffer size 0.032 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.732 nm, buffer size 0.032 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.041 0.021 199.0 66: (ns/day) (hour/ns) 66: Performance: 70.488 0.340 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.043 0.022 197.4 66: (ns/day) (hour/ns) 66: Performance: 35.908 0.668 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.029 0.014 198.6 66: (ns/day) (hour/ns) 66: Performance: 54.182 0.443 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (143 ms) 66: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/5 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 100, rlist from 0.728 to 0.806 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps. 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.040 0.020 198.9 66: (ns/day) (hour/ns) 66: Performance: 73.517 0.326 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 100, rlist from 0.728 to 0.806 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.033 0.017 198.3 66: (ns/day) (hour/ns) 66: Performance: 46.734 0.514 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 100, rlist from 0.728 to 0.806 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.036 0.018 198.9 66: (ns/day) (hour/ns) 66: Performance: 43.060 0.557 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (321 ms) 66: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/6 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps. 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.048 0.024 199.1 66: (ns/day) (hour/ns) 66: Performance: 61.081 0.393 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.032 0.016 198.2 66: (ns/day) (hour/ns) 66: Performance: 48.214 0.498 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.034 0.017 198.8 66: (ns/day) (hour/ns) 66: Performance: 45.484 0.528 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (130 ms) 66: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/7 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 20, rlist from 0.749 to 0.842 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps. 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.053 0.026 199.2 66: (ns/day) (hour/ns) 66: Performance: 55.676 0.431 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 20, rlist from 0.749 to 0.842 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.039 0.020 198.6 66: (ns/day) (hour/ns) 66: Performance: 39.334 0.610 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 20, rlist from 0.749 to 0.843 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.093 0.047 199.6 66: (ns/day) (hour/ns) 66: Performance: 16.626 1.444 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (177 ms) 66: [----------] 8 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact (1411 ms total) 66: 66: [----------] 8 tests from NVT/MdrunNoAppendContinuationIsExact 66: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 1.026 0.513 200.0 66: (ns/day) (hour/ns) 66: Performance: 2.862 8.386 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 1.365 0.682 200.0 66: (ns/day) (hour/ns) 66: Performance: 1.139 21.062 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 1.859 0.930 200.0 66: (ns/day) (hour/ns) 66: Performance: 0.837 28.690 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (2288 ms) 66: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 1.175 0.587 200.0 66: (ns/day) (hour/ns) 66: Performance: 2.500 9.599 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.044 0.022 199.2 66: (ns/day) (hour/ns) 66: Performance: 35.080 0.684 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.030 0.015 198.8 66: (ns/day) (hour/ns) 66: Performance: 52.259 0.459 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (1022 ms) 66: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 66: 1 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 66: 1 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.024 0.012 198.5 66: (ns/day) (hour/ns) 66: Performance: 121.905 0.197 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.024 0.012 198.5 66: (ns/day) (hour/ns) 66: Performance: 63.425 0.378 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.021 0.011 198.5 66: (ns/day) (hour/ns) 66: Performance: 72.044 0.333 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (57 ms) 66: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 66: 1 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 66: 1 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.026 0.013 197.3 66: (ns/day) (hour/ns) 66: Performance: 109.510 0.219 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.025 0.013 198.7 66: (ns/day) (hour/ns) 66: Performance: 60.819 0.395 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.020 0.010 198.6 66: (ns/day) (hour/ns) 66: Performance: 76.846 0.312 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (61 ms) 66: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.026 0.013 199.0 66: (ns/day) (hour/ns) 66: Performance: 111.110 0.216 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.028 0.014 199.1 66: (ns/day) (hour/ns) 66: Performance: 54.800 0.438 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.026 0.013 198.4 66: (ns/day) (hour/ns) 66: Performance: 58.636 0.409 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (58 ms) 66: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.036 0.019 191.6 66: (ns/day) (hour/ns) 66: Performance: 79.102 0.303 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.032 0.016 198.8 66: (ns/day) (hour/ns) 66: Performance: 47.715 0.503 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.028 0.014 198.4 66: (ns/day) (hour/ns) 66: Performance: 54.748 0.438 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (69 ms) 66: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.034 0.017 197.6 66: (ns/day) (hour/ns) 66: Performance: 85.649 0.280 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.046 0.023 199.4 66: (ns/day) (hour/ns) 66: Performance: 33.729 0.712 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.051 0.026 199.1 66: (ns/day) (hour/ns) 66: Performance: 30.135 0.796 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (88 ms) 66: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.033 0.017 199.0 66: (ns/day) (hour/ns) 66: Performance: 87.893 0.273 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.029 0.014 198.6 66: (ns/day) (hour/ns) 66: Performance: 53.904 0.445 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.060 0.030 197.1 66: (ns/day) (hour/ns) 66: Performance: 25.524 0.940 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (85 ms) 66: [----------] 8 tests from NVT/MdrunNoAppendContinuationIsExact (3732 ms total) 66: 66: [----------] 2 tests from NPH/MdrunNoAppendContinuationIsExact 66: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: NVE simulation: will use the initial temperature of 68.810 K for 66: determining the Verlet buffer size 66: 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: NVE simulation: will use the initial temperature of 68.810 K for 66: determining the Verlet buffer size 66: 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.030 0.015 198.9 66: (ns/day) (hour/ns) 66: Performance: 98.562 0.244 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.025 0.012 198.6 66: (ns/day) (hour/ns) 66: Performance: 62.318 0.385 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.030 0.015 198.7 66: (ns/day) (hour/ns) 66: Performance: 50.724 0.473 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (63 ms) 66: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: NVE simulation: will use the initial temperature of 68.810 K for 66: determining the Verlet buffer size 66: 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: NVE simulation: will use the initial temperature of 68.810 K for 66: determining the Verlet buffer size 66: 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.042 0.021 199.4 66: (ns/day) (hour/ns) 66: Performance: 69.225 0.347 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.032 0.016 199.3 66: (ns/day) (hour/ns) 66: Performance: 48.389 0.496 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.062 0.031 199.3 66: (ns/day) (hour/ns) 66: Performance: 24.936 0.962 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (90 ms) 66: [----------] 2 tests from NPH/MdrunNoAppendContinuationIsExact (154 ms total) 66: 66: [----------] 8 tests from NPT/MdrunNoAppendContinuationIsExact 66: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.077 0.038 199.6 66: (ns/day) (hour/ns) 66: Performance: 38.273 0.627 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.049 0.025 199.3 66: (ns/day) (hour/ns) 66: Performance: 31.343 0.766 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.036 0.018 198.9 66: (ns/day) (hour/ns) 66: Performance: 43.399 0.553 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (109 ms) 66: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.029 0.014 198.8 66: (ns/day) (hour/ns) 66: Performance: 101.574 0.236 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.112 0.056 199.7 66: (ns/day) (hour/ns) 66: Performance: 13.920 1.724 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.025 0.012 198.3 66: (ns/day) (hour/ns) 66: Performance: 62.289 0.385 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (104 ms) 66: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 66: 1 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 66: 1 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.024 0.012 197.6 66: (ns/day) (hour/ns) 66: Performance: 118.692 0.202 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.024 0.012 198.2 66: (ns/day) (hour/ns) 66: Performance: 64.926 0.370 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.039 0.020 199.1 66: (ns/day) (hour/ns) 66: Performance: 39.602 0.606 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (66 ms) 66: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 66: 1 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 66: 1 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.046 0.023 199.1 66: (ns/day) (hour/ns) 66: Performance: 63.894 0.376 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.026 0.013 198.6 66: (ns/day) (hour/ns) 66: Performance: 59.550 0.403 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.024 0.012 198.5 66: (ns/day) (hour/ns) 66: Performance: 63.916 0.375 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (70 ms) 66: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.035 0.018 199.2 66: (ns/day) (hour/ns) 66: Performance: 83.739 0.287 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.049 0.024 199.4 66: (ns/day) (hour/ns) 66: Performance: 31.841 0.754 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.035 0.018 198.7 66: (ns/day) (hour/ns) 66: Performance: 43.618 0.550 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (90 ms) 66: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.049 0.025 199.4 66: (ns/day) (hour/ns) 66: Performance: 59.853 0.401 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.066 0.033 199.6 66: (ns/day) (hour/ns) 66: Performance: 23.528 1.020 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.082 0.041 199.4 66: (ns/day) (hour/ns) 66: Performance: 18.848 1.273 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (121 ms) 66: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 66: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (0 ms) 66: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.046 0.023 199.5 66: (ns/day) (hour/ns) 66: Performance: 63.523 0.378 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.034 0.017 199.0 66: (ns/day) (hour/ns) 66: Performance: 45.223 0.531 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.037 0.018 198.7 66: (ns/day) (hour/ns) 66: Performance: 42.085 0.570 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (80 ms) 66: [----------] 8 tests from NPT/MdrunNoAppendContinuationIsExact (643 ms total) 66: 66: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact 66: [ RUN ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: MTTK coupling is deprecated and will soon be removed 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: MTTK coupling is deprecated and will soon be removed 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.034 0.017 199.1 66: (ns/day) (hour/ns) 66: Performance: 86.637 0.277 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.026 0.013 198.8 66: (ns/day) (hour/ns) 66: Performance: 60.145 0.399 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.031 0.016 198.4 66: (ns/day) (hour/ns) 66: Performance: 49.930 0.481 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (66 ms) 66: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact (66 ms total) 66: 66: [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact 66: [ RUN ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/0 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Pull group 1 'FirstWaterMolecule' has 3 atoms 66: Pull group 2 'SecondWaterMolecule' has 3 atoms 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: Pull group natoms pbc atom distance at start reference at t=0 66: 1 3 2 66: 2 3 5 1.112 nm 1.000 nm 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Pull group 1 'FirstWaterMolecule' has 3 atoms 66: Pull group 2 'SecondWaterMolecule' has 3 atoms 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: Pull group natoms pbc atom distance at start reference at t=0 66: 1 3 2 66: 2 3 5 1.112 nm 1.000 nm 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps. 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.057 0.028 199.1 66: (ns/day) (hour/ns) 66: Performance: 51.716 0.464 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.042 0.021 198.9 66: (ns/day) (hour/ns) 66: Performance: 37.258 0.644 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.048 0.024 199.0 66: (ns/day) (hour/ns) 66: Performance: 32.445 0.740 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (98 ms) 66: [ RUN ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/1 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Pull group 1 'FirstWaterMolecule' has 3 atoms 66: Pull group 2 'SecondWaterMolecule' has 3 atoms 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: Pull group natoms pbc atom distance at start reference at t=0 66: 1 3 2 66: 2 3 5 1.112 nm 1.000 nm 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Pull group 1 'FirstWaterMolecule' has 3 atoms 66: Pull group 2 'SecondWaterMolecule' has 3 atoms 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: Pull group natoms pbc atom distance at start reference at t=0 66: 1 3 2 66: 2 3 5 1.112 nm 1.000 nm 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps. 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.045 0.023 199.3 66: (ns/day) (hour/ns) 66: Performance: 64.593 0.372 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.037 0.018 198.9 66: (ns/day) (hour/ns) 66: Performance: 42.226 0.568 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.057 0.029 199.2 66: (ns/day) (hour/ns) 66: Performance: 27.002 0.889 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (95 ms) 66: [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact (193 ms total) 66: 66: [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact 66: [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 66: Setting the AWH bias MC random seed to -75499049 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Pull group 1 'C_&_r_1' has 1 atoms 66: Pull group 2 'N_&_r_2' has 1 atoms 66: Pull group 3 'CA' has 1 atoms 66: Pull group 4 'C_&_r_2' has 1 atoms 66: Pull group 5 'N_&_r_3' has 1 atoms 66: Number of degrees of freedom in T-Coupling group System is 51.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: Pull group natoms pbc atom distance at start reference at t=0 66: 1 1 0 66: 2 1 0 179.098 deg 0.000 deg 66: 2 1 0 66: 3 1 0 158.667 deg 0.000 deg 66: 66: There were 3 NOTEs 66: Setting the AWH bias MC random seed to -285491241 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Pull group 1 'C_&_r_1' has 1 atoms 66: Pull group 2 'N_&_r_2' has 1 atoms 66: Pull group 3 'CA' has 1 atoms 66: Pull group 4 'C_&_r_2' has 1 atoms 66: Pull group 5 'N_&_r_3' has 1 atoms 66: Number of degrees of freedom in T-Coupling group System is 51.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: Pull group natoms pbc atom distance at start reference at t=0 66: 1 1 0 66: 2 1 0 179.098 deg 0.000 deg 66: 2 1 0 66: 3 1 0 158.667 deg 0.000 deg 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine-dipeptide' 66: 16 steps, 0.0 ps. 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.053 0.027 198.0 66: (ns/day) (hour/ns) 66: Performance: 54.484 0.440 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine-dipeptide' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.047 0.024 198.3 66: (ns/day) (hour/ns) 66: Performance: 32.947 0.728 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine-dipeptide' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.046 0.023 198.5 66: (ns/day) (hour/ns) 66: Performance: 33.677 0.713 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (137 ms) 66: [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 66: Setting the AWH bias MC random seed to 1865408287 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Pull group 1 'C_&_r_1' has 1 atoms 66: Pull group 2 'N_&_r_2' has 1 atoms 66: Pull group 3 'CA' has 1 atoms 66: Pull group 4 'C_&_r_2' has 1 atoms 66: Pull group 5 'N_&_r_3' has 1 atoms 66: Number of degrees of freedom in T-Coupling group System is 51.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: Pull group natoms pbc atom distance at start reference at t=0 66: 1 1 0 66: 2 1 0 179.098 deg 0.000 deg 66: 2 1 0 66: 3 1 0 158.667 deg 0.000 deg 66: 66: There were 3 NOTEs 66: Setting the AWH bias MC random seed to 234307071 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Pull group 1 'C_&_r_1' has 1 atoms 66: Pull group 2 'N_&_r_2' has 1 atoms 66: Pull group 3 'CA' has 1 atoms 66: Pull group 4 'C_&_r_2' has 1 atoms 66: Pull group 5 'N_&_r_3' has 1 atoms 66: Number of degrees of freedom in T-Coupling group System is 51.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: Pull group natoms pbc atom distance at start reference at t=0 66: 1 1 0 66: 2 1 0 179.098 deg 0.000 deg 66: 2 1 0 66: 3 1 0 158.667 deg 0.000 deg 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine-dipeptide' 66: 16 steps, 0.0 ps. 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.055 0.028 198.5 66: (ns/day) (hour/ns) 66: Performance: 52.871 0.454 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine-dipeptide' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.043 0.022 198.5 66: (ns/day) (hour/ns) 66: Performance: 36.077 0.665 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine-dipeptide' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.041 0.021 197.8 66: (ns/day) (hour/ns) 66: Performance: 37.840 0.634 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (136 ms) 66: [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact (274 ms total) 66: 66: [----------] 1 test from ExpandedEnsemble/MdrunNoAppendContinuationIsExact 66: [ RUN ] ExpandedEnsemble/MdrunNoAppendContinuationIsExact.WithinTolerances/0 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 2 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 2 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps. 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.055 0.028 199.4 66: (ns/day) (hour/ns) 66: Performance: 52.977 0.453 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.039 0.019 199.3 66: (ns/day) (hour/ns) 66: Performance: 39.968 0.600 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.049 0.025 198.6 66: (ns/day) (hour/ns) 66: Performance: 31.557 0.761 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] ExpandedEnsemble/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (150 ms) 66: [----------] 1 test from ExpandedEnsemble/MdrunNoAppendContinuationIsExact (150 ms total) 66: 66: [----------] 3 tests from Checking/InitialConstraintsTest 66: [ RUN ] Checking/InitialConstraintsTest.Works/0 66: Number of degrees of freedom in T-Coupling group rest is 11.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 66: NVE simulation: will use the initial temperature of 1141.954 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 2 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc-and-methanol' 66: 1 steps, 0.0 ps. 66: Setting the LD random seed to -84116521 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.045 0.022 199.2 66: (ns/day) (hour/ns) 66: Performance: 7.723 3.108 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_spc-and-methanol.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/0 (35 ms) 66: [ RUN ] Checking/InitialConstraintsTest.Works/1 66: Number of degrees of freedom in T-Coupling group rest is 11.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 66: NVE simulation: will use the initial temperature of 1141.954 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 2 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc-and-methanol' 66: 1 steps, 0.0 ps. 66: Setting the LD random seed to -1617051681 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.030 0.015 198.9 66: (ns/day) (hour/ns) 66: Performance: 11.313 2.121 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_spc-and-methanol.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/1 (24 ms) 66: [ RUN ] Checking/InitialConstraintsTest.Works/2 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 66: Integrator method md-vv-avek is implemented primarily for validation 66: purposes; for molecular dynamics, you should probably be using md or 66: md-vv 66: 66: Number of degrees of freedom in T-Coupling group rest is 11.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 66: NVE simulation: will use the initial temperature of 1141.954 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc-and-methanol' 66: 1 steps, 0.0 ps. 66: Setting the LD random seed to -25780744 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.014 0.007 197.5 66: (ns/day) (hour/ns) 66: Performance: 24.540 0.978 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_spc-and-methanol.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/2 (19 ms) 66: [----------] 3 tests from Checking/InitialConstraintsTest (80 ms total) 66: 66: [----------] Global test environment tear-down 66: [==========] 76 tests from 13 test suites ran. (12905 ms total) 66: [ PASSED ] 76 tests. 66/90 Test #66: MdrunIOTests .............................. Passed 12.95 sec test 67 Start 67: MdrunTestsOneRank 67: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/mdrun-test "-ntomp" "2" "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/MdrunTestsOneRank.xml" 67: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests 67: Test timeout computed to be: 600 67: [==========] Running 29 tests from 8 test suites. 67: [----------] Global test environment set-up. 67: [----------] 1 test from CompelTest 67: [ RUN ] CompelTest.SwapCanRun 67: Generating 1-4 interactions: fudge = 0.5 67: Split0 group 'Ch0' contains 83 atoms. 67: Split1 group 'Ch1' contains 83 atoms. 67: Solvent group 'SOL' contains 11931 atoms. 67: Swap group 'NA+' contains 19 atoms. 67: Swap group 'CL-' contains 19 atoms. 67: Number of degrees of freedom in T-Coupling group System is 27869.00 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 67: Removing center of mass motion in the presence of position restraints 67: might cause artifacts. When you are using position restraints to 67: equilibrate a macro-molecule, the artifacts are usually negligible. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 2 NOTEs 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Update groups can not be used for this system because there are three or more consecutively coupled constraints 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: SWAP: Determining initial numbers of ions per compartment. 67: SWAP: Setting pointers for checkpoint writing 67: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 67: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 67: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 67: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 67: starting mdrun 'Channel_coco in octane membrane' 67: 2 steps, 0.0 ps. 67: Setting the LD random seed to -35199057 67: 67: Generated 330891 of the 330891 non-bonded parameter combinations 67: 67: Generated 330891 of the 330891 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Protein' 67: 67: turning all bonds into constraints... 67: 67: Excluding 3 bonded neighbours molecule type 'OCT' 67: 67: turning all bonds into constraints... 67: 67: Excluding 1 bonded neighbours molecule type 'NA' 67: 67: turning all bonds into constraints... 67: 67: Excluding 1 bonded neighbours molecule type 'CL' 67: 67: turning all bonds into constraints... 67: 67: Excluding 3 bonded neighbours molecule type 'Protein' 67: 67: Excluding 3 bonded neighbours molecule type 'OCT' 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: turning all bonds into constraints... 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/OctaneSandwich.gro' 67: 67: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 67: 67: Calculated rlist for 1x1 atom pair-list as 1.316 nm, buffer size 0.316 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 1.262 nm, buffer size 0.262 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 1 Mb of data 67: 67: Writing final coordinates. 67: 67: NOTE: 27 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.514 0.257 199.8 67: (ns/day) (hour/ns) 67: Performance: 5.037 4.765 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps 67: 67: Update groups can not be used for this system because there are three or more consecutively coupled constraints 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: SWAP: Setting pointers for checkpoint writing 67: SWAP: Copying channel fluxes from checkpoint file data 67: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 67: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 67: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 67: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 67: starting mdrun 'Channel_coco in octane membrane' 67: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 67: 67: Writing final coordinates. 67: 67: NOTE: 25 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.494 0.247 199.8 67: (ns/day) (hour/ns) 67: Performance: 5.239 4.581 67: [ OK ] CompelTest.SwapCanRun (1123 ms) 67: [----------] 1 test from CompelTest (1123 ms total) 67: 67: [----------] 6 tests from BondedInteractionsTest 67: [ RUN ] BondedInteractionsTest.NormalBondWorks 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: 67: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: 67: In moleculetype 'butane' 2 atoms are not bound by a potential or 67: constraint to any other atom in the same moleculetype. Although 67: technically this might not cause issues in a simulation, this often means 67: that the user forgot to add a bond/potential/constraint or put multiple 67: molecules in the same moleculetype definition by mistake. Run with -v to 67: get information for each atom. 67: 67: Number of degrees of freedom in T-Coupling group rest is 9.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 67: NVE simulation with an initial temperature of zero: will use a Verlet 67: buffer of 10%. Check your energy drift! 67: 67: 67: There were 3 NOTEs 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 67: 67: Reading frames from gro file 'A single butane', 4 atoms. 67: Reading frame 0 time 0.000 Last frame 0 time 0.000 67: 67: NOTE: 23 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.001 0.000 189.0 67: (ns/day) (hour/ns) 67: Performance: 201.663 0.119 67: Setting the LD random seed to -156303361 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'butane' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] BondedInteractionsTest.NormalBondWorks (17 ms) 67: [ RUN ] BondedInteractionsTest.TabulatedBondWorks 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: 67: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: 67: In moleculetype 'butane' 2 atoms are not bound by a potential or 67: constraint to any other atom in the same moleculetype. Although 67: technically this might not cause issues in a simulation, this often means 67: that the user forgot to add a bond/potential/constraint or put multiple 67: molecules in the same moleculetype definition by mistake. Run with -v to 67: get information for each atom. 67: 67: Number of degrees of freedom in T-Coupling group rest is 9.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 67: NVE simulation with an initial temperature of zero: will use a Verlet 67: buffer of 10%. Check your energy drift! 67: 67: 67: There were 3 NOTEs 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 67: 67: Reading frames from gro file 'A single butane', 4 atoms. 67: Reading frame 0 time 0.000 Last frame 0 time 0.000 67: 67: NOTE: 26 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.001 0.000 188.9 67: (ns/day) (hour/ns) 67: Performance: 249.235 0.096 67: Setting the LD random seed to -314704719 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'butane' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] BondedInteractionsTest.TabulatedBondWorks (18 ms) 67: [ RUN ] BondedInteractionsTest.NormalAngleWorks 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: 67: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: 67: In moleculetype 'butane' 4 atoms are not bound by a potential or 67: constraint to any other atom in the same moleculetype. Although 67: technically this might not cause issues in a simulation, this often means 67: that the user forgot to add a bond/potential/constraint or put multiple 67: molecules in the same moleculetype definition by mistake. Run with -v to 67: get information for each atom. 67: 67: Number of degrees of freedom in T-Coupling group rest is 9.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 67: NVE simulation with an initial temperature of zero: will use a Verlet 67: buffer of 10%. Check your energy drift! 67: 67: 67: There were 3 NOTEs 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 67: 67: Reading frames from gro file 'A single butane', 4 atoms. 67: Reading frame 0 time 0.000 Last frame 0 time 0.000 67: 67: NOTE: 26 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.001 0.000 188.6 67: (ns/day) (hour/ns) 67: Performance: 179.667 0.134 67: Setting the LD random seed to 566230431 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'butane' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] BondedInteractionsTest.NormalAngleWorks (13 ms) 67: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: 67: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: 67: In moleculetype 'butane' 4 atoms are not bound by a potential or 67: constraint to any other atom in the same moleculetype. Although 67: technically this might not cause issues in a simulation, this often means 67: that the user forgot to add a bond/potential/constraint or put multiple 67: molecules in the same moleculetype definition by mistake. Run with -v to 67: get information for each atom. 67: 67: Number of degrees of freedom in T-Coupling group rest is 9.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 67: NVE simulation with an initial temperature of zero: will use a Verlet 67: buffer of 10%. Check your energy drift! 67: 67: 67: There were 3 NOTEs 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 67: 67: Reading frames from gro file 'A single butane', 4 atoms. 67: Reading frame 0 time 0.000 Last frame 0 time 0.000 67: 67: NOTE: 24 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.001 0.000 188.2 67: (ns/day) (hour/ns) 67: Performance: 183.209 0.131 67: Setting the LD random seed to -270012501 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'butane' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (11 ms) 67: [ RUN ] BondedInteractionsTest.NormalDihedralWorks 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: 67: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]: 67: In moleculetype 'butane' 4 atoms are not bound by a potential or 67: constraint to any other atom in the same moleculetype. Although 67: technically this might not cause issues in a simulation, this often means 67: that the user forgot to add a bond/potential/constraint or put multiple 67: molecules in the same moleculetype definition by mistake. Run with -v to 67: get information for each atom. 67: 67: Number of degrees of freedom in T-Coupling group rest is 9.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 67: NVE simulation with an initial temperature of zero: will use a Verlet 67: buffer of 10%. Check your energy drift! 67: 67: 67: There were 3 NOTEs 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 67: 67: Reading frames from gro file 'A single butane', 4 atoms. 67: Reading frame 0 time 0.000 Last frame 0 time 0.000 67: 67: NOTE: 28 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.001 0.000 185.7 67: (ns/day) (hour/ns) 67: Performance: 251.833 0.095 67: Setting the LD random seed to -34603905 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'butane' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] BondedInteractionsTest.NormalDihedralWorks (10 ms) 67: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: 67: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]: 67: In moleculetype 'butane' 4 atoms are not bound by a potential or 67: constraint to any other atom in the same moleculetype. Although 67: technically this might not cause issues in a simulation, this often means 67: that the user forgot to add a bond/potential/constraint or put multiple 67: molecules in the same moleculetype definition by mistake. Run with -v to 67: get information for each atom. 67: 67: Number of degrees of freedom in T-Coupling group rest is 9.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 67: NVE simulation with an initial temperature of zero: will use a Verlet 67: buffer of 10%. Check your energy drift! 67: 67: 67: There were 3 NOTEs 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 67: 67: Reading frames from gro file 'A single butane', 4 atoms. 67: Reading frame 0 time 0.000 Last frame 0 time 0.000 67: 67: NOTE: 27 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.001 0.000 189.6 67: (ns/day) (hour/ns) 67: Performance: 265.291 0.090 67: Setting the LD random seed to -1128595585 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'butane' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (15 ms) 67: [----------] 6 tests from BondedInteractionsTest (87 ms total) 67: 67: [----------] 2 tests from BoxDeformationTest 67: [ RUN ] BoxDeformationTest.flowDoesNotAffectEkin 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (10) 67: 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: Number of degrees of freedom in T-Coupling group rest is 33.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: There were 3 NOTEs 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Argon' 67: 0 steps, 0.0 ps. 67: 67: NOTE: 32 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.001 0.000 173.3 67: (ns/day) (hour/ns) 67: Performance: 416.538 0.058 67: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -1275120681 67: 67: Generated 1 of the 1 non-bonded parameter combinations 67: 67: Excluding 1 bonded neighbours molecule type 'Argon' 67: 67: Setting gen_seed to 1601658355 67: 67: Velocities were taken from a Maxwell distribution at 0 K 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] BoxDeformationTest.flowDoesNotAffectEkin (17 ms) 67: [ RUN ] BoxDeformationTest.EnergiesWithinTolerances 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (10) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Number of degrees of freedom in T-Coupling group rest is 1293.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: There were 2 NOTEs 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'spc2' 67: 20 steps, 0.0 ps. 67: Setting the LD random seed to -35585 67: 67: Generated 330891 of the 330891 non-bonded parameter combinations 67: 67: Generated 330891 of the 330891 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc216.gro' 67: 67: The largest distance between excluded atoms is 0.152 nm between atom 41 and 42 67: Calculating fourier grid dimensions for X Y Z 67: Using a fourier grid of 16x16x16, spacing 0.116 0.116 0.116 67: 67: Estimate for the relative computational load of the PME mesh part: 0.20 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: NOTE: 1 % of the run time was spent in domain decomposition, 67: 11 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.132 0.066 199.5 67: (ns/day) (hour/ns) 67: Performance: 55.024 0.436 67: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Reading energy frame 2 time 0.040 Last energy frame read 2 time 0.040 [ OK ] BoxDeformationTest.EnergiesWithinTolerances (730 ms) 67: [----------] 2 tests from BoxDeformationTest (748 ms total) 67: 67: [----------] 1 test from PositionRestraintCommTest 67: [ RUN ] PositionRestraintCommTest.PositionRestraintsTwoCOMs 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 67: You have set rlist larger than the interaction cut-off, but you also have 67: verlet-buffer-tolerance > 0. Will set rlist using 67: verlet-buffer-tolerance. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (10) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 67: 13489 atoms are not part of any of the VCM groups 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 67: 13489 atoms are not part of any center of mass motion removal group. 67: This may lead to artifacts. 67: In most cases one should use one group for the whole system. 67: 67: Number of degrees of freedom in T-Coupling group System is 29527.73 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 67: Removing center of mass motion in the presence of position restraints 67: might cause artifacts. When you are using position restraints to 67: equilibrate a macro-molecule, the artifacts are usually negligible. 67: 67: 67: There were 4 NOTEs 67: 67: There was 1 WARNING 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Changing nstlist from 10 to 20, rlist from 0.965 to 1.066 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Channel_coco in octane membrane' 67: 10 steps, 0.0 ps. 67: Setting the LD random seed to -138839077 67: 67: Generated 330891 of the 330891 non-bonded parameter combinations 67: 67: Generated 330891 of the 330891 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Protein' 67: 67: Excluding 3 bonded neighbours molecule type 'OCT' 67: 67: Excluding 1 bonded neighbours molecule type 'NA' 67: 67: Excluding 1 bonded neighbours molecule type 'CL' 67: 67: Excluding 3 bonded neighbours molecule type 'Protein' 67: 67: Excluding 3 bonded neighbours molecule type 'OCT' 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/OctaneSandwich.gro' 67: 67: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.990 nm, buffer size 0.090 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.965 nm, buffer size 0.065 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: Chain0: 2.207 2.168 7.330 67: Chain1: 2.228 2.186 2.401 67: Chain0: 2.207 2.168 7.330 67: Chain1: 2.228 2.186 2.401 67: 67: This run will generate roughly 1 Mb of data 67: 67: Writing final coordinates. 67: 67: NOTE: 15 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.921 0.461 199.9 67: (ns/day) (hour/ns) 67: Performance: 4.127 5.816 67: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Last energy frame read 1 time 0.020 [ OK ] PositionRestraintCommTest.PositionRestraintsTwoCOMs (1137 ms) 67: [----------] 1 test from PositionRestraintCommTest (1137 ms total) 67: 67: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest 67: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 2 [file ala.top, line 256]: 67: For energy conservation with LINCS, lincs_iter should be 2 or larger. 67: 67: 67: Number of degrees of freedom in T-Coupling group rest is 54.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 67: The optimal PME mesh load for parallel simulations is below 0.5 67: and for highly parallel simulations between 0.25 and 0.33, 67: for higher performance, increase the cut-off and the PME grid spacing. 67: 67: 67: 67: There were 3 NOTEs 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'UNNAMED in water' 67: 4 steps, 0.0 ps. 67: Setting the LD random seed to 1404501943 67: 67: Generated 2211 of the 2211 non-bonded parameter combinations 67: 67: Generated 2211 of the 2211 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 67: 67: turning H bonds into constraints... 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 67: 67: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 67: Calculating fourier grid dimensions for X Y Z 67: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 67: 67: Estimate for the relative computational load of the PME mesh part: 0.94 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.066 0.033 199.3 67: (ns/day) (hour/ns) 67: Performance: 13.091 1.833 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 2 [file ala.top, line 256]: 67: For energy conservation with LINCS, lincs_iter should be 2 or larger. 67: 67: 67: Number of degrees of freedom in T-Coupling group rest is 54.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 67: The optimal PME mesh load for parallel simulations is below 0.5 67: and for highly parallel simulations between 0.25 and 0.33, 67: for higher performance, increase the cut-off and the PME grid spacing. 67: 67: 67: 67: There were 3 NOTEs 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'UNNAMED in water' 67: 4 steps, 0.0 ps. 67: Setting the LD random seed to -738610178 67: 67: Generated 2211 of the 2211 non-bonded parameter combinations 67: 67: Generated 2211 of the 2211 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 67: 67: turning H bonds into constraints... 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 67: 67: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 67: Calculating fourier grid dimensions for X Y Z 67: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 67: 67: Estimate for the relative computational load of the PME mesh part: 0.94 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.074 0.037 199.2 67: (ns/day) (hour/ns) 67: Performance: 11.690 2.053 67: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 67: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 trr version: GMX_trn_file (single precision) 67: 67: 67: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 67: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (788 ms) 67: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 2 [file ala.top, line 256]: 67: For energy conservation with LINCS, lincs_iter should be 2 or larger. 67: 67: 67: Number of degrees of freedom in T-Coupling group rest is 54.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 67: The optimal PME mesh load for parallel simulations is below 0.5 67: and for highly parallel simulations between 0.25 and 0.33, 67: for higher performance, increase the cut-off and the PME grid spacing. 67: 67: 67: 67: There were 3 NOTEs 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'UNNAMED in water' 67: 4 steps, 0.0 ps. 67: Setting the LD random seed to -1078288501 67: 67: Generated 2211 of the 2211 non-bonded parameter combinations 67: 67: Generated 2211 of the 2211 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 67: 67: turning H bonds into constraints... 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 67: 67: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 67: Calculating fourier grid dimensions for X Y Z 67: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 67: 67: Estimate for the relative computational load of the PME mesh part: 0.94 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.177 0.089 199.6 67: (ns/day) (hour/ns) 67: Performance: 4.879 4.919 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 2 [file ala.top, line 256]: 67: For energy conservation with LINCS, lincs_iter should be 2 or larger. 67: 67: 67: Number of degrees of freedom in T-Coupling group rest is 54.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 67: The optimal PME mesh load for parallel simulations is below 0.5 67: and for highly parallel simulations between 0.25 and 0.33, 67: for higher performance, increase the cut-off and the PME grid spacing. 67: 67: 67: 67: There were 3 NOTEs 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 67: Can not increase nstlist because an NVE ensemble is used 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'UNNAMED in water' 67: 4 steps, 0.0 ps. 67: Setting the LD random seed to -671813797 67: 67: Generated 2211 of the 2211 non-bonded parameter combinations 67: 67: Generated 2211 of the 2211 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 67: 67: turning H bonds into constraints... 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 67: 67: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 67: Calculating fourier grid dimensions for X Y Z 67: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 67: 67: Estimate for the relative computational load of the PME mesh part: 0.94 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.111 0.056 199.4 67: (ns/day) (hour/ns) 67: Performance: 7.734 3.103 67: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 67: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 67: 67: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 67: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (577 ms) 67: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (1365 ms total) 67: 67: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest 67: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Pull group 1 'FirstWaterMolecule' has 3 atoms 67: Pull group 2 'SecondWaterMolecule' has 3 atoms 67: Number of degrees of freedom in T-Coupling group rest is 9.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: Pull group natoms pbc atom distance at start reference at t=0 67: 1 3 2 67: 2 3 5 1.112 nm 1.000 nm 67: 67: There was 1 NOTE 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'spc2' 67: 4 steps, 0.0 ps. 67: Setting the LD random seed to -16785585 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Generated 3 of the 3 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: turning H bonds into constraints... 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.171 0.086 199.6 67: (ns/day) (hour/ns) 67: Performance: 5.029 4.773 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Pull group 1 'FirstWaterMolecule' has 3 atoms 67: Pull group 2 'SecondWaterMolecule' has 3 atoms 67: Number of degrees of freedom in T-Coupling group rest is 9.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: Pull group natoms pbc atom distance at start reference at t=0 67: 1 3 2 67: 2 3 5 1.112 nm 1.000 nm 67: 67: There was 1 NOTE 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 67: Can not increase nstlist because an NVE ensemble is used 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'spc2' 67: 4 steps, 0.0 ps. 67: Setting the LD random seed to -228682833 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Generated 3 of the 3 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: turning H bonds into constraints... 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.124 0.062 199.2 67: (ns/day) (hour/ns) 67: Performance: 6.945 3.456 67: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 67: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 67: 67: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 67: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (197 ms) 67: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (197 ms total) 67: 67: [----------] 12 tests from FreezeWorks/FreezeGroupTest 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 33.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 67: NVE simulation: will use the initial temperature of 246.451 K for 67: determining the Verlet buffer size 67: 67: 67: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 5 NOTEs 67: 67: There was 1 WARNING 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.079 0.040 199.4 67: (ns/day) (hour/ns) 67: Performance: 19.623 1.223 67: 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (80 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 33.00 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 67: NVE simulation: will use the initial temperature of 246.451 K for 67: determining the Verlet buffer size 67: 67: 67: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 5 NOTEs 67: 67: There was 1 WARNING 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.727 0.363 199.9 67: (ns/day) (hour/ns) 67: Performance: 2.139 11.218 67: 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (425 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 33.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 67: NVE simulation: will use the initial temperature of 246.451 K for 67: determining the Verlet buffer size 67: 67: 67: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 5 NOTEs 67: 67: There was 1 WARNING 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.079 0.039 198.9 67: (ns/day) (hour/ns) 67: Performance: 19.703 1.218 67: 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (103 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 33.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 67: NVE simulation: will use the initial temperature of 246.451 K for 67: determining the Verlet buffer size 67: 67: 67: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 5 NOTEs 67: 67: There was 1 WARNING 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.095 0.047 199.4 67: (ns/day) (hour/ns) 67: Performance: 16.399 1.464 67: 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 (107 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 33.00 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 67: NVE simulation: will use the initial temperature of 246.451 K for 67: determining the Verlet buffer size 67: 67: 67: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 5 NOTEs 67: 67: There was 1 WARNING 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.071 0.035 199.2 67: (ns/day) (hour/ns) 67: Performance: 21.906 1.096 67: 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (83 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 67: ./src/programs/mdrun/tests/freezegroups.cpp:209: Skipped 67: Parrinello-Rahman is not implemented in md-vv. 67: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (0 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 33.00 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 4 NOTEs 67: 67: There was 1 WARNING 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.081 0.041 199.3 67: (ns/day) (hour/ns) 67: Performance: 19.094 1.257 67: 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (75 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 33.00 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 4 NOTEs 67: 67: There was 1 WARNING 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.032 0.016 198.4 67: (ns/day) (hour/ns) 67: Performance: 48.680 0.493 67: 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (67 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 33.00 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 4 NOTEs 67: 67: There was 1 WARNING 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.081 0.041 199.3 67: (ns/day) (hour/ns) 67: Performance: 19.050 1.260 67: 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 (72 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 33.00 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 4 NOTEs 67: 67: There was 1 WARNING 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.127 0.064 199.5 67: (ns/day) (hour/ns) 67: Performance: 12.241 1.961 67: 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 (207 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 33.00 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 4 NOTEs 67: 67: There was 1 WARNING 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.128 0.064 199.5 67: (ns/day) (hour/ns) 67: Performance: 12.131 1.978 67: 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 (240 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 33.00 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 4 NOTEs 67: 67: There was 1 WARNING 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.088 0.044 199.3 67: (ns/day) (hour/ns) 67: Performance: 17.655 1.359 67: 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 (147 ms) 67: [----------] 12 tests from FreezeWorks/FreezeGroupTest (1613 ms total) 67: 67: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest 67: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 67: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: Net Acceleration in X direction, will not be corrected 67: Net Acceleration in Y direction, will not be corrected 67: Net Acceleration in Z direction, will not be corrected 67: 67: There were 3 NOTEs 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'spc2' 67: 8 steps, 0.0 ps. 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Generated 3 of the 3 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Setting gen_seed to 519462783 67: 67: Velocities were taken from a Maxwell distribution at 0 K 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.079 0.040 199.4 67: (ns/day) (hour/ns) 67: Performance: 39.130 0.613 67: 67: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (58 ms) 67: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 67: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 67: Net Acceleration in X direction, will not be corrected 67: Net Acceleration in Y direction, will not be corrected 67: Net Acceleration in Z direction, will not be corrected 67: 67: There were 3 NOTEs 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Can not increase nstlist because verlet-buffer-tolerance is not set or used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'spc2' 67: 8 steps, 0.0 ps. 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Generated 3 of the 3 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Setting gen_seed to 1660810879 67: 67: Velocities were taken from a Maxwell distribution at 0 K 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.055 0.027 199.2 67: (ns/day) (hour/ns) 67: Performance: 56.634 0.424 67: 67: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (63 ms) 67: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 67: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: Net Acceleration in X direction, will not be corrected 67: Net Acceleration in Y direction, will not be corrected 67: Net Acceleration in Z direction, will not be corrected 67: 67: There were 3 NOTEs 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'spc2' 67: 8 steps, 0.0 ps. 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Generated 3 of the 3 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Setting gen_seed to 855473201 67: 67: Velocities were taken from a Maxwell distribution at 0 K 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.037 0.018 198.9 67: (ns/day) (hour/ns) 67: Performance: 84.199 0.285 67: 67: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 (36 ms) 67: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 67: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 67: Net Acceleration in X direction, will not be corrected 67: Net Acceleration in Y direction, will not be corrected 67: Net Acceleration in Z direction, will not be corrected 67: 67: There were 3 NOTEs 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Can not increase nstlist because verlet-buffer-tolerance is not set or used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'spc2' 67: 8 steps, 0.0 ps. 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Generated 3 of the 3 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Setting gen_seed to 2129072127 67: 67: Velocities were taken from a Maxwell distribution at 0 K 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.047 0.024 199.0 67: (ns/day) (hour/ns) 67: Performance: 65.375 0.367 67: 67: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (48 ms) 67: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (207 ms total) 67: 67: [----------] Global test environment tear-down 67: [==========] 29 tests from 8 test suites ran. (7926 ms total) 67: [ PASSED ] 28 tests. 67: [ SKIPPED ] 1 test, listed below: 67: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 67/90 Test #67: MdrunTestsOneRank ......................... Passed 7.99 sec test 68 Start 68: MdrunTestsTwoRanks 68: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/mdrun-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/MdrunTestsTwoRanks.xml" 68: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests 68: Test timeout computed to be: 600 68: [==========] Running 29 tests from 8 test suites. 68: [----------] Global test environment set-up. 68: [----------] 1 test from CompelTest 68: [ RUN ] CompelTest.SwapCanRun 68: Generating 1-4 interactions: fudge = 0.5 68: Split0 group 'Ch0' contains 83 atoms. 68: Split1 group 'Ch1' contains 83 atoms. 68: Solvent group 'SOL' contains 11931 atoms. 68: Swap group 'NA+' contains 19 atoms. 68: Swap group 'CL-' contains 19 atoms. 68: Number of degrees of freedom in T-Coupling group System is 27869.00 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 68: Removing center of mass motion in the presence of position restraints 68: might cause artifacts. When you are using position restraints to 68: equilibrate a macro-molecule, the artifacts are usually negligible. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 2 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Update groups can not be used for this system because there are three or more consecutively coupled constraints 68: 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: SWAP: Determining initial numbers of ions per compartment. 68: SWAP: Setting pointers for checkpoint writing 68: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 68: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 68: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 68: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 68: starting mdrun 'Channel_coco in octane membrane' 68: 2 steps, 0.0 ps. 68: Setting the LD random seed to -239405573 68: 68: Generated 330891 of the 330891 non-bonded parameter combinations 68: 68: Generated 330891 of the 330891 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Protein' 68: 68: turning all bonds into constraints... 68: 68: Excluding 3 bonded neighbours molecule type 'OCT' 68: 68: turning all bonds into constraints... 68: 68: Excluding 1 bonded neighbours molecule type 'NA' 68: 68: turning all bonds into constraints... 68: 68: Excluding 1 bonded neighbours molecule type 'CL' 68: 68: turning all bonds into constraints... 68: 68: Excluding 3 bonded neighbours molecule type 'Protein' 68: 68: Excluding 3 bonded neighbours molecule type 'OCT' 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/OctaneSandwich.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.316 nm, buffer size 0.316 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.262 nm, buffer size 0.262 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 1 Mb of data 68: 68: Writing final coordinates. 68: 68: 68: Dynamic load balancing report: 68: DLB was off during the run due to low measured imbalance. 68: Average load imbalance: 29.0%. 68: The balanceable part of the MD step is 15%, load imbalance is computed from this. 68: Part of the total run time spent waiting due to load imbalance: 4.2%. 68: 68: 68: NOTE: 18 % of the run time was spent in domain decomposition, 68: 26 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 1.734 0.441 393.0 68: (ns/day) (hour/ns) 68: Performance: 2.937 8.171 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps 68: 68: Update groups can not be used for this system because there are three or more consecutively coupled constraints 68: 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: SWAP: Setting pointers for checkpoint writing 68: SWAP: Copying channel fluxes from checkpoint file data 68: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 68: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 68: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 68: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 68: starting mdrun 'Channel_coco in octane membrane' 68: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 16 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 1.458 0.365 399.8 68: (ns/day) (hour/ns) 68: Performance: 3.554 6.753 68: [ OK ] CompelTest.SwapCanRun (2005 ms) 68: [----------] 1 test from CompelTest (2006 ms total) 68: 68: [----------] 6 tests from BondedInteractionsTest 68: [ RUN ] BondedInteractionsTest.NormalBondWorks 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 68: For a correct single-point energy evaluation with nsteps = 0, use 68: continuation = yes to avoid constraining the input coordinates. 68: 68: 68: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: 68: In moleculetype 'butane' 2 atoms are not bound by a potential or 68: constraint to any other atom in the same moleculetype. Although 68: technically this might not cause issues in a simulation, this often means 68: that the user forgot to add a bond/potential/constraint or put multiple 68: molecules in the same moleculetype definition by mistake. Run with -v to 68: get information for each atom. 68: 68: Number of degrees of freedom in T-Coupling group rest is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 68: NVE simulation with an initial temperature of zero: will use a Verlet 68: buffer of 10%. Check your energy drift! 68: 68: 68: There were 3 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 68: 68: Reading frames from gro file 'A single butane', 4 atoms. 68: Reading frame 0 time 0.000 Last frame 0 time 0.000 68: 68: NOTE: 20 % of the run time was spent in domain decomposition, 68: 16 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: NOTE: 6 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.002 0.001 381.4 68: (ns/day) (hour/ns) 68: Performance: 165.701 0.145 68: Setting the LD random seed to -14682477 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'butane' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] BondedInteractionsTest.NormalBondWorks (33 ms) 68: [ RUN ] BondedInteractionsTest.TabulatedBondWorks 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 68: For a correct single-point energy evaluation with nsteps = 0, use 68: continuation = yes to avoid constraining the input coordinates. 68: 68: 68: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: 68: In moleculetype 'butane' 2 atoms are not bound by a potential or 68: constraint to any other atom in the same moleculetype. Although 68: technically this might not cause issues in a simulation, this often means 68: that the user forgot to add a bond/potential/constraint or put multiple 68: molecules in the same moleculetype definition by mistake. Run with -v to 68: get information for each atom. 68: 68: Number of degrees of freedom in T-Coupling group rest is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 68: NVE simulation with an initial temperature of zero: will use a Verlet 68: buffer of 10%. Check your energy drift! 68: 68: 68: There were 3 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 68: 68: Reading frames from gro file 'A single butane', 4 atoms. 68: Reading frame 0 time 0.000 Last frame 0 time 0.000 68: 68: NOTE: 21 % of the run time was spent in domain decomposition, 68: 17 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: NOTE: 6 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.002 0.001 377.5 68: (ns/day) (hour/ns) 68: Performance: 143.805 0.167 68: Setting the LD random seed to -68158612 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'butane' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] BondedInteractionsTest.TabulatedBondWorks (203 ms) 68: [ RUN ] BondedInteractionsTest.NormalAngleWorks 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 68: For a correct single-point energy evaluation with nsteps = 0, use 68: continuation = yes to avoid constraining the input coordinates. 68: 68: 68: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: 68: In moleculetype 'butane' 4 atoms are not bound by a potential or 68: constraint to any other atom in the same moleculetype. Although 68: technically this might not cause issues in a simulation, this often means 68: that the user forgot to add a bond/potential/constraint or put multiple 68: molecules in the same moleculetype definition by mistake. Run with -v to 68: get information for each atom. 68: 68: Number of degrees of freedom in T-Coupling group rest is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 68: NVE simulation with an initial temperature of zero: will use a Verlet 68: buffer of 10%. Check your energy drift! 68: 68: 68: There were 3 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 68: 68: Reading frames from gro file 'A single butane', 4 atoms. 68: Reading frame 0 time 0.000 Last frame 0 time 0.000 68: 68: NOTE: 23 % of the run time was spent in domain decomposition, 68: 13 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.003 0.001 380.2 68: (ns/day) (hour/ns) 68: Performance: 102.645 0.234 68: Setting the LD random seed to -33642501 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'butane' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] BondedInteractionsTest.NormalAngleWorks (147 ms) 68: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 68: For a correct single-point energy evaluation with nsteps = 0, use 68: continuation = yes to avoid constraining the input coordinates. 68: 68: 68: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: 68: In moleculetype 'butane' 4 atoms are not bound by a potential or 68: constraint to any other atom in the same moleculetype. Although 68: technically this might not cause issues in a simulation, this often means 68: that the user forgot to add a bond/potential/constraint or put multiple 68: molecules in the same moleculetype definition by mistake. Run with -v to 68: get information for each atom. 68: 68: Number of degrees of freedom in T-Coupling group rest is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 68: NVE simulation with an initial temperature of zero: will use a Verlet 68: buffer of 10%. Check your energy drift! 68: 68: 68: There were 3 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 68: 68: Reading frames from gro file 'A single butane', 4 atoms. 68: Reading frame 0 time 0.000 Last frame 0 time 0.000 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.028 0.007 398.1 68: (ns/day) (hour/ns) 68: Performance: 12.332 1.946 68: Setting the LD random seed to 2055184366 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'butane' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (237 ms) 68: [ RUN ] BondedInteractionsTest.NormalDihedralWorks 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 68: For a correct single-point energy evaluation with nsteps = 0, use 68: continuation = yes to avoid constraining the input coordinates. 68: 68: 68: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]: 68: In moleculetype 'butane' 4 atoms are not bound by a potential or 68: constraint to any other atom in the same moleculetype. Although 68: technically this might not cause issues in a simulation, this often means 68: that the user forgot to add a bond/potential/constraint or put multiple 68: molecules in the same moleculetype definition by mistake. Run with -v to 68: get information for each atom. 68: 68: Number of degrees of freedom in T-Coupling group rest is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 68: NVE simulation with an initial temperature of zero: will use a Verlet 68: buffer of 10%. Check your energy drift! 68: 68: 68: There were 3 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 68: 68: Reading frames from gro file 'A single butane', 4 atoms. 68: Reading frame 0 time 0.000 Last frame 0 time 0.000 68: 68: NOTE: 13 % of the run time was spent in domain decomposition, 68: 11 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.004 0.001 378.8 68: (ns/day) (hour/ns) 68: Performance: 85.550 0.281 68: Setting the LD random seed to 2074984390 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'butane' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] BondedInteractionsTest.NormalDihedralWorks (36 ms) 68: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 68: For a correct single-point energy evaluation with nsteps = 0, use 68: continuation = yes to avoid constraining the input coordinates. 68: 68: 68: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]: 68: In moleculetype 'butane' 4 atoms are not bound by a potential or 68: constraint to any other atom in the same moleculetype. Although 68: technically this might not cause issues in a simulation, this often means 68: that the user forgot to add a bond/potential/constraint or put multiple 68: molecules in the same moleculetype definition by mistake. Run with -v to 68: get information for each atom. 68: 68: Number of degrees of freedom in T-Coupling group rest is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 68: NVE simulation with an initial temperature of zero: will use a Verlet 68: buffer of 10%. Check your energy drift! 68: 68: 68: There were 3 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 68: 68: Reading frames from gro file 'A single butane', 4 atoms. 68: Reading frame 0 time 0.000 Last frame 0 time 0.000 68: 68: NOTE: 19 % of the run time was spent in domain decomposition, 68: 13 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.002 0.001 368.9 68: (ns/day) (hour/ns) 68: Performance: 131.086 0.183 68: Setting the LD random seed to 2142970727 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'butane' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (61 ms) 68: [----------] 6 tests from BondedInteractionsTest (720 ms total) 68: 68: [----------] 2 tests from BoxDeformationTest 68: [ RUN ] BoxDeformationTest.flowDoesNotAffectEkin 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 68: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 68: < 0 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (10) 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 68: For a correct single-point energy evaluation with nsteps = 0, use 68: continuation = yes to avoid constraining the input coordinates. 68: 68: Number of degrees of freedom in T-Coupling group rest is 33.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: There were 3 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 0 steps, 0.0 ps. 68: 68: NOTE: 28 % of the run time was spent in domain decomposition, 68: 18 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.002 0.001 324.3 68: (ns/day) (hour/ns) 68: Performance: 251.353 0.095 68: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 2070457959 68: 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Setting gen_seed to -536873001 68: 68: Velocities were taken from a Maxwell distribution at 0 K 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] BoxDeformationTest.flowDoesNotAffectEkin (65 ms) 68: [ RUN ] BoxDeformationTest.EnergiesWithinTolerances 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 68: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 68: < 0 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (10) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group rest is 1293.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: There were 2 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 20 steps, 0.0 ps. 68: Setting the LD random seed to 1005812890 68: 68: Generated 330891 of the 330891 non-bonded parameter combinations 68: 68: Generated 330891 of the 330891 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc216.gro' 68: 68: The largest distance between excluded atoms is 0.152 nm between atom 41 and 42 68: Calculating fourier grid dimensions for X Y Z 68: Using a fourier grid of 16x16x16, spacing 0.116 0.116 0.116 68: 68: Estimate for the relative computational load of the PME mesh part: 0.20 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: 68: Dynamic load balancing report: 68: DLB was off during the run due to low measured imbalance. 68: Average load imbalance: 34.0%. 68: The balanceable part of the MD step is 3%, load imbalance is computed from this. 68: Part of the total run time spent waiting due to load imbalance: 1.1%. 68: 68: 68: Core t (s) Wall t (s) (%) 68: Time: 1.767 0.442 399.8 68: (ns/day) (hour/ns) 68: Performance: 8.212 2.923 68: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Reading energy frame 2 time 0.040 Last energy frame read 2 time 0.040 [ OK ] BoxDeformationTest.EnergiesWithinTolerances (1137 ms) 68: [----------] 2 tests from BoxDeformationTest (1203 ms total) 68: 68: [----------] 1 test from PositionRestraintCommTest 68: [ RUN ] PositionRestraintCommTest.PositionRestraintsTwoCOMs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 68: You have set rlist larger than the interaction cut-off, but you also have 68: verlet-buffer-tolerance > 0. Will set rlist using 68: verlet-buffer-tolerance. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (10) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 68: 13489 atoms are not part of any of the VCM groups 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 68: 13489 atoms are not part of any center of mass motion removal group. 68: This may lead to artifacts. 68: In most cases one should use one group for the whole system. 68: 68: Number of degrees of freedom in T-Coupling group System is 29527.73 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 68: Removing center of mass motion in the presence of position restraints 68: might cause artifacts. When you are using position restraints to 68: equilibrate a macro-molecule, the artifacts are usually negligible. 68: 68: 68: There were 4 NOTEs 68: 68: There was 1 WARNING 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 10 to 20, rlist from 0.965 to 1.066 68: 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Channel_coco in octane membrane' 68: 10 steps, 0.0 ps. 68: Setting the LD random seed to -1365811233 68: 68: Generated 330891 of the 330891 non-bonded parameter combinations 68: 68: Generated 330891 of the 330891 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Protein' 68: 68: Excluding 3 bonded neighbours molecule type 'OCT' 68: 68: Excluding 1 bonded neighbours molecule type 'NA' 68: 68: Excluding 1 bonded neighbours molecule type 'CL' 68: 68: Excluding 3 bonded neighbours molecule type 'Protein' 68: 68: Excluding 3 bonded neighbours molecule type 'OCT' 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/OctaneSandwich.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.990 nm, buffer size 0.090 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.965 nm, buffer size 0.065 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: Chain0: 2.207 2.168 7.330 68: Chain1: 2.228 2.186 2.401 68: Chain0: 2.207 2.168 7.330 68: Chain1: 2.228 2.186 2.401 68: 68: This run will generate roughly 1 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 18 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.889 0.223 399.6 68: (ns/day) (hour/ns) 68: Performance: 8.542 2.809 68: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Last energy frame read 1 time 0.020 [ OK ] PositionRestraintCommTest.PositionRestraintsTwoCOMs (1522 ms) 68: [----------] 1 test from PositionRestraintCommTest (1522 ms total) 68: 68: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest 68: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 68: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 68: < 0 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 2 [file ala.top, line 256]: 68: For energy conservation with LINCS, lincs_iter should be 2 or larger. 68: 68: 68: Number of degrees of freedom in T-Coupling group rest is 54.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 68: The optimal PME mesh load for parallel simulations is below 0.5 68: and for highly parallel simulations between 0.25 and 0.33, 68: for higher performance, increase the cut-off and the PME grid spacing. 68: 68: 68: 68: There were 3 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'UNNAMED in water' 68: 4 steps, 0.0 ps. 68: Setting the LD random seed to 2080374763 68: 68: Generated 2211 of the 2211 non-bonded parameter combinations 68: 68: Generated 2211 of the 2211 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 68: 68: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 68: Calculating fourier grid dimensions for X Y Z 68: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 68: 68: Estimate for the relative computational load of the PME mesh part: 0.94 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 21 % of the run time was spent in domain decomposition, 68: 0 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: NOTE: 28 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.977 0.245 399.5 68: (ns/day) (hour/ns) 68: Performance: 1.767 13.585 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 68: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 68: < 0 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 2 [file ala.top, line 256]: 68: For energy conservation with LINCS, lincs_iter should be 2 or larger. 68: 68: 68: Number of degrees of freedom in T-Coupling group rest is 54.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 68: The optimal PME mesh load for parallel simulations is below 0.5 68: and for highly parallel simulations between 0.25 and 0.33, 68: for higher performance, increase the cut-off and the PME grid spacing. 68: 68: 68: 68: There were 3 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'UNNAMED in water' 68: 4 steps, 0.0 ps. 68: Setting the LD random seed to -697434657 68: 68: Generated 2211 of the 2211 non-bonded parameter combinations 68: 68: Generated 2211 of the 2211 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 68: 68: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 68: Calculating fourier grid dimensions for X Y Z 68: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 68: 68: Estimate for the relative computational load of the PME mesh part: 0.94 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 39 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.096 0.024 397.6 68: (ns/day) (hour/ns) 68: Performance: 17.946 1.337 68: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 trr version: GMX_trn_file (single precision) 68: 68: 68: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (975 ms) 68: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 68: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 68: < 0 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 2 [file ala.top, line 256]: 68: For energy conservation with LINCS, lincs_iter should be 2 or larger. 68: 68: 68: Number of degrees of freedom in T-Coupling group rest is 54.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 68: The optimal PME mesh load for parallel simulations is below 0.5 68: and for highly parallel simulations between 0.25 and 0.33, 68: for higher performance, increase the cut-off and the PME grid spacing. 68: 68: 68: 68: There were 3 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'UNNAMED in water' 68: 4 steps, 0.0 ps. 68: Setting the LD random seed to -2105347 68: 68: Generated 2211 of the 2211 non-bonded parameter combinations 68: 68: Generated 2211 of the 2211 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 68: 68: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 68: Calculating fourier grid dimensions for X Y Z 68: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 68: 68: Estimate for the relative computational load of the PME mesh part: 0.94 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 62 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.239 0.078 307.9 68: (ns/day) (hour/ns) 68: Performance: 5.571 4.308 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 68: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 68: < 0 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 2 [file ala.top, line 256]: 68: For energy conservation with LINCS, lincs_iter should be 2 or larger. 68: 68: 68: Number of degrees of freedom in T-Coupling group rest is 54.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 68: The optimal PME mesh load for parallel simulations is below 0.5 68: and for highly parallel simulations between 0.25 and 0.33, 68: for higher performance, increase the cut-off and the PME grid spacing. 68: 68: 68: 68: There were 3 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 68: Can not increase nstlist because an NVE ensemble is used 68: 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'UNNAMED in water' 68: 4 steps, 0.0 ps. 68: Setting the LD random seed to -1746109265 68: 68: Generated 2211 of the 2211 non-bonded parameter combinations 68: 68: Generated 2211 of the 2211 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 68: 68: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 68: Calculating fourier grid dimensions for X Y Z 68: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 68: 68: Estimate for the relative computational load of the PME mesh part: 0.94 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 25 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.275 0.069 398.8 68: (ns/day) (hour/ns) 68: Performance: 6.259 3.834 68: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 68: 68: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (416 ms) 68: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (1392 ms total) 68: 68: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest 68: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 68: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 68: < 0 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Pull group 1 'FirstWaterMolecule' has 3 atoms 68: Pull group 2 'SecondWaterMolecule' has 3 atoms 68: Number of degrees of freedom in T-Coupling group rest is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 3 2 68: 2 3 5 1.112 nm 1.000 nm 68: 68: There was 1 NOTE 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 4 steps, 0.0 ps. 68: Setting the LD random seed to 973068222 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 49 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.254 0.064 398.5 68: (ns/day) (hour/ns) 68: Performance: 6.789 3.535 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 68: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 68: < 0 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Pull group 1 'FirstWaterMolecule' has 3 atoms 68: Pull group 2 'SecondWaterMolecule' has 3 atoms 68: Number of degrees of freedom in T-Coupling group rest is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 3 2 68: 2 3 5 1.112 nm 1.000 nm 68: 68: There was 1 NOTE 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 68: Can not increase nstlist because an NVE ensemble is used 68: 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 4 steps, 0.0 ps. 68: Setting the LD random seed to -1092620673 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 23 % of the run time was spent in domain decomposition, 68: 0 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: NOTE: 26 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.776 0.194 399.5 68: (ns/day) (hour/ns) 68: Performance: 2.223 10.797 68: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 68: 68: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (509 ms) 68: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (509 ms total) 68: 68: [----------] 12 tests from FreezeWorks/FreezeGroupTest 68: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 68: There are 5 atoms that are fully frozen and part of COMM removal 68: group(s), removing these atoms from the COMM removal group(s) 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 68: There are 3 atoms that are frozen along less then 3 dimensions and part 68: of COMM removal group(s), due to limitations in the code these still 68: contribute to the mass of the COM along frozen dimensions and therefore 68: the COMM correction will be too small. 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 246.451 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: 68: There was 1 WARNING 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 8 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: 68: Dynamic load balancing report: 68: DLB was off during the run due to low measured imbalance. 68: Average load imbalance: 12.3%. 68: The balanceable part of the MD step is 41%, load imbalance is computed from this. 68: Part of the total run time spent waiting due to load imbalance: 5.1%. 68: 68: NOTE: 5.1 % of the available CPU time was lost due to load imbalance 68: in the domain decomposition. 68: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 68: You can also consider manually changing the decomposition (option -dd); 68: e.g. by using fewer domains along the box dimension in which there is 68: considerable inhomogeneity in the simulated system. 68: 68: NOTE: 45 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.129 0.034 381.2 68: (ns/day) (hour/ns) 68: Performance: 22.892 1.048 68: 68: 68: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (189 ms) 68: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 68: There are 5 atoms that are fully frozen and part of COMM removal 68: group(s), removing these atoms from the COMM removal group(s) 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 68: There are 3 atoms that are frozen along less then 3 dimensions and part 68: of COMM removal group(s), due to limitations in the code these still 68: contribute to the mass of the COM along frozen dimensions and therefore 68: the COMM correction will be too small. 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 246.451 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: 68: There was 1 WARNING 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 8 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: 68: Dynamic load balancing report: 68: DLB was off during the run due to low measured imbalance. 68: Average load imbalance: 12.7%. 68: The balanceable part of the MD step is 42%, load imbalance is computed from this. 68: Part of the total run time spent waiting due to load imbalance: 5.4%. 68: 68: NOTE: 5.4 % of the available CPU time was lost due to load imbalance 68: in the domain decomposition. 68: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 68: You can also consider manually changing the decomposition (option -dd); 68: e.g. by using fewer domains along the box dimension in which there is 68: considerable inhomogeneity in the simulated system. 68: 68: NOTE: 47 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.193 0.054 357.9 68: (ns/day) (hour/ns) 68: Performance: 14.427 1.664 68: 68: 68: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (105 ms) 68: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 68: There are 5 atoms that are fully frozen and part of COMM removal 68: group(s), removing these atoms from the COMM removal group(s) 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 68: There are 3 atoms that are frozen along less then 3 dimensions and part 68: of COMM removal group(s), due to limitations in the code these still 68: contribute to the mass of the COM along frozen dimensions and therefore 68: the COMM correction will be too small. 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 68: NVE simulation: will use the initial temperature of 246.451 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: 68: There was 1 WARNING 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 8 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: 68: Dynamic load balancing report: 68: DLB was off during the run due to low measured imbalance. 68: Average load imbalance: 22.1%. 68: The balanceable part of the MD step is 44%, load imbalance is computed from this. 68: Part of the total run time spent waiting due to load imbalance: 9.8%. 68: 68: NOTE: 9.8 % of the available CPU time was lost due to load imbalance 68: in the domain decomposition. 68: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 68: You can also consider manually changing the decomposition (option -dd); 68: e.g. by using fewer domains along the box dimension in which there is 68: considerable inhomogeneity in the simulated system. 68: 68: NOTE: 41 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.055 0.015 375.3 68: (ns/day) (hour/ns) 68: Performance: 53.347 0.450 68: 68: 68: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (167 ms) 68: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 68: There are 5 atoms that are fully frozen and part of COMM removal 68: group(s), removing these atoms from the COMM removal group(s) 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 68: There are 3 atoms that are frozen along less then 3 dimensions and part 68: of COMM removal group(s), due to limitations in the code these still 68: contribute to the mass of the COM along frozen dimensions and therefore 68: the COMM correction will be too small. 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 68: NVE simulation: will use the initial temperature of 246.451 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: 68: There was 1 WARNING 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 8 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: 68: Dynamic load balancing report: 68: DLB was off during the run due to low measured imbalance. 68: Average load imbalance: 10.5%. 68: The balanceable part of the MD step is 49%, load imbalance is computed from this. 68: Part of the total run time spent waiting due to load imbalance: 5.2%. 68: 68: NOTE: 5.2 % of the available CPU time was lost due to load imbalance 68: in the domain decomposition. 68: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 68: You can also consider manually changing the decomposition (option -dd); 68: e.g. by using fewer domains along the box dimension in which there is 68: considerable inhomogeneity in the simulated system. 68: 68: NOTE: 47 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.106 0.027 397.0 68: (ns/day) (hour/ns) 68: Performance: 28.998 0.828 68: 68: 68: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 (67 ms) 68: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 68: There are 5 atoms that are fully frozen and part of COMM removal 68: group(s), removing these atoms from the COMM removal group(s) 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 68: There are 3 atoms that are frozen along less then 3 dimensions and part 68: of COMM removal group(s), due to limitations in the code these still 68: contribute to the mass of the COM along frozen dimensions and therefore 68: the COMM correction will be too small. 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 68: NVE simulation: will use the initial temperature of 246.451 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: 68: There was 1 WARNING 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 8 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: 68: Dynamic load balancing report: 68: DLB was off during the run due to low measured imbalance. 68: Average load imbalance: 11.4%. 68: The balanceable part of the MD step is 48%, load imbalance is computed from this. 68: Part of the total run time spent waiting due to load imbalance: 5.5%. 68: 68: NOTE: 5.5 % of the available CPU time was lost due to load imbalance 68: in the domain decomposition. 68: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 68: You can also consider manually changing the decomposition (option -dd); 68: e.g. by using fewer domains along the box dimension in which there is 68: considerable inhomogeneity in the simulated system. 68: 68: NOTE: 45 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.053 0.013 395.9 68: (ns/day) (hour/ns) 68: Performance: 58.380 0.411 68: 68: 68: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (68 ms) 68: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 68: ./src/programs/mdrun/tests/freezegroups.cpp:209: Skipped 68: Parrinello-Rahman is not implemented in md-vv. 68: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (0 ms) 68: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 68: There are 5 atoms that are fully frozen and part of COMM removal 68: group(s), removing these atoms from the COMM removal group(s) 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 68: There are 3 atoms that are frozen along less then 3 dimensions and part 68: of COMM removal group(s), due to limitations in the code these still 68: contribute to the mass of the COM along frozen dimensions and therefore 68: the COMM correction will be too small. 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: There was 1 WARNING 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 68: 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 8 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 46 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.188 0.049 385.8 68: (ns/day) (hour/ns) 68: Performance: 15.986 1.501 68: 68: 68: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (154 ms) 68: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 68: There are 5 atoms that are fully frozen and part of COMM removal 68: group(s), removing these atoms from the COMM removal group(s) 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 68: There are 3 atoms that are frozen along less then 3 dimensions and part 68: of COMM removal group(s), due to limitations in the code these still 68: contribute to the mass of the COM along frozen dimensions and therefore 68: the COMM correction will be too small. 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: There was 1 WARNING 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 68: 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 8 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 41 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.109 0.035 314.4 68: (ns/day) (hour/ns) 68: Performance: 22.508 1.066 68: 68: 68: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (100 ms) 68: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 68: There are 5 atoms that are fully frozen and part of COMM removal 68: group(s), removing these atoms from the COMM removal group(s) 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 68: There are 3 atoms that are frozen along less then 3 dimensions and part 68: of COMM removal group(s), due to limitations in the code these still 68: contribute to the mass of the COM along frozen dimensions and therefore 68: the COMM correction will be too small. 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: There was 1 WARNING 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 68: 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 8 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 10 % of the run time was spent in domain decomposition, 68: 0 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: NOTE: 27 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 1.448 0.365 397.1 68: (ns/day) (hour/ns) 68: Performance: 2.132 11.255 68: 68: 68: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 (520 ms) 68: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 68: There are 5 atoms that are fully frozen and part of COMM removal 68: group(s), removing these atoms from the COMM removal group(s) 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 68: There are 3 atoms that are frozen along less then 3 dimensions and part 68: of COMM removal group(s), due to limitations in the code these still 68: contribute to the mass of the COM along frozen dimensions and therefore 68: the COMM correction will be too small. 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: There was 1 WARNING 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 68: 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 8 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 57 % of the run time was spent in domain decomposition, 68: 0 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: NOTE: 13 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.223 0.056 398.9 68: (ns/day) (hour/ns) 68: Performance: 13.923 1.724 68: 68: 68: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 (247 ms) 68: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 68: There are 5 atoms that are fully frozen and part of COMM removal 68: group(s), removing these atoms from the COMM removal group(s) 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 68: There are 3 atoms that are frozen along less then 3 dimensions and part 68: of COMM removal group(s), due to limitations in the code these still 68: contribute to the mass of the COM along frozen dimensions and therefore 68: the COMM correction will be too small. 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: There was 1 WARNING 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 68: 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 8 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 44 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 6.284 1.575 399.0 68: (ns/day) (hour/ns) 68: Performance: 0.494 48.614 68: 68: 68: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 (1996 ms) 68: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 68: There are 5 atoms that are fully frozen and part of COMM removal 68: group(s), removing these atoms from the COMM removal group(s) 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 68: There are 3 atoms that are frozen along less then 3 dimensions and part 68: of COMM removal group(s), due to limitations in the code these still 68: contribute to the mass of the COM along frozen dimensions and therefore 68: the COMM correction will be too small. 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: There was 1 WARNING 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 68: 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 8 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 39 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 3.609 0.908 397.5 68: (ns/day) (hour/ns) 68: Performance: 0.856 28.022 68: 68: 68: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 (1250 ms) 68: [----------] 12 tests from FreezeWorks/FreezeGroupTest (4868 ms total) 68: 68: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest 68: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 68: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 68: < 0 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 68: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: Net Acceleration in X direction, will not be corrected 68: Net Acceleration in Y direction, will not be corrected 68: Net Acceleration in Z direction, will not be corrected 68: 68: There were 3 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Setting gen_seed to -570568709 68: 68: Velocities were taken from a Maxwell distribution at 0 K 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: 68: Dynamic load balancing report: 68: DLB was off during the run due to low measured imbalance. 68: Average load imbalance: 2.0%. 68: The balanceable part of the MD step is 44%, load imbalance is computed from this. 68: Part of the total run time spent waiting due to load imbalance: 0.9%. 68: 68: 68: NOTE: 50 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 3.645 0.912 399.9 68: (ns/day) (hour/ns) 68: Performance: 1.706 14.067 68: 68: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (1096 ms) 68: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 68: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 68: < 0 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 68: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 68: Net Acceleration in X direction, will not be corrected 68: Net Acceleration in Y direction, will not be corrected 68: Net Acceleration in Z direction, will not be corrected 68: 68: There were 3 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because verlet-buffer-tolerance is not set or used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Setting gen_seed to -71368739 68: 68: Velocities were taken from a Maxwell distribution at 0 K 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: 68: Dynamic load balancing report: 68: DLB was off during the run due to low measured imbalance. 68: Average load imbalance: 1.2%. 68: The balanceable part of the MD step is 38%, load imbalance is computed from this. 68: Part of the total run time spent waiting due to load imbalance: 0.5%. 68: 68: 68: NOTE: 50 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 3.922 0.981 399.9 68: (ns/day) (hour/ns) 68: Performance: 1.586 15.133 68: 68: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (1220 ms) 68: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 68: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 68: < 0 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 68: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: Net Acceleration in X direction, will not be corrected 68: Net Acceleration in Y direction, will not be corrected 68: Net Acceleration in Z direction, will not be corrected 68: 68: There were 3 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Setting gen_seed to -20031141 68: 68: Velocities were taken from a Maxwell distribution at 0 K 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: 68: Dynamic load balancing report: 68: DLB was off during the run due to low measured imbalance. 68: Average load imbalance: 2.5%. 68: The balanceable part of the MD step is 35%, load imbalance is computed from this. 68: Part of the total run time spent waiting due to load imbalance: 0.9%. 68: 68: 68: NOTE: 50 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 1.166 0.292 399.7 68: (ns/day) (hour/ns) 68: Performance: 5.333 4.500 68: 68: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 (866 ms) 68: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 68: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 68: < 0 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 68: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 68: Net Acceleration in X direction, will not be corrected 68: Net Acceleration in Y direction, will not be corrected 68: Net Acceleration in Z direction, will not be corrected 68: 68: There were 3 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because verlet-buffer-tolerance is not set or used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Setting gen_seed to -806430241 68: 68: Velocities were taken from a Maxwell distribution at 0 K 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: 68: Dynamic load balancing report: 68: DLB was off during the run due to low measured imbalance. 68: Average load imbalance: 1.7%. 68: The balanceable part of the MD step is 10%, load imbalance is computed from this. 68: Part of the total run time spent waiting due to load imbalance: 0.2%. 68: 68: 68: NOTE: 17 % of the run time was spent in domain decomposition, 68: 3 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: NOTE: 38 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.235 0.059 398.7 68: (ns/day) (hour/ns) 68: Performance: 26.341 0.911 68: 68: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (131 ms) 68: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (3314 ms total) 68: 68: [----------] Global test environment tear-down 68: [==========] 29 tests from 8 test suites ran. (16854 ms total) 68: [ PASSED ] 28 tests. 68: [ SKIPPED ] 1 test, listed below: 68: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 68/90 Test #68: MdrunTestsTwoRanks ........................ Passed 16.91 sec test 69 Start 69: MdrunSingleRankAlgorithmsTests 69: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/mdrun-single-rank-algorithms-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/MdrunSingleRankAlgorithmsTests.xml" 69: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests 69: Test timeout computed to be: 600 69: [==========] Running 5 tests from 3 test suites. 69: [----------] Global test environment set-up. 69: [----------] 1 test from DispersionCorrectionTest 69: [ RUN ] DispersionCorrectionTest.DispersionCorrectionCanRun 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 30.00 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]: 69: There are 9 non-linear virtual site constructions. Their contribution to 69: the energy error is approximated. In most cases this does not affect the 69: error significantly. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 2 NOTEs 69: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Changing nstlist from 10 to 40, rlist from 1.023 to 1.158 69: 69: Update groups can not be used for this system because an incompatible virtual site type is used 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine dipeptide in vacuo' 69: 200 steps, 0.4 ps. 69: Setting the LD random seed to -1343819969 69: 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 69: 69: Cleaning up constraints and constant bonded interactions with virtual sites 69: 69: Converted 3 Bonds with virtual sites to connections, 7 left 69: 69: Removed 18 Angles with virtual sites, 21 left 69: 69: Removed 10 Proper Dih.s with virtual sites, 44 left 69: 69: Converted 12 Constraints with virtual sites to connections, 0 left 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 69: 69: Calculated rlist for 1x1 atom pair-list as 1.038 nm, buffer size 0.038 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 1.023 nm, buffer size 0.023 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.231 0.116 199.8 69: (ns/day) (hour/ns) 69: Performance: 300.140 0.080 69: [ OK ] DispersionCorrectionTest.DispersionCorrectionCanRun (244 ms) 69: [----------] 1 test from DispersionCorrectionTest (244 ms total) 69: 69: [----------] 1 test from OriresTest 69: [ RUN ] OriresTest.OriresCanRun 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 518.00 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There was 1 NOTE 69: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Orientation restraints only supports a single rank. Choosing to use only a single thread-MPI rank. 69: Changing nstlist from 10 to 25, rlist from 1.07 to 1.203 69: 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-1' 69: 10 steps, 0.0 ps. 69: Setting the LD random seed to 1207434223 69: 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/orires_1lvz.gro' 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 69: 69: Calculated rlist for 1x1 atom pair-list as 1.093 nm, buffer size 0.093 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 1.070 nm, buffer size 0.070 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.103 0.051 199.3 69: (ns/day) (hour/ns) 69: Performance: 36.943 0.650 69: [ OK ] OriresTest.OriresCanRun (993 ms) 69: [----------] 1 test from OriresTest (993 ms total) 69: 69: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest 69: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 69: Number of degrees of freedom in T-Coupling group rest is 10.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]: 69: NVE simulation with an initial temperature of zero: will use a Verlet 69: buffer of 10%. Check your energy drift! 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]: 69: The optimal PME mesh load for parallel simulations is below 0.5 69: and for highly parallel simulations between 0.25 and 0.33, 69: for higher performance, increase the cut-off and the PME grid spacing. 69: 69: 69: 69: There were 2 NOTEs 69: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Dipoles' 69: 20 steps, 0.1 ps. 69: Setting the LD random seed to -805348226 69: 69: Generated 1 of the 1 non-bonded parameter combinations 69: 69: Excluding 1 bonded neighbours molecule type 'Dipole' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/dipoles.gro', all velocities are zero 69: 69: Searching the wall atom type(s) 69: 69: The largest distance between excluded atoms is 0.344 nm between atom 1 and 2 69: Calculating fourier grid dimensions for X Y Z 69: Using a fourier grid of 20x20x40, spacing 0.200 0.200 0.200 69: 69: Estimate for the relative computational load of the PME mesh part: 1.00 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.097 0.049 199.4 69: (ns/day) (hour/ns) 69: Performance: 93.106 0.258 69: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Last energy frame read 5 time 0.050 trr version: GMX_trn_file (single precision) 69: 69: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 (813 ms) 69: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 69: Test system 'epsilon-surface-constraint' cannot run with 1 ranks. 69: The supported numbers are > 1. 69: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 (0 ms) 69: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 69: With epsilon_surface > 0 all molecules should be neutral. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 69: With epsilon_surface > 0 you can only use domain decomposition when there 69: are only small molecules with all bonds constrained (mdrun will check for 69: this). 69: 69: Number of degrees of freedom in T-Coupling group rest is 9.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 69: NVE simulation with an initial temperature of zero: will use a Verlet 69: buffer of 10%. Check your energy drift! 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 69: The optimal PME mesh load for parallel simulations is below 0.5 69: and for highly parallel simulations between 0.25 and 0.33, 69: for higher performance, increase the cut-off and the PME grid spacing. 69: 69: 69: 69: There were 4 NOTEs 69: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Dipoles' 69: 20 steps, 0.1 ps. 69: Setting the LD random seed to -43102793 69: 69: Generated 1 of the 1 non-bonded parameter combinations 69: 69: Excluding 1 bonded neighbours molecule type 'Dipole' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/dipoles.gro', all velocities are zero 69: 69: The largest distance between excluded atoms is 0.344 nm between atom 1 and 2 69: Calculating fourier grid dimensions for X Y Z 69: Using a fourier grid of 20x20x20, spacing 0.200 0.200 0.200 69: 69: Estimate for the relative computational load of the PME mesh part: 1.00 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.132 0.066 199.4 69: (ns/day) (hour/ns) 69: Performance: 68.342 0.351 69: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Last energy frame read 5 time 0.050 69: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 (352 ms) 69: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest (1166 ms total) 69: 69: [----------] Global test environment tear-down 69: [==========] 5 tests from 3 test suites ran. (2918 ms total) 69: [ PASSED ] 5 tests. 69/90 Test #69: MdrunSingleRankAlgorithmsTests ............ Passed 2.96 sec test 70 Start 70: Minimize1RankTests 70: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/minimize-test "-ntomp" "2" "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/Minimize1RankTests.xml" 70: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests 70: Test timeout computed to be: 600 70: [==========] Running 12 tests from 2 test suites. 70: [----------] Global test environment set-up. 70: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 70: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group System is 27.00 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 4 NOTEs 70: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Using 1 MPI thread 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Steepest Descents: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: 70: Energy minimization reached the maximum number of steps before the forces 70: reached the requested precision Fmax < 10. 70: 70: writing lowest energy coordinates. 70: 70: Steepest Descents did not converge to Fmax < 10 in 5 steps. 70: Potential Energy = -4.7991047e+01 70: Maximum force = 1.8629713e+02 on atom 13 70: Norm of force = 8.7721867e+01 70: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 70: 70: Generated 330891 of the 330891 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (599 ms) 70: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group System is 27.00 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 4 NOTEs 70: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Using 1 MPI thread 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Polak-Ribiere Conjugate Gradients: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: F-max = 3.02331e+02 on atom 3 70: F-Norm = 1.18024e+02 70: 70: 70: Energy minimization reached the maximum number of steps before the forces 70: reached the requested precision Fmax < 10. 70: 70: writing lowest energy coordinates. 70: 70: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 70: Potential Energy = -5.5862484e+01 70: Maximum force = 4.2726132e+02 on atom 13 70: Norm of force = 1.8452547e+02 70: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 70: 70: Generated 330891 of the 330891 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (608 ms) 70: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: Generating 1-4 interactions: fudge = 1 70: Number of degrees of freedom in T-Coupling group System is 22.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 4 NOTEs 70: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Using 1 MPI thread 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Steepest Descents: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: 70: Energy minimization reached the maximum number of steps before the forces 70: reached the requested precision Fmax < 10. 70: 70: writing lowest energy coordinates. 70: 70: Steepest Descents did not converge to Fmax < 10 in 5 steps. 70: Potential Energy = 3.1937714e+02 70: Maximum force = 9.9988643e+03 on atom 9 70: Norm of force = 4.6166996e+03 70: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 70: 70: Generated 17396 of the 20503 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Glycine' 70: 70: turning H bonds into constraints... 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (141 ms) 70: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: Generating 1-4 interactions: fudge = 1 70: 70: NOTE 3 [file glycine_vacuo.top, line 12]: 70: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 70: 70: Number of degrees of freedom in T-Coupling group System is 22.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 5 NOTEs 70: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Using 1 MPI thread 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Polak-Ribiere Conjugate Gradients: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: F-max = 2.41575e+04 on atom 10 70: F-Norm = 1.18451e+04 70: 70: 70: Energy minimization reached the maximum number of steps before the forces 70: reached the requested precision Fmax < 10. 70: 70: writing lowest energy coordinates. 70: 70: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 70: Potential Energy = 1.5174426e+02 70: Maximum force = 7.4208862e+03 on atom 9 70: Norm of force = 3.5692992e+03 70: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 70: 70: Generated 17396 of the 20503 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Glycine' 70: 70: turning H bonds into constraints... 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (132 ms) 70: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file unknown]: 70: You are using constraints on all bonds, whereas the forcefield has been 70: parametrized only with constraints involving hydrogen atoms. We suggest 70: using constraints = h-bonds instead, this will also improve performance. 70: 70: Number of degrees of freedom in T-Coupling group System is 23.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 5 NOTEs 70: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Update groups can not be used for this system because an incompatible virtual site type is used 70: 70: Using 1 MPI thread 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Steepest Descents: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: 70: Energy minimization reached the maximum number of steps before the forces 70: reached the requested precision Fmax < 10. 70: 70: writing lowest energy coordinates. 70: 70: Steepest Descents did not converge to Fmax < 10 in 5 steps. 70: Potential Energy = -1.5698431e+02 70: Maximum force = 4.5699695e+02 on atom 17 70: Norm of force = 1.8327127e+02 70: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 70: 70: turning all bonds into constraints... 70: 70: Cleaning up constraints and constant bonded interactions with virtual sites 70: 70: Removed 18 Angles with virtual sites, 21 left 70: 70: Removed 10 Proper Dih.s with virtual sites, 44 left 70: 70: Converted 15 Constraints with virtual sites to connections, 7 left 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (24 ms) 70: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file unknown]: 70: You are using constraints on all bonds, whereas the forcefield has been 70: parametrized only with constraints involving hydrogen atoms. We suggest 70: using constraints = h-bonds instead, this will also improve performance. 70: 70: 70: NOTE 4 [file unknown]: 70: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 70: 70: Number of degrees of freedom in T-Coupling group System is 23.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 6 NOTEs 70: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Update groups can not be used for this system because an incompatible virtual site type is used 70: 70: Using 1 MPI thread 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Polak-Ribiere Conjugate Gradients: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: F-max = 1.06801e+03 on atom 28 70: F-Norm = 4.26922e+02 70: 70: 70: Energy minimization reached the maximum number of steps before the forces 70: reached the requested precision Fmax < 10. 70: 70: writing lowest energy coordinates. 70: 70: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 70: Potential Energy = -1.6941071e+02 70: Maximum force = 2.1830020e+02 on atom 17 70: Norm of force = 7.9207704e+01 70: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 70: 70: turning all bonds into constraints... 70: 70: Cleaning up constraints and constant bonded interactions with virtual sites 70: 70: Removed 18 Angles with virtual sites, 21 left 70: 70: Removed 10 Proper Dih.s with virtual sites, 44 left 70: 70: Converted 15 Constraints with virtual sites to connections, 7 left 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (27 ms) 70: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (1533 ms total) 70: 70: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 70: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 3 NOTEs 70: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Using 1 MPI thread 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Steepest Descents: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: 70: writing lowest energy coordinates. 70: 70: Steepest Descents converged to Fmax < 10 in 1 steps 70: Potential Energy = -9.7425687e-01 70: Maximum force = 4.0132279e+00 on atom 1 70: Norm of force = 1.6383933e+00 70: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (23 ms) 70: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 3 NOTEs 70: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Using 1 MPI thread 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Polak-Ribiere Conjugate Gradients: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: F-max = 4.01323e+00 on atom 1 70: F-Norm = 1.63839e+00 70: 70: 70: writing lowest energy coordinates. 70: 70: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 70: Potential Energy = -9.9064195e-01 70: Maximum force = 2.5781672e+00 on atom 1 70: Norm of force = 1.0525324e+00 70: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (26 ms) 70: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 70: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 3 NOTEs 70: 70: There was 1 WARNING 70: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. 70: 70: Using 1 MPI thread 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Low-Memory BFGS Minimizer: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: Using 10 BFGS correction steps. 70: 70: F-max = 4.01323e+00 on atom 1 70: F-Norm = 1.63839e+00 70: 70: 70: writing lowest energy coordinates. 70: 70: Low-Memory BFGS Minimizer converged to Fmax < 10 in -1 steps 70: Potential Energy = -9.9064195e-01 70: Maximum force = 2.5781672e+00 on atom 1 70: Norm of force = 1.0525324e+00 70: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (25 ms) 70: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: Generating 1-4 interactions: fudge = 1 70: Number of degrees of freedom in T-Coupling group System is 27.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 4 NOTEs 70: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Using 1 MPI thread 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Steepest Descents: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: 70: Energy minimization reached the maximum number of steps before the forces 70: reached the requested precision Fmax < 10. 70: 70: writing lowest energy coordinates. 70: 70: Steepest Descents did not converge to Fmax < 10 in 5 steps. 70: Potential Energy = 3.1939697e+02 70: Maximum force = 9.9704248e+03 on atom 9 70: Norm of force = 4.6227540e+03 70: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 70: 70: Generated 17396 of the 20503 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Glycine' 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (116 ms) 70: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: Generating 1-4 interactions: fudge = 1 70: Number of degrees of freedom in T-Coupling group System is 27.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 4 NOTEs 70: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Using 1 MPI thread 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Polak-Ribiere Conjugate Gradients: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: F-max = 2.41672e+04 on atom 10 70: F-Norm = 1.19357e+04 70: 70: 70: Energy minimization reached the maximum number of steps before the forces 70: reached the requested precision Fmax < 10. 70: 70: writing lowest energy coordinates. 70: 70: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 70: Potential Energy = 1.5625757e+02 70: Maximum force = 7.5018242e+03 on atom 9 70: Norm of force = 3.6139019e+03 70: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 70: 70: Generated 17396 of the 20503 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Glycine' 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (103 ms) 70: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 70: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 70: 70: Generating 1-4 interactions: fudge = 1 70: Number of degrees of freedom in T-Coupling group System is 27.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 4 NOTEs 70: 70: There was 1 WARNING 70: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. 70: 70: Using 1 MPI thread 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Low-Memory BFGS Minimizer: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: Using 10 BFGS correction steps. 70: 70: F-max = 2.41672e+04 on atom 10 70: F-Norm = 1.19357e+04 70: 70: 70: Energy minimization has stopped, but the forces have not converged to the 70: requested precision Fmax < 10 (which may not be possible for your system). It 70: stopped because the algorithm tried to make a new step whose size was too 70: small, or there was no change in the energy since last step. Either way, we 70: regard the minimization as converged to within the available machine 70: precision, given your starting configuration and EM parameters. 70: 70: Double precision normally gives you higher accuracy, but this is often not 70: needed for preparing to run molecular dynamics. 70: 70: writing lowest energy coordinates. 70: 70: Low-Memory BFGS Minimizer converged to machine precision in 0 steps, 70: but did not reach the requested Fmax < 10. 70: Potential Energy = 5.6111731e+02 70: Maximum force = 1.2685497e+04 on atom 10 70: Norm of force = 6.0643635e+03 70: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 70: 70: Generated 17396 of the 20503 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Glycine' 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (103 ms) 70: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (400 ms total) 70: 70: [----------] Global test environment tear-down 70: [==========] 12 tests from 2 test suites ran. (2256 ms total) 70: [ PASSED ] 12 tests. 70/90 Test #70: Minimize1RankTests ........................ Passed 2.29 sec test 71 Start 71: Minimize2RankTests 71: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/minimize-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/Minimize2RankTests.xml" 71: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests 71: Test timeout computed to be: 600 71: [==========] Running 12 tests from 2 test suites. 71: [----------] Global test environment set-up. 71: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 71: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 71: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 71: setting nstcomm equal to nstcalcenergy for less overhead 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 27.00 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 71: COM removal frequency is set to (4). 71: Other settings require a global communication frequency of 100. 71: Note that this will require additional global communication steps, 71: which will reduce performance when using multiple ranks. 71: Consider setting nstcomm to a multiple of 100. 71: 71: 71: There were 4 NOTEs 71: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: 71: Steepest Descents: 71: Tolerance (Fmax) = 1.00000e+01 71: Number of steps = 4 71: 71: Energy minimization reached the maximum number of steps before the forces 71: reached the requested precision Fmax < 10. 71: 71: writing lowest energy coordinates. 71: 71: Steepest Descents did not converge to Fmax < 10 in 5 steps. 71: Potential Energy = -4.7991032e+01 71: Maximum force = 1.8629765e+02 on atom 13 71: Norm of force = 8.7722064e+01 71: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 71: 71: Generated 330891 of the 330891 1-4 parameter combinations 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (556 ms) 71: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 71: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 71: setting nstcomm equal to nstcalcenergy for less overhead 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 27.00 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 71: COM removal frequency is set to (4). 71: Other settings require a global communication frequency of 100. 71: Note that this will require additional global communication steps, 71: which will reduce performance when using multiple ranks. 71: Consider setting nstcomm to a multiple of 100. 71: 71: 71: There were 4 NOTEs 71: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: 71: Polak-Ribiere Conjugate Gradients: 71: Tolerance (Fmax) = 1.00000e+01 71: Number of steps = 4 71: F-max = 3.02331e+02 on atom 3 71: F-Norm = 1.18024e+02 71: 71: 71: Energy minimization reached the maximum number of steps before the forces 71: reached the requested precision Fmax < 10. 71: 71: writing lowest energy coordinates. 71: 71: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 71: Potential Energy = -5.5862144e+01 71: Maximum force = 4.2727667e+02 on atom 13 71: Norm of force = 1.8453053e+02 71: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 71: 71: Generated 330891 of the 330891 1-4 parameter combinations 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (675 ms) 71: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 71: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 71: setting nstcomm equal to nstcalcenergy for less overhead 71: 71: Generating 1-4 interactions: fudge = 1 71: Number of degrees of freedom in T-Coupling group System is 22.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 71: COM removal frequency is set to (4). 71: Other settings require a global communication frequency of 100. 71: Note that this will require additional global communication steps, 71: which will reduce performance when using multiple ranks. 71: Consider setting nstcomm to a multiple of 100. 71: 71: 71: There were 4 NOTEs 71: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: 71: Steepest Descents: 71: Tolerance (Fmax) = 1.00000e+01 71: Number of steps = 4 71: 71: Energy minimization reached the maximum number of steps before the forces 71: reached the requested precision Fmax < 10. 71: 71: writing lowest energy coordinates. 71: 71: Steepest Descents did not converge to Fmax < 10 in 5 steps. 71: Potential Energy = 3.1937704e+02 71: Maximum force = 9.9988633e+03 on atom 9 71: Norm of force = 4.6166993e+03 71: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 71: 71: Generated 17396 of the 20503 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Glycine' 71: 71: turning H bonds into constraints... 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (276 ms) 71: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 71: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 71: setting nstcomm equal to nstcalcenergy for less overhead 71: 71: Generating 1-4 interactions: fudge = 1 71: 71: NOTE 3 [file glycine_vacuo.top, line 12]: 71: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 71: 71: Number of degrees of freedom in T-Coupling group System is 22.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 71: COM removal frequency is set to (4). 71: Other settings require a global communication frequency of 100. 71: Note that this will require additional global communication steps, 71: which will reduce performance when using multiple ranks. 71: Consider setting nstcomm to a multiple of 100. 71: 71: 71: There were 5 NOTEs 71: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: 71: Polak-Ribiere Conjugate Gradients: 71: Tolerance (Fmax) = 1.00000e+01 71: Number of steps = 4 71: F-max = 2.41575e+04 on atom 10 71: F-Norm = 1.18451e+04 71: 71: 71: Energy minimization reached the maximum number of steps before the forces 71: reached the requested precision Fmax < 10. 71: 71: writing lowest energy coordinates. 71: 71: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 71: Potential Energy = 1.5174426e+02 71: Maximum force = 7.4208862e+03 on atom 9 71: Norm of force = 3.5692992e+03 71: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 71: 71: Generated 17396 of the 20503 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Glycine' 71: 71: turning H bonds into constraints... 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (306 ms) 71: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 71: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 71: setting nstcomm equal to nstcalcenergy for less overhead 71: 71: Generating 1-4 interactions: fudge = 0.5 71: 71: NOTE 3 [file unknown]: 71: You are using constraints on all bonds, whereas the forcefield has been 71: parametrized only with constraints involving hydrogen atoms. We suggest 71: using constraints = h-bonds instead, this will also improve performance. 71: 71: Number of degrees of freedom in T-Coupling group System is 23.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 71: COM removal frequency is set to (4). 71: Other settings require a global communication frequency of 100. 71: Note that this will require additional global communication steps, 71: which will reduce performance when using multiple ranks. 71: Consider setting nstcomm to a multiple of 100. 71: 71: 71: There were 5 NOTEs 71: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 71: Update groups can not be used for this system because an incompatible virtual site type is used 71: 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: 71: Steepest Descents: 71: Tolerance (Fmax) = 1.00000e+01 71: Number of steps = 4 71: 71: Energy minimization reached the maximum number of steps before the forces 71: reached the requested precision Fmax < 10. 71: 71: writing lowest energy coordinates. 71: 71: Steepest Descents did not converge to Fmax < 10 in 5 steps. 71: Potential Energy = -1.5698425e+02 71: Maximum force = 4.5699695e+02 on atom 17 71: Norm of force = 1.8327127e+02 71: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 Generated 2145 of the 2145 non-bonded parameter combinations 71: 71: Generated 2145 of the 2145 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 71: 71: turning all bonds into constraints... 71: 71: Cleaning up constraints and constant bonded interactions with virtual sites 71: 71: Removed 18 Angles with virtual sites, 21 left 71: 71: Removed 10 Proper Dih.s with virtual sites, 44 left 71: 71: Converted 15 Constraints with virtual sites to connections, 7 left 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (95 ms) 71: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 71: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 71: setting nstcomm equal to nstcalcenergy for less overhead 71: 71: Generating 1-4 interactions: fudge = 0.5 71: 71: NOTE 3 [file unknown]: 71: You are using constraints on all bonds, whereas the forcefield has been 71: parametrized only with constraints involving hydrogen atoms. We suggest 71: using constraints = h-bonds instead, this will also improve performance. 71: 71: 71: NOTE 4 [file unknown]: 71: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 71: 71: Number of degrees of freedom in T-Coupling group System is 23.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 71: COM removal frequency is set to (4). 71: Other settings require a global communication frequency of 100. 71: Note that this will require additional global communication steps, 71: which will reduce performance when using multiple ranks. 71: Consider setting nstcomm to a multiple of 100. 71: 71: 71: There were 6 NOTEs 71: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 71: Update groups can not be used for this system because an incompatible virtual site type is used 71: 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: 71: Polak-Ribiere Conjugate Gradients: 71: Tolerance (Fmax) = 1.00000e+01 71: Number of steps = 4 71: F-max = 1.06801e+03 on atom 28 71: F-Norm = 4.26922e+02 71: 71: 71: Energy minimization reached the maximum number of steps before the forces 71: reached the requested precision Fmax < 10. 71: 71: writing lowest energy coordinates. 71: 71: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 71: Potential Energy = -1.6941101e+02 71: Maximum force = 2.1832886e+02 on atom 17 71: Norm of force = 7.9206610e+01 71: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 2145 of the 2145 non-bonded parameter combinations 71: 71: Generated 2145 of the 2145 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 71: 71: turning all bonds into constraints... 71: 71: Cleaning up constraints and constant bonded interactions with virtual sites 71: 71: Removed 18 Angles with virtual sites, 21 left 71: 71: Removed 10 Proper Dih.s with virtual sites, 44 left 71: 71: Converted 15 Constraints with virtual sites to connections, 7 left 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (60 ms) 71: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (1971 ms total) 71: 71: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 71: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 71: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 71: setting nstcomm equal to nstcalcenergy for less overhead 71: 71: Number of degrees of freedom in T-Coupling group System is 33.00 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 71: COM removal frequency is set to (4). 71: Other settings require a global communication frequency of 100. 71: Note that this will require additional global communication steps, 71: which will reduce performance when using multiple ranks. 71: Consider setting nstcomm to a multiple of 100. 71: 71: 71: There were 3 NOTEs 71: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: 71: Steepest Descents: 71: Tolerance (Fmax) = 1.00000e+01 71: Number of steps = 4 71: 71: writing lowest energy coordinates. 71: 71: Steepest Descents converged to Fmax < 10 in 1 steps 71: Potential Energy = -9.7425687e-01 71: Maximum force = 4.0132279e+00 on atom 3 71: Norm of force = 1.6383933e+00 71: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 71: 71: Excluding 1 bonded neighbours molecule type 'Argon' 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (110 ms) 71: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 71: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 71: setting nstcomm equal to nstcalcenergy for less overhead 71: 71: Number of degrees of freedom in T-Coupling group System is 33.00 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 71: COM removal frequency is set to (4). 71: Other settings require a global communication frequency of 100. 71: Note that this will require additional global communication steps, 71: which will reduce performance when using multiple ranks. 71: Consider setting nstcomm to a multiple of 100. 71: 71: 71: There were 3 NOTEs 71: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: 71: Polak-Ribiere Conjugate Gradients: 71: Tolerance (Fmax) = 1.00000e+01 71: Number of steps = 4 71: F-max = 4.01323e+00 on atom 3 71: F-Norm = 1.63839e+00 71: 71: 71: writing lowest energy coordinates. 71: 71: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 71: Potential Energy = -9.9064195e-01 71: Maximum force = 2.5781672e+00 on atom 3 71: Norm of force = 1.0525324e+00 71: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 71: 71: Excluding 1 bonded neighbours molecule type 'Argon' 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (110 ms) 71: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 71: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 71: setting nstcomm equal to nstcalcenergy for less overhead 71: 71: 71: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 71: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 71: 71: Number of degrees of freedom in T-Coupling group System is 33.00 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 71: COM removal frequency is set to (4). 71: Other settings require a global communication frequency of 100. 71: Note that this will require additional global communication steps, 71: which will reduce performance when using multiple ranks. 71: Consider setting nstcomm to a multiple of 100. 71: 71: 71: There were 3 NOTEs 71: 71: There was 1 WARNING 71: Generated 1 of the 1 non-bonded parameter combinations 71: 71: Excluding 1 bonded neighbours molecule type 'Argon' 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (4 ms) 71: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 71: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 71: setting nstcomm equal to nstcalcenergy for less overhead 71: 71: Generating 1-4 interactions: fudge = 1 71: Number of degrees of freedom in T-Coupling group System is 27.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 71: COM removal frequency is set to (4). 71: Other settings require a global communication frequency of 100. 71: Note that this will require additional global communication steps, 71: which will reduce performance when using multiple ranks. 71: Consider setting nstcomm to a multiple of 100. 71: 71: 71: There were 4 NOTEs 71: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: 71: Steepest Descents: 71: Tolerance (Fmax) = 1.00000e+01 71: Number of steps = 4 71: 71: Energy minimization reached the maximum number of steps before the forces 71: reached the requested precision Fmax < 10. 71: 71: writing lowest energy coordinates. 71: 71: Steepest Descents did not converge to Fmax < 10 in 5 steps. 71: Potential Energy = 3.1939685e+02 71: Maximum force = 9.9704248e+03 on atom 9 71: Norm of force = 4.6227568e+03 71: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 71: 71: Generated 17396 of the 20503 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Glycine' 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (208 ms) 71: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 71: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 71: setting nstcomm equal to nstcalcenergy for less overhead 71: 71: Generating 1-4 interactions: fudge = 1 71: Number of degrees of freedom in T-Coupling group System is 27.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 71: COM removal frequency is set to (4). 71: Other settings require a global communication frequency of 100. 71: Note that this will require additional global communication steps, 71: which will reduce performance when using multiple ranks. 71: Consider setting nstcomm to a multiple of 100. 71: 71: 71: There were 4 NOTEs 71: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: 71: Polak-Ribiere Conjugate Gradients: 71: Tolerance (Fmax) = 1.00000e+01 71: Number of steps = 4 71: F-max = 2.41672e+04 on atom 10 71: F-Norm = 1.19357e+04 71: 71: 71: Energy minimization reached the maximum number of steps before the forces 71: reached the requested precision Fmax < 10. 71: 71: writing lowest energy coordinates. 71: 71: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 71: Potential Energy = 1.5625761e+02 71: Maximum force = 7.5018237e+03 on atom 9 71: Norm of force = 3.6139019e+03 71: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 71: 71: Generated 17396 of the 20503 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Glycine' 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (201 ms) 71: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 71: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 71: setting nstcomm equal to nstcalcenergy for less overhead 71: 71: 71: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 71: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 71: 71: Generating 1-4 interactions: fudge = 1 71: Number of degrees of freedom in T-Coupling group System is 27.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 71: COM removal frequency is set to (4). 71: Other settings require a global communication frequency of 100. 71: Note that this will require additional global communication steps, 71: which will reduce performance when using multiple ranks. 71: Consider setting nstcomm to a multiple of 100. 71: 71: 71: There were 4 NOTEs 71: 71: There was 1 WARNING 71: Generated 20503 of the 20503 non-bonded parameter combinations 71: 71: Generated 17396 of the 20503 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Glycine' 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (99 ms) 71: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (735 ms total) 71: 71: [----------] Global test environment tear-down 71: [==========] 12 tests from 2 test suites ran. (3058 ms total) 71: [ PASSED ] 12 tests. 71/90 Test #71: Minimize2RankTests ........................ Passed 3.10 sec test 72 Start 72: MdrunNonIntegratorTests 72: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/mdrun-non-integrator-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/MdrunNonIntegratorTests.xml" 72: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests 72: Test timeout computed to be: 600 72: [==========] Running 46 tests from 3 test suites. 72: [----------] Global test environment set-up. 72: [----------] 1 test from NonbondedBenchTest 72: [ RUN ] NonbondedBenchTest.BasicEndToEndTest 72: SIMD width: 4 72: System size: 3000 atoms 72: Cut-off radius: 1 nm 72: Number of threads: 1 72: Number of iterations: 1 72: Compute energies: no 72: Ewald excl. corr.: analytical 72: 72: Coulomb LJ comb. SIMD Mcycles Mcycles/it. pairs/cycle 72: total useful 72: Ewald all geom. 4xM 18.406 18.4061 0.0647 0.0342 72: [ OK ] NonbondedBenchTest.BasicEndToEndTest (26 ms) 72: [----------] 1 test from NonbondedBenchTest (26 ms total) 72: 72: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest 72: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Number of degrees of freedom in T-Coupling group System is 33.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 72: NVE simulation: will use the initial temperature of 68.810 K for 72: determining the Verlet buffer size 72: 72: 72: There were 3 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'Argon' 72: 16 steps, 0.0 ps. 72: Generated 1 of the 1 non-bonded parameter combinations 72: 72: Excluding 1 bonded neighbours molecule type 'Argon' 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.088 0.044 199.5 72: (ns/day) (hour/ns) 72: Performance: 33.368 0.719 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.trr' 72: 72: trr version: GMX_trn_file (single precision) 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.018 0.009 199.2 72: (ns/day) (hour/ns) 72: Performance: 161.171 0.149 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim2.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 (97 ms) 72: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Number of degrees of freedom in T-Coupling group System is 33.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 72: NVE simulation: will use the initial temperature of 68.810 K for 72: determining the Verlet buffer size 72: 72: 72: There were 3 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'Argon' 72: 16 steps, 0.0 ps. 72: Generated 1 of the 1 non-bonded parameter combinations 72: 72: Excluding 1 bonded neighbours molecule type 'Argon' 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.031 0.016 199.3 72: (ns/day) (hour/ns) 72: Performance: 93.034 0.258 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 93 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.018 0.009 198.8 72: (ns/day) (hour/ns) 72: Performance: 161.369 0.149 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim2.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 (40 ms) 72: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Number of degrees of freedom in T-Coupling group System is 33.00 72: 72: There were 2 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 100, rlist from 0.712 to 0.744 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'Argon' 72: 16 steps, 0.0 ps. 72: Generated 1 of the 1 non-bonded parameter combinations 72: 72: Excluding 1 bonded neighbours molecule type 'Argon' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.053 0.027 199.4 72: (ns/day) (hour/ns) 72: Performance: 54.884 0.437 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 100, rlist from 0.712 to 0.744 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 21 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.001 0.001 194.5 72: (ns/day) (hour/ns) 72: Performance: 2729.550 0.009 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim2.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 (57 ms) 72: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Number of degrees of freedom in T-Coupling group System is 33.00 72: 72: There were 2 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'Argon' 72: 16 steps, 0.0 ps. 72: Generated 1 of the 1 non-bonded parameter combinations 72: 72: Excluding 1 bonded neighbours molecule type 'Argon' 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.024 0.012 199.0 72: (ns/day) (hour/ns) 72: Performance: 120.061 0.200 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 21 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.001 0.001 194.0 72: (ns/day) (hour/ns) 72: Performance: 2673.869 0.009 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim2.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 (35 ms) 72: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 27.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 72: NVE simulation: will use the initial temperature of 398.997 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'spc2' 72: 16 steps, 0.0 ps. 72: Generated 330891 of the 330891 non-bonded parameter combinations 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.057 0.029 199.2 72: (ns/day) (hour/ns) 72: Performance: 51.039 0.470 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 31 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.002 0.001 193.5 72: (ns/day) (hour/ns) 72: Performance: 1733.425 0.014 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim2.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 (753 ms) 72: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 27.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 72: NVE simulation: will use the initial temperature of 398.997 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'spc2' 72: 16 steps, 0.0 ps. 72: Generated 330891 of the 330891 non-bonded parameter combinations 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.088 0.044 199.7 72: (ns/day) (hour/ns) 72: Performance: 33.169 0.724 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 24 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.003 0.002 193.4 72: (ns/day) (hour/ns) 72: Performance: 930.603 0.026 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim2.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 (630 ms) 72: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 27.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 3 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 100, rlist from 0.735 to 0.831 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'spc2' 72: 16 steps, 0.0 ps. 72: Generated 330891 of the 330891 non-bonded parameter combinations 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.738 nm, buffer size 0.038 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.309 0.154 199.9 72: (ns/day) (hour/ns) 72: Performance: 9.507 2.524 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 100, rlist from 0.735 to 0.831 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 28 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.002 0.001 191.6 72: (ns/day) (hour/ns) 72: Performance: 1668.181 0.014 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim2.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 (850 ms) 72: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 27.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 3 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'spc2' 72: 16 steps, 0.0 ps. 72: Generated 330891 of the 330891 non-bonded parameter combinations 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.044 0.022 199.2 72: (ns/day) (hour/ns) 72: Performance: 65.923 0.364 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 32 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.002 0.001 194.3 72: (ns/day) (hour/ns) 72: Performance: 1599.739 0.015 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim2.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 (1125 ms) 72: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: 72: NOTE 3 [file unknown]: 72: You are using constraints on all bonds, whereas the forcefield has been 72: parametrized only with constraints involving hydrogen atoms. We suggest 72: using constraints = h-bonds instead, this will also improve performance. 72: 72: Number of degrees of freedom in T-Coupling group System is 23.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 72: NVE simulation: will use the initial temperature of 456.887 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 72: There are 9 non-linear virtual site constructions. Their contribution to 72: the energy error is approximated. In most cases this does not affect the 72: error significantly. 72: 72: 72: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 6 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Update groups can not be used for this system because an incompatible virtual site type is used 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'Alanine dipeptide in vacuo' 72: 16 steps, 0.0 ps. 72: Generated 2145 of the 2145 non-bonded parameter combinations 72: 72: Generated 2145 of the 2145 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 72: 72: turning all bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 72: 72: Cleaning up constraints and constant bonded interactions with virtual sites 72: 72: Removed 18 Angles with virtual sites, 21 left 72: 72: Removed 10 Proper Dih.s with virtual sites, 44 left 72: 72: Converted 15 Constraints with virtual sites to connections, 7 left 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.070 0.035 199.3 72: (ns/day) (hour/ns) 72: Performance: 41.625 0.577 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Update groups can not be used for this system because an incompatible virtual site type is used 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 24 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.003 0.001 194.3 72: (ns/day) (hour/ns) 72: Performance: 1084.230 0.022 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim2.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 (73 ms) 72: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: 72: NOTE 3 [file unknown]: 72: You are using constraints on all bonds, whereas the forcefield has been 72: parametrized only with constraints involving hydrogen atoms. We suggest 72: using constraints = h-bonds instead, this will also improve performance. 72: 72: Number of degrees of freedom in T-Coupling group System is 23.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 72: NVE simulation: will use the initial temperature of 456.887 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 72: There are 9 non-linear virtual site constructions. Their contribution to 72: the energy error is approximated. In most cases this does not affect the 72: error significantly. 72: 72: 72: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 6 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Update groups can not be used for this system because an incompatible virtual site type is used 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'Alanine dipeptide in vacuo' 72: 16 steps, 0.0 ps. 72: Generated 2145 of the 2145 non-bonded parameter combinations 72: 72: Generated 2145 of the 2145 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 72: 72: turning all bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 72: 72: Cleaning up constraints and constant bonded interactions with virtual sites 72: 72: Removed 18 Angles with virtual sites, 21 left 72: 72: Removed 10 Proper Dih.s with virtual sites, 44 left 72: 72: Converted 15 Constraints with virtual sites to connections, 7 left 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.065 0.033 199.3 72: (ns/day) (hour/ns) 72: Performance: 45.186 0.531 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Update groups can not be used for this system because an incompatible virtual site type is used 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 19 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.005 0.003 196.4 72: (ns/day) (hour/ns) 72: Performance: 581.243 0.041 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim2.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 (66 ms) 72: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: 72: NOTE 3 [file unknown]: 72: You are using constraints on all bonds, whereas the forcefield has been 72: parametrized only with constraints involving hydrogen atoms. We suggest 72: using constraints = h-bonds instead, this will also improve performance. 72: 72: Number of degrees of freedom in T-Coupling group System is 23.00 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 72: There are 9 non-linear virtual site constructions. Their contribution to 72: the energy error is approximated. In most cases this does not affect the 72: error significantly. 72: 72: 72: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 5 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 80, rlist from 0.748 to 0.865 72: 72: Update groups can not be used for this system because an incompatible virtual site type is used 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'Alanine dipeptide in vacuo' 72: 16 steps, 0.0 ps. 72: Generated 2145 of the 2145 non-bonded parameter combinations 72: 72: Generated 2145 of the 2145 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 72: 72: turning all bonds into constraints... 72: 72: Cleaning up constraints and constant bonded interactions with virtual sites 72: 72: Removed 18 Angles with virtual sites, 21 left 72: 72: Removed 10 Proper Dih.s with virtual sites, 44 left 72: 72: Converted 15 Constraints with virtual sites to connections, 7 left 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.043 0.022 199.1 72: (ns/day) (hour/ns) 72: Performance: 67.680 0.355 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 80, rlist from 0.748 to 0.865 72: 72: Update groups can not be used for this system because an incompatible virtual site type is used 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 22 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.003 0.001 193.1 72: (ns/day) (hour/ns) 72: Performance: 1066.216 0.023 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim2.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 (239 ms) 72: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: 72: NOTE 3 [file unknown]: 72: You are using constraints on all bonds, whereas the forcefield has been 72: parametrized only with constraints involving hydrogen atoms. We suggest 72: using constraints = h-bonds instead, this will also improve performance. 72: 72: Number of degrees of freedom in T-Coupling group System is 23.00 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 72: There are 9 non-linear virtual site constructions. Their contribution to 72: the energy error is approximated. In most cases this does not affect the 72: error significantly. 72: 72: 72: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 5 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 25, rlist from 0.729 to 0.81 72: 72: Update groups can not be used for this system because an incompatible virtual site type is used 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'Alanine dipeptide in vacuo' 72: 16 steps, 0.0 ps. 72: Generated 2145 of the 2145 non-bonded parameter combinations 72: 72: Generated 2145 of the 2145 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 72: 72: turning all bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 72: 72: Cleaning up constraints and constant bonded interactions with virtual sites 72: 72: Removed 18 Angles with virtual sites, 21 left 72: 72: Removed 10 Proper Dih.s with virtual sites, 44 left 72: 72: Converted 15 Constraints with virtual sites to connections, 7 left 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.056 0.028 199.0 72: (ns/day) (hour/ns) 72: Performance: 52.536 0.457 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 25, rlist from 0.729 to 0.81 72: 72: Update groups can not be used for this system because an incompatible virtual site type is used 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 19 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.003 0.002 193.6 72: (ns/day) (hour/ns) 72: Performance: 813.494 0.030 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim2.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 (139 ms) 72: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest (4111 ms total) 72: 72: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.078 0.039 199.4 72: (ns/day) (hour/ns) 72: Performance: 37.464 0.641 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.020 0.010 191.4 72: (ns/day) (hour/ns) 72: Performance: 143.406 0.167 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim2.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 (91 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.110 0.055 199.5 72: (ns/day) (hour/ns) 72: Performance: 26.549 0.904 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 21 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.003 0.002 174.7 72: (ns/day) (hour/ns) 72: Performance: 828.705 0.029 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim2.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 (114 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.060 0.030 198.8 72: (ns/day) (hour/ns) 72: Performance: 48.531 0.495 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.022 0.011 188.5 72: (ns/day) (hour/ns) 72: Performance: 128.250 0.187 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim2.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 (118 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.089 0.045 199.4 72: (ns/day) (hour/ns) 72: Performance: 32.920 0.729 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.013 0.007 187.0 72: (ns/day) (hour/ns) 72: Performance: 205.175 0.117 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim2.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 (108 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.087 0.044 199.1 72: (ns/day) (hour/ns) 72: Performance: 33.755 0.711 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 91 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.046 0.023 195.3 72: (ns/day) (hour/ns) 72: Performance: 62.790 0.382 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim2.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 (115 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.101 0.051 199.5 72: (ns/day) (hour/ns) 72: Performance: 29.029 0.827 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 17 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.003 0.002 158.9 72: (ns/day) (hour/ns) 72: Performance: 760.379 0.032 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim2.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 (94 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.050 0.025 199.0 72: (ns/day) (hour/ns) 72: Performance: 58.274 0.412 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 52 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.006 0.004 173.1 72: (ns/day) (hour/ns) 72: Performance: 394.960 0.061 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim2.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 (65 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.084 0.042 198.8 72: (ns/day) (hour/ns) 72: Performance: 34.573 0.694 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 12 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.005 0.003 164.8 72: (ns/day) (hour/ns) 72: Performance: 451.094 0.053 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim2.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 (89 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.094 0.047 199.3 72: (ns/day) (hour/ns) 72: Performance: 31.180 0.770 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 20 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.003 0.002 178.4 72: (ns/day) (hour/ns) 72: Performance: 820.647 0.029 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim2.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 (105 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.177 0.089 199.6 72: (ns/day) (hour/ns) 72: Performance: 16.531 1.452 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.008 0.004 188.0 72: (ns/day) (hour/ns) 72: Performance: 329.849 0.073 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim2.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 (154 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.085 0.043 198.9 72: (ns/day) (hour/ns) 72: Performance: 34.216 0.701 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 11 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.005 0.003 173.8 72: (ns/day) (hour/ns) 72: Performance: 480.546 0.050 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim2.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 (92 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.082 0.041 199.7 72: (ns/day) (hour/ns) 72: Performance: 35.867 0.669 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 10 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.010 0.005 190.4 72: (ns/day) (hour/ns) 72: Performance: 274.316 0.087 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim2.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 (93 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.076 0.038 199.6 72: (ns/day) (hour/ns) 72: Performance: 38.411 0.625 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 15 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.003 0.002 140.4 72: (ns/day) (hour/ns) 72: Performance: 668.612 0.036 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim2.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 (90 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.087 0.044 199.6 72: (ns/day) (hour/ns) 72: Performance: 33.623 0.714 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 16 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.003 0.002 151.3 72: (ns/day) (hour/ns) 72: Performance: 781.702 0.031 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim2.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 (142 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.092 0.046 199.6 72: (ns/day) (hour/ns) 72: Performance: 31.886 0.753 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 19 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.003 0.002 178.4 72: (ns/day) (hour/ns) 72: Performance: 867.445 0.028 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim2.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 (92 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: NOTE: 26 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.490 0.245 199.9 72: (ns/day) (hour/ns) 72: Performance: 5.993 4.005 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 18 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.003 0.002 151.4 72: (ns/day) (hour/ns) 72: Performance: 723.159 0.033 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim2.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 (301 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: NOTE: 16 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.075 0.038 199.6 72: (ns/day) (hour/ns) 72: Performance: 38.871 0.617 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 21 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.003 0.002 179.9 72: (ns/day) (hour/ns) 72: Performance: 928.779 0.026 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim2.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 (100 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.225 0.113 199.9 72: (ns/day) (hour/ns) 72: Performance: 13.048 1.839 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 18 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.003 0.002 151.8 72: (ns/day) (hour/ns) 72: Performance: 675.726 0.036 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim2.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 (173 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.127 0.064 199.8 72: (ns/day) (hour/ns) 72: Performance: 23.088 1.039 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 19 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.003 0.002 169.5 72: (ns/day) (hour/ns) 72: Performance: 968.038 0.025 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim2.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 (116 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.120 0.060 199.8 72: (ns/day) (hour/ns) 72: Performance: 24.530 0.978 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.032 0.016 193.5 72: (ns/day) (hour/ns) 72: Performance: 89.093 0.269 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim2.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 (121 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: NOTE: 28 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.144 0.072 199.7 72: (ns/day) (hour/ns) 72: Performance: 20.365 1.179 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 18 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.002 0.002 147.4 72: (ns/day) (hour/ns) 72: Performance: 901.858 0.027 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim2.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 (130 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.114 0.057 199.8 72: (ns/day) (hour/ns) 72: Performance: 25.726 0.933 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.021 0.011 191.1 72: (ns/day) (hour/ns) 72: Performance: 134.776 0.178 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim2.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 (203 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 3 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.074 0.037 199.3 72: (ns/day) (hour/ns) 72: Performance: 39.335 0.610 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 17 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.004 0.002 161.0 72: (ns/day) (hour/ns) 72: Performance: 638.668 0.038 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim2.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 (101 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 3 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.123 0.061 199.5 72: (ns/day) (hour/ns) 72: Performance: 23.908 1.004 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.003 0.034 9.1 72: (ns/day) (hour/ns) 72: Performance: 42.906 0.559 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim2.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 (580 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 3 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 4.167 2.084 200.0 72: (ns/day) (hour/ns) 72: Performance: 0.705 34.046 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.139 0.237 58.8 72: (ns/day) (hour/ns) 72: Performance: 6.196 3.874 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim2.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 (3089 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 3 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 1.488 0.744 200.0 72: (ns/day) (hour/ns) 72: Performance: 1.974 12.157 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.021 0.097 21.3 72: (ns/day) (hour/ns) 72: Performance: 15.075 1.592 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim2.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 (1870 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 3 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.436 0.218 199.9 72: (ns/day) (hour/ns) 72: Performance: 6.728 3.567 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 17 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.004 0.002 177.3 72: (ns/day) (hour/ns) 72: Performance: 654.338 0.037 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim2.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 (419 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 3 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.117 0.059 199.5 72: (ns/day) (hour/ns) 72: Performance: 24.987 0.961 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 19 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.003 0.002 176.5 72: (ns/day) (hour/ns) 72: Performance: 893.228 0.027 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim2.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 (145 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 3 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.108 0.054 199.2 72: (ns/day) (hour/ns) 72: Performance: 27.163 0.884 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 17 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.003 0.002 177.9 72: (ns/day) (hour/ns) 72: Performance: 768.921 0.031 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim2.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 (154 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 3 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.110 0.055 199.5 72: (ns/day) (hour/ns) 72: Performance: 26.528 0.905 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 16 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.003 0.002 151.1 72: (ns/day) (hour/ns) 72: Performance: 810.071 0.030 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim2.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 (165 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 3 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.075 0.038 199.2 72: (ns/day) (hour/ns) 72: Performance: 38.960 0.616 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 14 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.003 0.002 145.8 72: (ns/day) (hour/ns) 72: Performance: 657.270 0.037 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim2.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 (107 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 3 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.062 0.031 197.0 72: (ns/day) (hour/ns) 72: Performance: 46.818 0.513 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 14 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.004 0.003 138.5 72: (ns/day) (hour/ns) 72: Performance: 498.833 0.048 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim2.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 (117 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 3 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.060 0.030 199.1 72: (ns/day) (hour/ns) 72: Performance: 48.926 0.491 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.013 0.007 191.3 72: (ns/day) (hour/ns) 72: Performance: 219.246 0.109 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim2.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 (111 ms) 72: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest (9582 ms total) 72: 72: [----------] Global test environment tear-down 72: [==========] 46 tests from 3 test suites ran. (14046 ms total) 72: [ PASSED ] 46 tests. 72/90 Test #72: MdrunNonIntegratorTests ................... Passed 14.09 sec test 73 Start 73: MdrunTpiTests 73: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/mdrun-tpi-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/MdrunTpiTests.xml" 73: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests 73: Test timeout computed to be: 600 73: [==========] Running 3 tests from 1 test suite. 73: [----------] Global test environment set-up. 73: [----------] 3 tests from Simple/TpiTest 73: [ RUN ] Simple/TpiTest.ReproducesOutput/0 73: Generating 1-4 interactions: fudge = 0.5 73: Number of degrees of freedom in T-Coupling group System is 1308.00 73: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 73: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 73: TPI is not implemented for GPUs. 73: 73: Using 1 MPI thread 73: Using 1 OpenMP thread 73: 73: 73: NOTE: Thread affinity was not set. 73: Reading frames from gro file '216 water molecules', 648 atoms. 73: Reading frame 0 time 0.000 mu 6.291e+01 6.291e+01 73: Last frame 0 time 0.000 73: Generated 331705 of the 331705 non-bonded parameter combinations 73: 73: Generated 331705 of the 331705 1-4 parameter combinations 73: 73: Excluding 2 bonded neighbours molecule type 'SOL' 73: 73: Excluding 3 bonded neighbours molecule type 'methane' 73: Analysing residue names: 73: There are: 216 Water residues 73: There are: 1 Other residues 73: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 73: 73: This run will generate roughly 0 Mb of data 73: [ OK ] Simple/TpiTest.ReproducesOutput/0 (680 ms) 73: [ RUN ] Simple/TpiTest.ReproducesOutput/1 73: Generating 1-4 interactions: fudge = 0.5 73: Number of degrees of freedom in T-Coupling group System is 1308.00 73: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 73: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 73: TPI is not implemented for GPUs. 73: 73: Using 1 MPI thread 73: Using 1 OpenMP thread 73: 73: 73: NOTE: Thread affinity was not set. 73: Reading frames from gro file '216 water molecules', 648 atoms. 73: Reading frame 0 time 0.000 mu 4.535e+01 4.535e+01 73: Last frame 0 time 0.000 73: Generated 331705 of the 331705 non-bonded parameter combinations 73: 73: Generated 331705 of the 331705 1-4 parameter combinations 73: 73: Excluding 2 bonded neighbours molecule type 'SOL' 73: 73: Excluding 3 bonded neighbours molecule type 'methane' 73: Analysing residue names: 73: There are: 216 Water residues 73: There are: 1 Other residues 73: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 73: 73: This run will generate roughly 0 Mb of data 73: [ OK ] Simple/TpiTest.ReproducesOutput/1 (486 ms) 73: [ RUN ] Simple/TpiTest.ReproducesOutput/2 73: Generating 1-4 interactions: fudge = 0.5 73: Number of degrees of freedom in T-Coupling group System is 1308.00 73: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 73: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 73: TPI is not implemented for GPUs. 73: 73: Using 1 MPI thread 73: Using 1 OpenMP thread 73: 73: 73: NOTE: Thread affinity was not set. 73: Reading frames from gro file '216 water molecules', 648 atoms. 73: Reading frame 0 time 0.000 mu 6.203e+01 6.203e+01 73: Last frame 0 time 0.000 73: Generated 331705 of the 331705 non-bonded parameter combinations 73: 73: Generated 331705 of the 331705 1-4 parameter combinations 73: 73: Excluding 2 bonded neighbours molecule type 'SOL' 73: 73: Excluding 3 bonded neighbours molecule type 'methane' 73: Analysing residue names: 73: There are: 216 Water residues 73: There are: 1 Other residues 73: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 73: 73: This run will generate roughly 0 Mb of data 73: [ OK ] Simple/TpiTest.ReproducesOutput/2 (498 ms) 73: [----------] 3 tests from Simple/TpiTest (1665 ms total) 73: 73: [----------] Global test environment tear-down 73: [==========] 3 tests from 1 test suite ran. (1852 ms total) 73: [ PASSED ] 3 tests. 73/90 Test #73: MdrunTpiTests ............................. Passed 1.90 sec test 74 Start 74: MdrunMpiTests 74: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/mdrun-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/MdrunMpiTests.xml" 74: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests 74: Test timeout computed to be: 600 74: [==========] Running 16 tests from 2 test suites. 74: [----------] Global test environment set-up. 74: [----------] 4 tests from MimicTest 74: [ RUN ] MimicTest.OneQuantumMol 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 74: For a correct single-point energy evaluation with nsteps = 0, use 74: continuation = yes to avoid constraining the input coordinates. 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group rest is 21.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 74: NVE simulation with an initial temperature of zero: will use a Verlet 74: buffer of 10%. Check your energy drift! 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 2 MPI threads 74: Using 2 OpenMP threads per tMPI thread 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro' 74: 74: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 74: Reading frame 0 time 0.000 Last frame 0 time 0.000 74: 74: NOTE: 27 % of the run time was spent in domain decomposition, 74: 11 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.001 380.7 74: (ns/day) (hour/ns) 74: Performance: 104.450 0.230 74: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 805298028 74: 74: Generated 10 of the 10 non-bonded parameter combinations 74: 74: Generated 10 of the 10 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 74: 74: This run will generate roughly 0 Mb of data 74: [ OK ] MimicTest.OneQuantumMol (68 ms) 74: [ RUN ] MimicTest.AllQuantumMol 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 74: For a correct single-point energy evaluation with nsteps = 0, use 74: continuation = yes to avoid constraining the input coordinates. 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group rest is 21.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 74: NVE simulation with an initial temperature of zero: will use a Verlet 74: buffer of 10%. Check your energy drift! 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 2 MPI threads 74: Using 2 OpenMP threads per tMPI thread 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro' 74: 74: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 74: Reading frame 0 time 0.000 Last frame 0 time 0.000 74: 74: NOTE: 23 % of the run time was spent in domain decomposition, 74: 16 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: NOTE: 5 % of the run time was spent communicating energies, 74: you might want to increase some nst* mdp options 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.001 377.6 74: (ns/day) (hour/ns) 74: Performance: 155.765 0.154 74: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -1073758225 74: 74: Generated 10 of the 10 non-bonded parameter combinations 74: 74: Generated 10 of the 10 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 74: 74: This run will generate roughly 0 Mb of data 74: [ OK ] MimicTest.AllQuantumMol (59 ms) 74: [ RUN ] MimicTest.TwoQuantumMol 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 74: For a correct single-point energy evaluation with nsteps = 0, use 74: continuation = yes to avoid constraining the input coordinates. 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group rest is 21.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 74: NVE simulation with an initial temperature of zero: will use a Verlet 74: buffer of 10%. Check your energy drift! 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 2 MPI threads 74: Using 2 OpenMP threads per tMPI thread 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro' 74: 74: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 74: Reading frame 0 time 0.000 Last frame 0 time 0.000 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.045 0.011 397.6 74: (ns/day) (hour/ns) 74: Performance: 7.572 3.170 74: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -1314137137 74: 74: Generated 10 of the 10 non-bonded parameter combinations 74: 74: Generated 10 of the 10 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 74: 74: This run will generate roughly 0 Mb of data 74: [ OK ] MimicTest.TwoQuantumMol (75 ms) 74: [ RUN ] MimicTest.BondCuts 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 74: For a correct single-point energy evaluation with nsteps = 0, use 74: continuation = yes to avoid constraining the input coordinates. 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group rest is 66.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 74: NVE simulation: will use the initial temperature of 300.368 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 2 MPI threads 74: Using 2 OpenMP threads per tMPI thread 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 74: 74: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 74: Reading frame 0 time 0.000 Last frame 0 time 0.000 74: 74: NOTE: 20 % of the run time was spent in domain decomposition, 74: 13 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: NOTE: 6 % of the run time was spent communicating energies, 74: you might want to increase some nst* mdp options 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.001 383.0 74: (ns/day) (hour/ns) 74: Performance: 109.615 0.219 74: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -168820737 74: 74: Generated 2211 of the 2211 non-bonded parameter combinations 74: 74: Generated 2211 of the 2211 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 74: 74: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 74: 74: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: [ OK ] MimicTest.BondCuts (91 ms) 74: [----------] 4 tests from MimicTest (296 ms total) 74: 74: [----------] 12 tests from DomainDecomposition/DomDecSpecialCasesTest 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group rest is 9.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 74: NVE simulation with an initial temperature of zero: will use a Verlet 74: buffer of 10%. Check your energy drift! 74: 74: 74: There was 1 NOTE 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 9.00 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group rest is 9.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 74: NVE simulation with an initial temperature of zero: will use a Verlet 74: buffer of 10%. Check your energy drift! 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 74: The optimal PME mesh load for parallel simulations is below 0.5 74: and for highly parallel simulations between 0.25 and 0.33, 74: for higher performance, increase the cut-off and the PME grid spacing. 74: 74: 74: 74: There were 2 NOTEs 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 9.00 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 74: The optimal PME mesh load for parallel simulations is below 0.5 74: and for highly parallel simulations between 0.25 and 0.33, 74: for higher performance, increase the cut-off and the PME grid spacing. 74: 74: 74: 74: There was 1 NOTE 74: Setting the LD random seed to -1007951873 74: 74: Generated 3 of the 3 non-bonded parameter combinations 74: 74: Generated 3 of the 3 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 74: 74: This run will generate roughly 0 Mb of data 74: Setting the LD random seed to -404750669 74: 74: Generated 3 of the 3 non-bonded parameter combinations 74: 74: Generated 3 of the 3 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 74: 74: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 1.017 nm, buffer size 0.017 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 1.005 nm, buffer size 0.005 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: Setting the LD random seed to -270666754 74: 74: Generated 3 of the 3 non-bonded parameter combinations 74: 74: Generated 3 of the 3 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 74: 74: The largest distance between excluded atoms is 0.164 nm between atom 2 and 3 74: Calculating fourier grid dimensions for X Y Z 74: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 74: 74: Estimate for the relative computational load of the PME mesh part: 1.00 74: 74: This run will generate roughly 0 Mb of data 74: Setting the LD random seed to -155648353 74: 74: Generated 3 of the 3 non-bonded parameter combinations 74: 74: Generated 3 of the 3 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 74: 74: The largest distance between excluded atoms is 0.164 nm between atom 2 and 3 74: 74: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: Calculating fourier grid dimensions for X Y Z 74: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 74: 74: Estimate for the relative computational load of the PME mesh part: 1.00 74: 74: This run will generate roughly 0 Mb of data 74: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme0 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_RF_No.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 2 MPI threads 74: Using 2 OpenMP threads per tMPI thread 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 20 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: 74: Dynamic load balancing report: 74: DLB was off during the run due to low measured imbalance. 74: Average load imbalance: 2.9%. 74: The balanceable part of the MD step is 51%, load imbalance is computed from this. 74: Part of the total run time spent waiting due to load imbalance: 1.5%. 74: 74: 74: NOTE: 42 % of the run time was spent communicating energies, 74: you might want to increase some nst* mdp options 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.125 0.055 228.3 74: (ns/day) (hour/ns) 74: Performance: 33.061 0.726 74: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme0 (105 ms) 74: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 74: ./src/programs/mdrun/tests/domain_decomposition.cpp:385: Skipped 74: Test configuration is invalid: 74: Cannot have separate PME ranks when PME is not used 74: 74: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 (0 ms) 74: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 74: ./src/programs/mdrun/tests/domain_decomposition.cpp:385: Skipped 74: Test configuration is invalid: 74: Cannot have separate PME ranks when PME is not used 74: Cannot use two separate PME ranks when there are less than four ranks total 74: 74: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 74: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_RF_TemperatureAndPressure.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 10 to 50, rlist from 1.005 to 1.136 74: 74: Using 2 MPI threads 74: Using 2 OpenMP threads per tMPI thread 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 20 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: NOTE: 18 % of the run time was spent in domain decomposition, 74: 0 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: NOTE: 35 % of the run time was spent communicating energies, 74: you might want to increase some nst* mdp options 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.458 0.116 394.3 74: (ns/day) (hour/ns) 74: Performance: 15.619 1.537 74: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 (191 ms) 74: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 74: ./src/programs/mdrun/tests/domain_decomposition.cpp:385: Skipped 74: Test configuration is invalid: 74: Cannot have separate PME ranks when PME is not used 74: 74: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 (0 ms) 74: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 74: ./src/programs/mdrun/tests/domain_decomposition.cpp:385: Skipped 74: Test configuration is invalid: 74: Cannot have separate PME ranks when PME is not used 74: Cannot use two separate PME ranks when there are less than four ranks total 74: 74: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 74: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme0 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_No.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 2 MPI threads 74: Using 2 OpenMP threads per tMPI thread 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 20 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: 74: Dynamic load balancing report: 74: DLB was off during the run due to low measured imbalance. 74: Average load imbalance: 12.5%. 74: The balanceable part of the MD step is 12%, load imbalance is computed from this. 74: Part of the total run time spent waiting due to load imbalance: 1.5%. 74: 74: 74: NOTE: 12 % of the run time was spent in domain decomposition, 74: 0 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 2.384 0.596 399.9 74: (ns/day) (hour/ns) 74: Performance: 3.043 7.886 74: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme0 (973 ms) 74: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme1 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_No.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 2 MPI threads 74: Using 2 OpenMP threads per tMPI thread 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 20 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.533 0.133 399.4 74: (ns/day) (hour/ns) 74: Performance: 13.600 1.765 74: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme1 (362 ms) 74: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 74: ./src/programs/mdrun/tests/domain_decomposition.cpp:385: Skipped 74: Test configuration is invalid: 74: Cannot use two separate PME ranks when there are less than four ranks total 74: 74: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 74: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_TemperatureAndPressure.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 10 to 100, rlist from 1 to 1 74: 74: Using 2 MPI threads 74: Using 2 OpenMP threads per tMPI thread 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 20 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: NOTE: 19 % of the run time was spent communicating energies, 74: you might want to increase some nst* mdp options 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.477 0.125 380.5 74: (ns/day) (hour/ns) 74: Performance: 14.460 1.660 74: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 (227 ms) 74: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_TemperatureAndPressure.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 10 to 100, rlist from 1 to 1 74: 74: Using 2 MPI threads 74: Using 2 OpenMP threads per tMPI thread 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 20 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.520 0.140 372.3 74: (ns/day) (hour/ns) 74: Performance: 12.999 1.846 74: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 (261 ms) 74: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 74: ./src/programs/mdrun/tests/domain_decomposition.cpp:385: Skipped 74: Test configuration is invalid: 74: Cannot use two separate PME ranks when there are less than four ranks total 74: 74: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 74: [----------] 12 tests from DomainDecomposition/DomDecSpecialCasesTest (2122 ms total) 74: 74: [----------] Global test environment tear-down 74: [==========] 16 tests from 2 test suites ran. (2810 ms total) 74: [ PASSED ] 10 tests. 74: [ SKIPPED ] 6 tests, listed below: 74: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 74: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 74: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 74: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 74: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 74: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 74/90 Test #74: MdrunMpiTests ............................. Passed 2.87 sec test 75 Start 75: MdrunMultiSimTests 75: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/mdrun-multisim-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/MdrunMultiSimTests.xml" 75: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests 75: Test timeout computed to be: 600 75: [==========] Running 2 tests from 1 test suite. 75: [----------] Global test environment set-up. 75: [----------] 2 tests from InNvt/MultiSimTerminationTest 75: [ RUN ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 75: [ OK ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 (0 ms) 75: [ RUN ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/1 75: [ OK ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/1 (0 ms) 75: [----------] 2 tests from InNvt/MultiSimTerminationTest (0 ms total) 75: 75: [----------] Global test environment tear-down 75: [==========] 2 tests from 1 test suite ran. (173 ms total) 75: [ PASSED ] 2 tests. 75: 75: YOU HAVE 4 DISABLED TESTS 75: 75/90 Test #75: MdrunMultiSimTests ........................ Passed 0.22 sec test 76 Start 76: MdrunMultiSimReplexTests 76: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/mdrun-multisim-replex-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/MdrunMultiSimReplexTests.xml" 76: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests 76: Test timeout computed to be: 600 76: [==========] Running 1 test from 1 test suite. 76: [----------] Global test environment set-up. 76: [----------] 1 test from InNvt/ReplicaExchangeTerminationTest 76: [ RUN ] InNvt/ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 76: [ OK ] InNvt/ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 (0 ms) 76: [----------] 1 test from InNvt/ReplicaExchangeTerminationTest (0 ms total) 76: 76: [----------] Global test environment tear-down 76: [==========] 1 test from 1 test suite ran. (194 ms total) 76: [ PASSED ] 1 test. 76: 76: YOU HAVE 4 DISABLED TESTS 76: 76/90 Test #76: MdrunMultiSimReplexTests .................. Passed 0.25 sec test 77 Start 77: MdrunMultiSimReplexEquivalenceTests 77: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/mdrun-multisim-replex-equivalence-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/MdrunMultiSimReplexEquivalenceTests.xml" 77: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests 77: Test timeout computed to be: 600 77: [==========] Running 0 tests from 0 test suites. 77: [==========] 0 tests from 0 test suites ran. (0 ms total) 77: [ PASSED ] 0 tests. 77: 77: YOU HAVE 10 DISABLED TESTS 77: 77/90 Test #77: MdrunMultiSimReplexEquivalenceTests ....... Passed 0.05 sec test 78 Start 78: MdrunMpi1RankPmeTests 78: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/mdrun-mpi-pme-test "-ntomp" "2" "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/MdrunMpi1RankPmeTests.xml" 78: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests 78: Test timeout computed to be: 600 78: [==========] Running 19 tests from 1 test suite. 78: [----------] Global test environment set-up. 78: [----------] 19 tests from ReproducesEnergies/PmeTest 78: Number of degrees of freedom in T-Coupling group rest is 12.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 78: NVE simulation: will use the initial temperature of 1046.791 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 78: The optimal PME mesh load for parallel simulations is below 0.5 78: and for highly parallel simulations between 0.25 and 0.33, 78: for higher performance, increase the cut-off and the PME grid spacing. 78: 78: 78: 78: There were 2 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 78: For a correct single-point energy evaluation with nsteps = 0, use 78: continuation = yes to avoid constraining the input coordinates. 78: 78: Number of degrees of freedom in T-Coupling group rest is 13.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 78: NVE simulation: will use the initial temperature of 966.268 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 78: The optimal PME mesh load for parallel simulations is below 0.5 78: and for highly parallel simulations between 0.25 and 0.33, 78: for higher performance, increase the cut-off and the PME grid spacing. 78: 78: 78: 78: There were 3 NOTEs 78: Setting the LD random seed to -270730379 78: 78: Generated 8 of the 10 non-bonded parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'Methanol' 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 78: 78: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: Calculating fourier grid dimensions for X Y Z 78: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 78: 78: Estimate for the relative computational load of the PME mesh part: 1.00 78: 78: This run will generate roughly 0 Mb of data 78: Setting the LD random seed to -1644340237 78: 78: Generated 8 of the 10 non-bonded parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'Methanol' 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 78: 78: Searching the wall atom type(s) 78: 78: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: Calculating fourier grid dimensions for X Y Z 78: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118 78: 78: Estimate for the relative computational load of the PME mesh part: 1.00 78: 78: This run will generate roughly 0 Mb of data 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu 78: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 78: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc-and-methanol' 78: 20 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.086 0.043 199.6 78: (ns/day) (hour/ns) 78: Performance: 42.172 0.569 78: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_cpu.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu (219 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto 78: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 78: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc-and-methanol' 78: 20 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.054 0.027 199.3 78: (ns/day) (hour/ns) 78: Performance: 67.474 0.356 78: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_auto.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto (35 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 78: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 78: Test is being skipped because: 78: it targets GPU execution, but no compatible devices were detected 78: PME GPU does not support: 78: Non-GPU build of GROMACS. 78: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 78: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 78: Test is being skipped because: 78: it targets GPU execution, but no compatible devices were detected 78: PME GPU does not support: 78: Non-GPU build of GROMACS. 78: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 78: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 78: Test is being skipped because: 78: it targets GPU execution, but no compatible devices were detected 78: PME GPU does not support: 78: Non-GPU build of GROMACS. 78: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu 78: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 78: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc-and-methanol' 78: 0 steps, 0.0 ps. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.010 0.005 195.0 78: (ns/day) (hour/ns) 78: Performance: 16.823 1.427 78: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_0__pme_cpu.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu (583 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 78: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 78: Test is being skipped because: 78: it targets GPU execution, but no compatible devices were detected 78: PME GPU does not support: 78: Non-GPU build of GROMACS. 78: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 78: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 78: Test is being skipped because: 78: it targets GPU execution, but no compatible devices were detected 78: PME GPU does not support: 78: Non-GPU build of GROMACS. 78: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu 78: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 78: Test is being skipped because: 78: it targets using PME rank(s) but the simulation is using only one rank 78: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto 78: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 78: Test is being skipped because: 78: it targets using PME rank(s) but the simulation is using only one rank 78: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 78: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 78: Test is being skipped because: 78: it targets using PME rank(s) but the simulation is using only one rank 78: it targets GPU execution, but no compatible devices were detected 78: PME GPU does not support: 78: Non-GPU build of GROMACS. 78: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 78: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 78: Test is being skipped because: 78: it targets using PME rank(s) but the simulation is using only one rank 78: it targets GPU execution, but no compatible devices were detected 78: PME GPU does not support: 78: Non-GPU build of GROMACS. 78: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 78: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 78: Test is being skipped because: 78: it targets using PME rank(s) but the simulation is using only one rank 78: it targets GPU execution, but no compatible devices were detected 78: PME GPU does not support: 78: Non-GPU build of GROMACS. 78: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu 78: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 78: Test is being skipped because: 78: it targets using PME rank(s) but the simulation is using only one rank 78: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu (2 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 78: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 78: Test is being skipped because: 78: it targets using PME rank(s) but the simulation is using only one rank 78: it targets GPU execution, but no compatible devices were detected 78: PME GPU does not support: 78: Non-GPU build of GROMACS. 78: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 78: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 78: Test is being skipped because: 78: it targets using PME rank(s) but the simulation is using only one rank 78: it targets GPU execution, but no compatible devices were detected 78: PME GPU does not support: 78: Non-GPU build of GROMACS. 78: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu 78: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 78: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc-and-methanol' 78: 20 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.322 0.161 199.8 78: (ns/day) (hour/ns) 78: Performance: 11.274 2.129 78: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__tunepme__npme_0__pme_cpu.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu (176 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 78: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 78: Test is being skipped because: 78: it targets GPU execution, but no compatible devices were detected 78: PME GPU does not support: 78: Non-GPU build of GROMACS. 78: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 78: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 78: Test is being skipped because: 78: it targets GPU execution, but no compatible devices were detected 78: PME GPU does not support: 78: Non-GPU build of GROMACS. 78: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 78: [----------] 19 tests from ReproducesEnergies/PmeTest (1018 ms total) 78: 78: [----------] Global test environment tear-down 78: [==========] 19 tests from 1 test suite ran. (1257 ms total) 78: [ PASSED ] 4 tests. 78: [ SKIPPED ] 15 tests, listed below: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 78/90 Test #78: MdrunMpi1RankPmeTests ..................... Passed 1.31 sec test 79 Start 79: MdrunMpi2RankPmeTests 79: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/mdrun-mpi-pme-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/MdrunMpi2RankPmeTests.xml" 79: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests 79: Test timeout computed to be: 600 79: [==========] Running 19 tests from 1 test suite. 79: [----------] Global test environment set-up. 79: [----------] 19 tests from ReproducesEnergies/PmeTest 79: Number of degrees of freedom in T-Coupling group rest is 12.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 79: NVE simulation: will use the initial temperature of 1046.791 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 79: The optimal PME mesh load for parallel simulations is below 0.5 79: and for highly parallel simulations between 0.25 and 0.33, 79: for higher performance, increase the cut-off and the PME grid spacing. 79: 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 79: For a correct single-point energy evaluation with nsteps = 0, use 79: continuation = yes to avoid constraining the input coordinates. 79: 79: Number of degrees of freedom in T-Coupling group rest is 13.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 79: NVE simulation: will use the initial temperature of 966.268 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 79: The optimal PME mesh load for parallel simulations is below 0.5 79: and for highly parallel simulations between 0.25 and 0.33, 79: for higher performance, increase the cut-off and the PME grid spacing. 79: 79: 79: 79: There were 3 NOTEs 79: Setting the LD random seed to 1438567735 79: 79: Generated 8 of the 10 non-bonded parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'Methanol' 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 79: 79: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: Calculating fourier grid dimensions for X Y Z 79: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 79: 79: Estimate for the relative computational load of the PME mesh part: 1.00 79: 79: This run will generate roughly 0 Mb of data 79: Setting the LD random seed to -520106658 79: 79: Generated 8 of the 10 non-bonded parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'Methanol' 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 79: 79: Searching the wall atom type(s) 79: 79: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: Calculating fourier grid dimensions for X Y Z 79: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118 79: 79: Estimate for the relative computational load of the PME mesh part: 1.00 79: 79: This run will generate roughly 0 Mb of data 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu 79: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 2 MPI threads 79: Using 2 OpenMP threads per tMPI thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc-and-methanol' 79: 20 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: 79: Dynamic load balancing report: 79: DLB was off during the run due to low measured imbalance. 79: Average load imbalance: 6.3%. 79: The balanceable part of the MD step is 2%, load imbalance is computed from this. 79: Part of the total run time spent waiting due to load imbalance: 0.2%. 79: 79: 79: NOTE: 12 % of the run time was spent communicating energies, 79: you might want to increase some nst* mdp options 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.526 0.132 399.6 79: (ns/day) (hour/ns) 79: Performance: 13.774 1.742 79: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_cpu.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu (534 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto 79: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 2 MPI threads 79: Using 2 OpenMP threads per tMPI thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc-and-methanol' 79: 20 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: 79: Dynamic load balancing report: 79: DLB was off during the run due to low measured imbalance. 79: Average load imbalance: 7.1%. 79: The balanceable part of the MD step is 4%, load imbalance is computed from this. 79: Part of the total run time spent waiting due to load imbalance: 0.3%. 79: 79: 79: NOTE: 10 % of the run time was spent communicating energies, 79: you might want to increase some nst* mdp options 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.349 0.087 399.1 79: (ns/day) (hour/ns) 79: Performance: 20.768 1.156 79: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_auto.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto (209 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 79: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 79: Test is being skipped because: 79: it targets GPU execution, but no compatible devices were detected 79: it targets PME decomposition, but that is not supported 79: PME GPU does not support: 79: Non-GPU build of GROMACS. 79: 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 79: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 79: Test is being skipped because: 79: it targets GPU execution, but no compatible devices were detected 79: it targets PME decomposition, but that is not supported 79: PME GPU does not support: 79: Non-GPU build of GROMACS. 79: 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 79: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 79: Test is being skipped because: 79: it targets GPU execution, but no compatible devices were detected 79: it targets PME decomposition, but that is not supported 79: PME GPU does not support: 79: Non-GPU build of GROMACS. 79: 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto (0 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu 79: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 2 MPI threads 79: Using 2 OpenMP threads per tMPI thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc-and-methanol' 79: 0 steps, 0.0 ps. 79: 79: NOTE: 14 % of the run time was spent communicating energies, 79: you might want to increase some nst* mdp options 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.067 0.017 395.3 79: (ns/day) (hour/ns) 79: Performance: 5.089 4.716 79: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_0__pme_cpu.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu (756 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 79: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 79: Test is being skipped because: 79: it targets GPU execution, but no compatible devices were detected 79: it targets PME decomposition, but that is not supported 79: PME GPU does not support: 79: Non-GPU build of GROMACS. 79: 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 79: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 79: Test is being skipped because: 79: it targets GPU execution, but no compatible devices were detected 79: it targets PME decomposition, but that is not supported 79: PME GPU does not support: 79: Non-GPU build of GROMACS. 79: 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu 79: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 2 MPI threads 79: Using 2 OpenMP threads per tMPI thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc-and-methanol' 79: 20 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.917 0.231 396.7 79: (ns/day) (hour/ns) 79: Performance: 7.852 3.056 79: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_1__pme_cpu.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu (514 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto 79: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 2 MPI threads 79: Using 2 OpenMP threads per tMPI thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc-and-methanol' 79: 20 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.415 0.104 399.1 79: (ns/day) (hour/ns) 79: Performance: 17.450 1.375 79: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_1__pme_auto.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto (161 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 79: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 79: Test is being skipped because: 79: it targets GPU execution, but no compatible devices were detected 79: PME GPU does not support: 79: Non-GPU build of GROMACS. 79: 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 79: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 79: Test is being skipped because: 79: it targets GPU execution, but no compatible devices were detected 79: PME GPU does not support: 79: Non-GPU build of GROMACS. 79: 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 79: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 79: Test is being skipped because: 79: it targets GPU execution, but no compatible devices were detected 79: PME GPU does not support: 79: Non-GPU build of GROMACS. 79: 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto (0 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu 79: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 2 MPI threads 79: Using 2 OpenMP threads per tMPI thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc-and-methanol' 79: 0 steps, 0.0 ps. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.055 0.014 386.5 79: (ns/day) (hour/ns) 79: Performance: 6.123 3.919 79: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_1__pme_cpu.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu (738 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 79: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 79: Test is being skipped because: 79: it targets GPU execution, but no compatible devices were detected 79: PME GPU does not support: 79: Non-GPU build of GROMACS. 79: 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 79: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 79: Test is being skipped because: 79: it targets GPU execution, but no compatible devices were detected 79: PME GPU does not support: 79: Non-GPU build of GROMACS. 79: 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu 79: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 2 MPI threads 79: Using 2 OpenMP threads per tMPI thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc-and-methanol' 79: 20 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: 79: Dynamic load balancing report: 79: DLB was off during the run due to low measured imbalance. 79: Average load imbalance: 8.9%. 79: The balanceable part of the MD step is 5%, load imbalance is computed from this. 79: Part of the total run time spent waiting due to load imbalance: 0.4%. 79: 79: 79: NOTE: 12 % of the run time was spent communicating energies, 79: you might want to increase some nst* mdp options 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.200 0.050 399.1 79: (ns/day) (hour/ns) 79: Performance: 36.187 0.663 79: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__tunepme__npme_0__pme_cpu.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu (124 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 79: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 79: Test is being skipped because: 79: it targets GPU execution, but no compatible devices were detected 79: it targets PME decomposition, but that is not supported 79: PME GPU does not support: 79: Non-GPU build of GROMACS. 79: 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 79: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 79: Test is being skipped because: 79: it targets GPU execution, but no compatible devices were detected 79: it targets PME decomposition, but that is not supported 79: PME GPU does not support: 79: Non-GPU build of GROMACS. 79: 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 79: [----------] 19 tests from ReproducesEnergies/PmeTest (3042 ms total) 79: 79: [----------] Global test environment tear-down 79: [==========] 19 tests from 1 test suite ran. (3207 ms total) 79: [ PASSED ] 7 tests. 79: [ SKIPPED ] 12 tests, listed below: 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 79/90 Test #79: MdrunMpi2RankPmeTests ..................... Passed 3.24 sec test 80 Start 80: MdrunCoordinationBasicTests1Rank 80: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/mdrun-coordination-basic-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/MdrunCoordinationBasicTests1Rank.xml" 80: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests 80: Test timeout computed to be: 1920 80: [==========] Running 1 test from 1 test suite. 80: [----------] Global test environment set-up. 80: [----------] 1 test from BasicPropagators/PeriodicActionsTest 80: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 1 OpenMP thread 80: 80: 80: NOTE: Thread affinity was not set. 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.024 0.024 99.7 80: (ns/day) (hour/ns) 80: Performance: 61.218 0.392 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 1 OpenMP thread 80: 80: 80: NOTE: Thread affinity was not set. 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.020 0.020 99.3 80: (ns/day) (hour/ns) 80: Performance: 73.447 0.327 80: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: COM removal frequency is set to (1). 80: Other settings require a global communication frequency of 4. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 4. 80: 80: 80: There were 5 NOTEs 80: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 1 OpenMP thread 80: 80: 80: NOTE: Thread affinity was not set. 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.015 0.015 99.5 80: (ns/day) (hour/ns) 80: Performance: 96.891 0.248 80: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: COM removal frequency is set to (1). 80: Other settings require a global communication frequency of 100. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 100. 80: 80: 80: There were 4 NOTEs 80: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 1 OpenMP thread 80: 80: 80: NOTE: Thread affinity was not set. 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.020 0.020 99.6 80: (ns/day) (hour/ns) 80: Performance: 74.359 0.323 80: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: COM removal frequency is set to (1). 80: Other settings require a global communication frequency of 100. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 100. 80: 80: 80: There were 4 NOTEs 80: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 1 OpenMP thread 80: 80: 80: NOTE: Thread affinity was not set. 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.013 0.013 99.5 80: (ns/day) (hour/ns) 80: Performance: 108.856 0.220 80: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: COM removal frequency is set to (1). 80: Other settings require a global communication frequency of 100. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 100. 80: 80: 80: There were 4 NOTEs 80: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 1 OpenMP thread 80: 80: 80: NOTE: Thread affinity was not set. 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.022 0.022 99.6 80: (ns/day) (hour/ns) 80: Performance: 65.446 0.367 80: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 80: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (174 ms) 80: [----------] 1 test from BasicPropagators/PeriodicActionsTest (174 ms total) 80: 80: [----------] Global test environment tear-down 80: [==========] 1 test from 1 test suite ran. (371 ms total) 80: [ PASSED ] 1 test. 80/90 Test #80: MdrunCoordinationBasicTests1Rank .......... Passed 0.42 sec test 81 Start 81: MdrunCoordinationBasicTests2Ranks 81: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/mdrun-coordination-basic-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/MdrunCoordinationBasicTests2Ranks.xml" 81: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests 81: Test timeout computed to be: 1920 81: [==========] Running 1 test from 1 test suite. 81: [----------] Global test environment set-up. 81: [----------] 1 test from BasicPropagators/PeriodicActionsTest 81: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 1 OpenMP thread per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 0.5%. 81: The balanceable part of the MD step is 53%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 0.3%. 81: 81: 81: NOTE: 49 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.127 0.064 199.7 81: (ns/day) (hour/ns) 81: Performance: 23.115 1.038 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 1 OpenMP thread per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 0.3%. 81: The balanceable part of the MD step is 54%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 0.1%. 81: 81: 81: NOTE: 49 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.045 0.023 199.2 81: (ns/day) (hour/ns) 81: Performance: 64.325 0.373 81: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: COM removal frequency is set to (1). 81: Other settings require a global communication frequency of 4. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 4. 81: 81: 81: There were 5 NOTEs 81: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 1 OpenMP thread per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 0.2%. 81: The balanceable part of the MD step is 47%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 0.1%. 81: 81: 81: NOTE: 51 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.021 0.011 198.5 81: (ns/day) (hour/ns) 81: Performance: 136.244 0.176 81: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: COM removal frequency is set to (1). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 1 OpenMP thread per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 1.9%. 81: The balanceable part of the MD step is 45%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 0.9%. 81: 81: 81: NOTE: 53 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.062 0.031 199.2 81: (ns/day) (hour/ns) 81: Performance: 46.812 0.513 81: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: COM removal frequency is set to (1). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 1 OpenMP thread per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 0.8%. 81: The balanceable part of the MD step is 43%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 0.4%. 81: 81: 81: NOTE: 48 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.056 0.028 199.3 81: (ns/day) (hour/ns) 81: Performance: 52.440 0.458 81: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: COM removal frequency is set to (1). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 1 OpenMP thread per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 0.7%. 81: The balanceable part of the MD step is 47%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 0.3%. 81: 81: 81: NOTE: 61 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.054 0.027 199.0 81: (ns/day) (hour/ns) 81: Performance: 54.415 0.441 81: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 81: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (368 ms) 81: [----------] 1 test from BasicPropagators/PeriodicActionsTest (368 ms total) 81: 81: [----------] Global test environment tear-down 81: [==========] 1 test from 1 test suite ran. (538 ms total) 81: [ PASSED ] 1 test. 81/90 Test #81: MdrunCoordinationBasicTests2Ranks ......... Passed 0.59 sec test 82 Start 82: MdrunCoordinationCouplingTests1Rank 82: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/mdrun-coordination-coupling-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/MdrunCoordinationCouplingTests1Rank.xml" 82: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests 82: Test timeout computed to be: 1920 82: [==========] Running 25 tests from 1 test suite. 82: [----------] Global test environment set-up. 82: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.032 0.032 99.8 82: (ns/day) (hour/ns) 82: Performance: 45.619 0.526 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.023 0.023 99.7 82: (ns/day) (hour/ns) 82: Performance: 63.386 0.379 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 4. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 4. 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.024 0.024 99.6 82: (ns/day) (hour/ns) 82: Performance: 61.878 0.388 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.034 0.034 99.8 82: (ns/day) (hour/ns) 82: Performance: 43.218 0.555 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.032 0.032 99.7 82: (ns/day) (hour/ns) 82: Performance: 45.345 0.529 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.032 0.032 99.8 82: (ns/day) (hour/ns) 82: Performance: 45.896 0.523 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (241 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.025 0.025 99.7 82: (ns/day) (hour/ns) 82: Performance: 59.126 0.406 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.007 0.007 99.1 82: (ns/day) (hour/ns) 82: Performance: 205.107 0.117 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.007 0.007 99.1 82: (ns/day) (hour/ns) 82: Performance: 202.332 0.119 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.020 0.020 99.7 82: (ns/day) (hour/ns) 82: Performance: 73.169 0.328 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.730 0.730 100.0 82: (ns/day) (hour/ns) 82: Performance: 2.012 11.929 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.245 0.245 100.0 82: (ns/day) (hour/ns) 82: Performance: 6.005 3.997 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (1390 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.051 0.051 99.8 82: (ns/day) (hour/ns) 82: Performance: 28.976 0.828 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.036 0.036 99.6 82: (ns/day) (hour/ns) 82: Performance: 40.815 0.588 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.034 0.034 99.8 82: (ns/day) (hour/ns) 82: Performance: 43.378 0.553 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.014 0.014 99.4 82: (ns/day) (hour/ns) 82: Performance: 102.169 0.235 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.020 0.020 99.5 82: (ns/day) (hour/ns) 82: Performance: 74.645 0.322 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.015 0.015 99.1 82: (ns/day) (hour/ns) 82: Performance: 97.522 0.246 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (272 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.016 0.016 99.4 82: (ns/day) (hour/ns) 82: Performance: 90.813 0.264 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.011 0.011 98.9 82: (ns/day) (hour/ns) 82: Performance: 128.098 0.187 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.010 0.010 99.1 82: (ns/day) (hour/ns) 82: Performance: 146.426 0.164 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.017 0.017 99.5 82: (ns/day) (hour/ns) 82: Performance: 87.931 0.273 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.014 0.014 99.2 82: (ns/day) (hour/ns) 82: Performance: 103.314 0.232 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.012 0.012 99.3 82: (ns/day) (hour/ns) 82: Performance: 119.973 0.200 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (139 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.013 0.013 99.4 82: (ns/day) (hour/ns) 82: Performance: 112.759 0.213 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.013 0.013 99.4 82: (ns/day) (hour/ns) 82: Performance: 115.953 0.207 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.011 0.011 99.2 82: (ns/day) (hour/ns) 82: Performance: 128.740 0.186 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.012 0.012 99.2 82: (ns/day) (hour/ns) 82: Performance: 118.566 0.202 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.024 0.024 99.7 82: (ns/day) (hour/ns) 82: Performance: 60.069 0.400 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.019 0.019 99.6 82: (ns/day) (hour/ns) 82: Performance: 77.730 0.309 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (163 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.015 0.015 99.4 82: (ns/day) (hour/ns) 82: Performance: 96.292 0.249 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.012 0.012 99.2 82: (ns/day) (hour/ns) 82: Performance: 124.321 0.193 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.012 0.013 99.0 82: (ns/day) (hour/ns) 82: Performance: 116.385 0.206 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.020 0.020 99.6 82: (ns/day) (hour/ns) 82: Performance: 74.402 0.323 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.034 0.034 99.6 82: (ns/day) (hour/ns) 82: Performance: 43.146 0.556 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.020 0.020 99.6 82: (ns/day) (hour/ns) 82: Performance: 74.262 0.323 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (223 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.021 0.021 99.5 82: (ns/day) (hour/ns) 82: Performance: 68.416 0.351 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.034 0.034 99.8 82: (ns/day) (hour/ns) 82: Performance: 43.210 0.555 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.020 0.020 99.6 82: (ns/day) (hour/ns) 82: Performance: 72.778 0.330 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.026 0.027 98.9 82: (ns/day) (hour/ns) 82: Performance: 55.422 0.433 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.030 0.030 99.6 82: (ns/day) (hour/ns) 82: Performance: 48.927 0.491 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.031 0.031 99.7 82: (ns/day) (hour/ns) 82: Performance: 47.291 0.507 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (242 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.030 0.030 99.7 82: (ns/day) (hour/ns) 82: Performance: 49.645 0.483 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.080 0.080 99.9 82: (ns/day) (hour/ns) 82: Performance: 18.444 1.301 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.023 0.023 98.9 82: (ns/day) (hour/ns) 82: Performance: 63.223 0.380 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.023 0.024 99.6 82: (ns/day) (hour/ns) 82: Performance: 62.492 0.384 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.033 0.033 99.7 82: (ns/day) (hour/ns) 82: Performance: 44.636 0.538 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.020 0.020 99.5 82: (ns/day) (hour/ns) 82: Performance: 73.950 0.325 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (276 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.024 0.024 99.4 82: (ns/day) (hour/ns) 82: Performance: 60.685 0.395 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.022 0.022 99.6 82: (ns/day) (hour/ns) 82: Performance: 67.216 0.357 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.012 0.013 99.2 82: (ns/day) (hour/ns) 82: Performance: 117.220 0.205 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.033 0.033 99.6 82: (ns/day) (hour/ns) 82: Performance: 44.705 0.537 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.028 0.028 99.7 82: (ns/day) (hour/ns) 82: Performance: 52.742 0.455 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.039 0.039 99.8 82: (ns/day) (hour/ns) 82: Performance: 37.704 0.637 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (248 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.037 0.038 99.7 82: (ns/day) (hour/ns) 82: Performance: 39.166 0.613 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.016 0.016 99.5 82: (ns/day) (hour/ns) 82: Performance: 94.108 0.255 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.026 0.026 99.7 82: (ns/day) (hour/ns) 82: Performance: 55.851 0.430 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.031 0.031 99.6 82: (ns/day) (hour/ns) 82: Performance: 47.616 0.504 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.031 0.031 99.6 82: (ns/day) (hour/ns) 82: Performance: 47.294 0.507 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.048 0.048 99.8 82: (ns/day) (hour/ns) 82: Performance: 30.765 0.780 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (289 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 1.251 1.251 100.0 82: (ns/day) (hour/ns) 82: Performance: 1.174 20.443 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.694 0.694 100.0 82: (ns/day) (hour/ns) 82: Performance: 2.117 11.337 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 1.030 1.030 100.0 82: (ns/day) (hour/ns) 82: Performance: 1.426 16.832 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 1.306 1.307 100.0 82: (ns/day) (hour/ns) 82: Performance: 1.124 21.348 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 1.483 1.484 100.0 82: (ns/day) (hour/ns) 82: Performance: 0.990 24.242 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 1.668 1.668 100.0 82: (ns/day) (hour/ns) 82: Performance: 0.881 27.254 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (9037 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.849 0.849 100.0 82: (ns/day) (hour/ns) 82: Performance: 1.731 13.866 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 1.617 1.618 100.0 82: (ns/day) (hour/ns) 82: Performance: 0.908 26.431 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.818 0.818 100.0 82: (ns/day) (hour/ns) 82: Performance: 1.795 13.369 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 1.440 1.440 100.0 82: (ns/day) (hour/ns) 82: Performance: 1.020 23.533 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 2.244 2.244 100.0 82: (ns/day) (hour/ns) 82: Performance: 0.654 36.671 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 1.930 1.930 100.0 82: (ns/day) (hour/ns) 82: Performance: 0.761 31.542 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (11819 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 1.957 1.958 100.0 82: (ns/day) (hour/ns) 82: Performance: 0.750 31.986 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 1.022 1.022 100.0 82: (ns/day) (hour/ns) 82: Performance: 1.437 16.702 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 4. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 4. 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.460 0.461 100.0 82: (ns/day) (hour/ns) 82: Performance: 3.189 7.525 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.033 0.033 99.8 82: (ns/day) (hour/ns) 82: Performance: 44.772 0.536 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.015 0.015 99.6 82: (ns/day) (hour/ns) 82: Performance: 100.509 0.239 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.013 0.013 99.6 82: (ns/day) (hour/ns) 82: Performance: 109.074 0.220 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (4059 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.030 0.030 99.8 82: (ns/day) (hour/ns) 82: Performance: 49.333 0.486 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.010 0.010 99.2 82: (ns/day) (hour/ns) 82: Performance: 146.447 0.164 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.014 0.014 99.3 82: (ns/day) (hour/ns) 82: Performance: 103.628 0.232 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.039 0.039 99.7 82: (ns/day) (hour/ns) 82: Performance: 37.952 0.632 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.040 0.040 99.8 82: (ns/day) (hour/ns) 82: Performance: 37.068 0.647 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.029 0.029 99.7 82: (ns/day) (hour/ns) 82: Performance: 50.184 0.478 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (229 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.032 0.032 99.8 82: (ns/day) (hour/ns) 82: Performance: 45.457 0.528 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.024 0.025 99.6 82: (ns/day) (hour/ns) 82: Performance: 59.846 0.401 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.027 0.027 99.7 82: (ns/day) (hour/ns) 82: Performance: 54.827 0.438 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.034 0.034 99.6 82: (ns/day) (hour/ns) 82: Performance: 43.117 0.557 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.083 0.083 99.9 82: (ns/day) (hour/ns) 82: Performance: 17.718 1.355 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.393 0.393 99.9 82: (ns/day) (hour/ns) 82: Performance: 3.735 6.425 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (704 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.144 0.145 99.9 82: (ns/day) (hour/ns) 82: Performance: 10.164 2.361 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.023 0.024 99.6 82: (ns/day) (hour/ns) 82: Performance: 62.443 0.384 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.014 0.014 99.5 82: (ns/day) (hour/ns) 82: Performance: 106.977 0.224 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.018 0.019 99.6 82: (ns/day) (hour/ns) 82: Performance: 79.227 0.303 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.022 0.022 99.5 82: (ns/day) (hour/ns) 82: Performance: 67.165 0.357 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.032 0.033 99.8 82: (ns/day) (hour/ns) 82: Performance: 45.185 0.531 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (359 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.070 0.070 99.9 82: (ns/day) (hour/ns) 82: Performance: 20.920 1.147 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.031 0.031 99.8 82: (ns/day) (hour/ns) 82: Performance: 46.889 0.512 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 4. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 4. 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.034 0.034 99.8 82: (ns/day) (hour/ns) 82: Performance: 43.715 0.549 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.062 0.062 99.9 82: (ns/day) (hour/ns) 82: Performance: 23.667 1.014 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.041 0.041 99.8 82: (ns/day) (hour/ns) 82: Performance: 35.546 0.675 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.029 0.029 99.8 82: (ns/day) (hour/ns) 82: Performance: 49.974 0.480 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (335 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.020 0.020 99.7 82: (ns/day) (hour/ns) 82: Performance: 74.895 0.320 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.019 0.019 99.7 82: (ns/day) (hour/ns) 82: Performance: 76.306 0.315 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.022 0.022 99.1 82: (ns/day) (hour/ns) 82: Performance: 66.629 0.360 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.023 0.023 99.7 82: (ns/day) (hour/ns) 82: Performance: 62.832 0.382 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.018 0.018 99.6 82: (ns/day) (hour/ns) 82: Performance: 82.255 0.292 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.017 0.017 99.6 82: (ns/day) (hour/ns) 82: Performance: 87.120 0.275 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (188 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.019 0.019 99.7 82: (ns/day) (hour/ns) 82: Performance: 76.698 0.313 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.018 0.018 99.6 82: (ns/day) (hour/ns) 82: Performance: 83.286 0.288 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.024 0.024 99.7 82: (ns/day) (hour/ns) 82: Performance: 60.658 0.396 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.034 0.034 99.8 82: (ns/day) (hour/ns) 82: Performance: 42.657 0.563 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.015 0.015 99.6 82: (ns/day) (hour/ns) 82: Performance: 98.606 0.243 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.027 0.027 99.7 82: (ns/day) (hour/ns) 82: Performance: 54.074 0.444 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (209 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.020 0.020 99.6 82: (ns/day) (hour/ns) 82: Performance: 74.211 0.323 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.009 0.009 99.2 82: (ns/day) (hour/ns) 82: Performance: 163.885 0.146 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.010 0.010 99.3 82: (ns/day) (hour/ns) 82: Performance: 140.849 0.170 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.016 0.016 99.4 82: (ns/day) (hour/ns) 82: Performance: 93.590 0.256 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.019 0.019 99.5 82: (ns/day) (hour/ns) 82: Performance: 77.484 0.310 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.018 0.018 99.5 82: (ns/day) (hour/ns) 82: Performance: 79.623 0.301 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (158 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.028 0.028 99.6 82: (ns/day) (hour/ns) 82: Performance: 53.122 0.452 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.041 0.041 99.8 82: (ns/day) (hour/ns) 82: Performance: 35.897 0.669 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.014 0.014 99.4 82: (ns/day) (hour/ns) 82: Performance: 102.439 0.234 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.023 0.023 99.6 82: (ns/day) (hour/ns) 82: Performance: 62.571 0.384 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.034 0.034 99.7 82: (ns/day) (hour/ns) 82: Performance: 42.934 0.559 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.578 0.578 100.0 82: (ns/day) (hour/ns) 82: Performance: 2.542 9.441 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (1168 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.036 0.036 99.7 82: (ns/day) (hour/ns) 82: Performance: 40.394 0.594 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.028 0.028 99.7 82: (ns/day) (hour/ns) 82: Performance: 52.569 0.457 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.023 0.023 99.7 82: (ns/day) (hour/ns) 82: Performance: 63.496 0.378 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.030 0.030 99.7 82: (ns/day) (hour/ns) 82: Performance: 49.333 0.486 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.018 0.018 99.6 82: (ns/day) (hour/ns) 82: Performance: 81.224 0.295 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.023 0.023 99.7 82: (ns/day) (hour/ns) 82: Performance: 63.234 0.380 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (237 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.032 0.032 99.7 82: (ns/day) (hour/ns) 82: Performance: 46.123 0.520 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.015 0.015 99.4 82: (ns/day) (hour/ns) 82: Performance: 94.938 0.253 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.014 0.014 99.4 82: (ns/day) (hour/ns) 82: Performance: 105.051 0.228 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.032 0.032 99.7 82: (ns/day) (hour/ns) 82: Performance: 45.722 0.525 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.070 0.070 99.8 82: (ns/day) (hour/ns) 82: Performance: 20.877 1.150 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.030 0.030 99.7 82: (ns/day) (hour/ns) 82: Performance: 49.474 0.485 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 (317 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: MTTK coupling is deprecated and will soon be removed 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: for current Trotter decomposition methods with vv, nsttcouple and 82: nstpcouple must be equal. Both have been reset to 82: min(nsttcouple,nstpcouple) = 2 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.106 0.106 99.9 82: (ns/day) (hour/ns) 82: Performance: 13.846 1.733 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: MTTK coupling is deprecated and will soon be removed 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: for current Trotter decomposition methods with vv, nsttcouple and 82: nstpcouple must be equal. Both have been reset to 82: min(nsttcouple,nstpcouple) = 2 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.022 0.022 99.5 82: (ns/day) (hour/ns) 82: Performance: 66.838 0.359 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: MTTK coupling is deprecated and will soon be removed 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: for current Trotter decomposition methods with vv, nsttcouple and 82: nstpcouple must be equal. Both have been reset to 82: min(nsttcouple,nstpcouple) = 2 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 5 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.024 0.024 99.6 82: (ns/day) (hour/ns) 82: Performance: 60.987 0.394 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: MTTK coupling is deprecated and will soon be removed 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: for current Trotter decomposition methods with vv, nsttcouple and 82: nstpcouple must be equal. Both have been reset to 82: min(nsttcouple,nstpcouple) = 2 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 5 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.023 0.023 99.4 82: (ns/day) (hour/ns) 82: Performance: 63.994 0.375 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: MTTK coupling is deprecated and will soon be removed 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: for current Trotter decomposition methods with vv, nsttcouple and 82: nstpcouple must be equal. Both have been reset to 82: min(nsttcouple,nstpcouple) = 2 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 5 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.036 0.036 99.8 82: (ns/day) (hour/ns) 82: Performance: 40.724 0.589 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: MTTK coupling is deprecated and will soon be removed 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: for current Trotter decomposition methods with vv, nsttcouple and 82: nstpcouple must be equal. Both have been reset to 82: min(nsttcouple,nstpcouple) = 2 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 5 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.017 0.017 99.3 82: (ns/day) (hour/ns) 82: Performance: 85.365 0.281 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 (319 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.038 0.039 99.7 82: (ns/day) (hour/ns) 82: Performance: 38.119 0.630 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.034 0.034 99.7 82: (ns/day) (hour/ns) 82: Performance: 42.976 0.558 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.038 0.038 99.8 82: (ns/day) (hour/ns) 82: Performance: 38.495 0.623 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.016 0.016 99.4 82: (ns/day) (hour/ns) 82: Performance: 91.580 0.262 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.052 0.052 99.8 82: (ns/day) (hour/ns) 82: Performance: 28.198 0.851 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.019 0.019 99.5 82: (ns/day) (hour/ns) 82: Performance: 78.735 0.305 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 (288 ms) 82: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest (32922 ms total) 82: 82: [----------] Global test environment tear-down 82: [==========] 25 tests from 1 test suite ran. (33097 ms total) 82: [ PASSED ] 25 tests. 82/90 Test #82: MdrunCoordinationCouplingTests1Rank ....... Passed 33.13 sec test 83 Start 83: MdrunCoordinationCouplingTests2Ranks 83: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/mdrun-coordination-coupling-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/MdrunCoordinationCouplingTests2Ranks.xml" 83: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests 83: Test timeout computed to be: 1920 83: [==========] Running 25 tests from 1 test suite. 83: [----------] Global test environment set-up. 83: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 3.2%. 83: The balanceable part of the MD step is 20%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.6%. 83: 83: 83: NOTE: 42 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.038 0.019 199.0 83: (ns/day) (hour/ns) 83: Performance: 76.222 0.315 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.9%. 83: The balanceable part of the MD step is 49%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.9%. 83: 83: 83: NOTE: 45 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.020 0.010 198.4 83: (ns/day) (hour/ns) 83: Performance: 149.274 0.161 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 4. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 4. 83: 83: 83: There were 4 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.4%. 83: The balanceable part of the MD step is 38%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.9%. 83: 83: 83: NOTE: 50 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 1.396 0.698 200.0 83: (ns/day) (hour/ns) 83: Performance: 2.104 11.405 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 4 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.9%. 83: The balanceable part of the MD step is 7%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.1%. 83: 83: 83: NOTE: 43 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.075 0.037 199.5 83: (ns/day) (hour/ns) 83: Performance: 39.228 0.612 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 4 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.8%. 83: The balanceable part of the MD step is 37%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.0%. 83: 83: 83: NOTE: 47 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.033 0.017 197.9 83: (ns/day) (hour/ns) 83: Performance: 87.936 0.273 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 4 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was turned on during the run due to measured imbalance. 83: Average load imbalance: 6.4%. 83: The balanceable part of the MD step is 33%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 2.1%. 83: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 83: 83: 83: NOTE: 53 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.068 0.034 198.9 83: (ns/day) (hour/ns) 83: Performance: 42.702 0.562 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (1373 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.1%. 83: The balanceable part of the MD step is 49%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.0%. 83: 83: 83: NOTE: 48 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.072 0.036 199.4 83: (ns/day) (hour/ns) 83: Performance: 40.505 0.593 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.3%. 83: The balanceable part of the MD step is 49%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.1%. 83: 83: 83: NOTE: 48 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.048 0.024 198.8 83: (ns/day) (hour/ns) 83: Performance: 60.722 0.395 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 0.8%. 83: The balanceable part of the MD step is 43%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.3%. 83: 83: 83: NOTE: 55 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.064 0.032 199.1 83: (ns/day) (hour/ns) 83: Performance: 45.481 0.528 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 0.9%. 83: The balanceable part of the MD step is 42%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.4%. 83: 83: 83: NOTE: 61 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.055 0.028 198.0 83: (ns/day) (hour/ns) 83: Performance: 53.225 0.451 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.1%. 83: The balanceable part of the MD step is 5%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.1%. 83: 83: 83: NOTE: 67 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.055 0.028 199.2 83: (ns/day) (hour/ns) 83: Performance: 53.067 0.452 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 0.8%. 83: The balanceable part of the MD step is 42%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.3%. 83: 83: 83: NOTE: 48 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.036 0.026 135.7 83: (ns/day) (hour/ns) 83: Performance: 55.837 0.430 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (593 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 0.9%. 83: The balanceable part of the MD step is 52%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.5%. 83: 83: 83: NOTE: 47 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.048 0.024 199.1 83: (ns/day) (hour/ns) 83: Performance: 61.428 0.391 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 0.4%. 83: The balanceable part of the MD step is 50%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.2%. 83: 83: 83: NOTE: 67 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.060 0.030 198.9 83: (ns/day) (hour/ns) 83: Performance: 48.947 0.490 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 0.5%. 83: The balanceable part of the MD step is 43%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.2%. 83: 83: 83: NOTE: 49 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.068 0.034 199.1 83: (ns/day) (hour/ns) 83: Performance: 42.740 0.562 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 0.4%. 83: The balanceable part of the MD step is 43%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.2%. 83: 83: 83: NOTE: 50 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.028 0.014 198.2 83: (ns/day) (hour/ns) 83: Performance: 102.589 0.234 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.2%. 83: The balanceable part of the MD step is 41%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.5%. 83: 83: 83: NOTE: 48 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.057 0.029 198.7 83: (ns/day) (hour/ns) 83: Performance: 51.030 0.470 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.1%. 83: The balanceable part of the MD step is 45%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.0%. 83: 83: 83: NOTE: 1 % of the run time was spent in domain decomposition, 83: 11 % of the run time was spent in pair search, 83: you might want to increase nstlist (this has no effect on accuracy) 83: 83: NOTE: 38 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.075 0.037 198.9 83: (ns/day) (hour/ns) 83: Performance: 39.214 0.612 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (451 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.0%. 83: The balanceable part of the MD step is 42%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.9%. 83: 83: 83: NOTE: 47 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.062 0.031 198.9 83: (ns/day) (hour/ns) 83: Performance: 46.758 0.513 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.1%. 83: The balanceable part of the MD step is 49%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.0%. 83: 83: 83: NOTE: 48 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.052 0.026 199.0 83: (ns/day) (hour/ns) 83: Performance: 56.526 0.425 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.4%. 83: The balanceable part of the MD step is 44%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.6%. 83: 83: 83: NOTE: 77 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.095 0.048 199.0 83: (ns/day) (hour/ns) 83: Performance: 30.892 0.777 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.3%. 83: The balanceable part of the MD step is 42%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.5%. 83: 83: 83: NOTE: 50 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 3.245 1.623 200.0 83: (ns/day) (hour/ns) 83: Performance: 0.905 26.517 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.0%. 83: The balanceable part of the MD step is 43%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.4%. 83: 83: 83: NOTE: 48 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 2.636 1.363 193.5 83: (ns/day) (hour/ns) 83: Performance: 1.078 22.266 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 3.1%. 83: The balanceable part of the MD step is 38%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.2%. 83: 83: 83: NOTE: 50 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 2.788 1.394 200.0 83: (ns/day) (hour/ns) 83: Performance: 1.054 22.779 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (6774 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 50 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 2.620 1.310 200.0 83: (ns/day) (hour/ns) 83: Performance: 1.121 21.411 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 50 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 1.194 0.597 200.0 83: (ns/day) (hour/ns) 83: Performance: 2.459 9.759 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 48 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 2.798 1.442 193.9 83: (ns/day) (hour/ns) 83: Performance: 1.018 23.570 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 50 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 3.662 1.832 199.8 83: (ns/day) (hour/ns) 83: Performance: 0.802 29.939 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 50 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.301 0.151 199.9 83: (ns/day) (hour/ns) 83: Performance: 9.754 2.460 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 48 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.032 0.016 198.6 83: (ns/day) (hour/ns) 83: Performance: 90.536 0.265 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (6886 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 45 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.027 0.014 197.7 83: (ns/day) (hour/ns) 83: Performance: 105.978 0.226 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 46 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.023 0.011 198.1 83: (ns/day) (hour/ns) 83: Performance: 128.274 0.187 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 49 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.150 0.075 199.7 83: (ns/day) (hour/ns) 83: Performance: 19.497 1.231 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 47 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.024 0.012 197.0 83: (ns/day) (hour/ns) 83: Performance: 121.241 0.198 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 48 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.046 0.023 198.7 83: (ns/day) (hour/ns) 83: Performance: 63.327 0.379 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 46 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.027 0.014 192.0 83: (ns/day) (hour/ns) 83: Performance: 105.845 0.227 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (244 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 44 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.021 0.011 197.9 83: (ns/day) (hour/ns) 83: Performance: 139.764 0.172 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 39 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.019 0.010 198.1 83: (ns/day) (hour/ns) 83: Performance: 152.637 0.157 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 45 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.018 0.009 197.2 83: (ns/day) (hour/ns) 83: Performance: 158.919 0.151 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 47 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.023 0.012 198.2 83: (ns/day) (hour/ns) 83: Performance: 125.608 0.191 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 46 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.024 0.012 198.3 83: (ns/day) (hour/ns) 83: Performance: 123.417 0.194 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 47 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.026 0.013 198.0 83: (ns/day) (hour/ns) 83: Performance: 110.994 0.216 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (139 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 45 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.025 0.013 197.8 83: (ns/day) (hour/ns) 83: Performance: 115.245 0.208 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 38 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.016 0.008 194.9 83: (ns/day) (hour/ns) 83: Performance: 177.209 0.135 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 45 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.017 0.009 195.6 83: (ns/day) (hour/ns) 83: Performance: 169.017 0.142 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 48 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.034 0.017 198.9 83: (ns/day) (hour/ns) 83: Performance: 85.770 0.280 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 47 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.022 0.011 194.2 83: (ns/day) (hour/ns) 83: Performance: 130.072 0.185 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 50 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.301 0.150 199.8 83: (ns/day) (hour/ns) 83: Performance: 9.766 2.458 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (284 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 50 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.952 0.476 200.0 83: (ns/day) (hour/ns) 83: Performance: 3.085 7.779 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 49 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.191 0.096 199.8 83: (ns/day) (hour/ns) 83: Performance: 15.359 1.563 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 4 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 47 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.023 0.012 198.3 83: (ns/day) (hour/ns) 83: Performance: 124.213 0.193 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 4 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 48 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.037 0.019 198.5 83: (ns/day) (hour/ns) 83: Performance: 78.901 0.304 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 4 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 48 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.034 0.017 198.7 83: (ns/day) (hour/ns) 83: Performance: 85.507 0.281 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 4 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 47 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.027 0.014 198.0 83: (ns/day) (hour/ns) 83: Performance: 108.792 0.221 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (735 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 45 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.024 0.012 197.7 83: (ns/day) (hour/ns) 83: Performance: 122.413 0.196 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 50 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.757 0.379 199.9 83: (ns/day) (hour/ns) 83: Performance: 3.878 6.188 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 46 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.057 0.028 199.2 83: (ns/day) (hour/ns) 83: Performance: 51.712 0.464 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 48 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.029 0.015 197.5 83: (ns/day) (hour/ns) 83: Performance: 101.036 0.238 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 42 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.038 0.021 178.1 83: (ns/day) (hour/ns) 83: Performance: 68.957 0.348 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 47 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.048 0.024 199.0 83: (ns/day) (hour/ns) 83: Performance: 61.147 0.392 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (569 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 46 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.039 0.020 198.5 83: (ns/day) (hour/ns) 83: Performance: 74.426 0.322 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 46 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.027 0.014 198.0 83: (ns/day) (hour/ns) 83: Performance: 107.420 0.223 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 46 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.020 0.010 197.0 83: (ns/day) (hour/ns) 83: Performance: 145.417 0.165 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 47 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.028 0.014 198.2 83: (ns/day) (hour/ns) 83: Performance: 104.598 0.229 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 47 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.023 0.011 197.8 83: (ns/day) (hour/ns) 83: Performance: 128.867 0.186 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 47 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.025 0.013 197.9 83: (ns/day) (hour/ns) 83: Performance: 116.204 0.207 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (165 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 45 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.022 0.011 197.8 83: (ns/day) (hour/ns) 83: Performance: 130.186 0.184 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 45 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.016 0.008 197.2 83: (ns/day) (hour/ns) 83: Performance: 179.724 0.134 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 44 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.020 0.010 197.4 83: (ns/day) (hour/ns) 83: Performance: 147.451 0.163 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 48 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.028 0.014 198.4 83: (ns/day) (hour/ns) 83: Performance: 103.197 0.233 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 47 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.026 0.013 198.6 83: (ns/day) (hour/ns) 83: Performance: 113.591 0.211 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 48 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.039 0.020 198.9 83: (ns/day) (hour/ns) 83: Performance: 74.124 0.324 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (153 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 46 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.028 0.014 198.5 83: (ns/day) (hour/ns) 83: Performance: 103.367 0.232 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 47 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.024 0.012 198.6 83: (ns/day) (hour/ns) 83: Performance: 120.429 0.199 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 4. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 4. 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 43 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.017 0.009 197.6 83: (ns/day) (hour/ns) 83: Performance: 171.478 0.140 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 47 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.022 0.011 198.4 83: (ns/day) (hour/ns) 83: Performance: 133.540 0.180 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 47 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.028 0.014 197.7 83: (ns/day) (hour/ns) 83: Performance: 102.700 0.234 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 47 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.023 0.012 198.3 83: (ns/day) (hour/ns) 83: Performance: 126.661 0.189 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (142 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 46 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.027 0.014 198.4 83: (ns/day) (hour/ns) 83: Performance: 108.169 0.222 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 44 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.015 0.007 196.1 83: (ns/day) (hour/ns) 83: Performance: 196.379 0.122 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 47 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.024 0.012 198.4 83: (ns/day) (hour/ns) 83: Performance: 120.349 0.199 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 49 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.058 0.029 199.3 83: (ns/day) (hour/ns) 83: Performance: 50.309 0.477 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 48 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.045 0.023 195.0 83: (ns/day) (hour/ns) 83: Performance: 63.750 0.376 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 47 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.024 0.012 194.5 83: (ns/day) (hour/ns) 83: Performance: 121.529 0.197 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (170 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 46 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.043 0.022 198.5 83: (ns/day) (hour/ns) 83: Performance: 67.200 0.357 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 46 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.025 0.013 198.5 83: (ns/day) (hour/ns) 83: Performance: 116.822 0.205 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 46 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.020 0.010 198.0 83: (ns/day) (hour/ns) 83: Performance: 143.650 0.167 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 48 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.035 0.018 198.4 83: (ns/day) (hour/ns) 83: Performance: 82.784 0.290 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 47 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.030 0.015 198.7 83: (ns/day) (hour/ns) 83: Performance: 98.356 0.244 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 51 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.083 0.041 199.4 83: (ns/day) (hour/ns) 83: Performance: 35.491 0.676 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (212 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 48 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.062 0.031 199.4 83: (ns/day) (hour/ns) 83: Performance: 47.152 0.509 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 48 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.047 0.024 199.1 83: (ns/day) (hour/ns) 83: Performance: 61.868 0.388 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 54 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.062 0.031 199.1 83: (ns/day) (hour/ns) 83: Performance: 47.543 0.505 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 25 % of the run time was spent in domain decomposition, 83: 0 % of the run time was spent in pair search, 83: you might want to increase nstlist (this has no effect on accuracy) 83: 83: NOTE: 45 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.128 0.084 152.5 83: (ns/day) (hour/ns) 83: Performance: 17.503 1.371 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 57 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.097 0.063 155.5 83: (ns/day) (hour/ns) 83: Performance: 23.476 1.022 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 57 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.087 0.044 198.6 83: (ns/day) (hour/ns) 83: Performance: 33.356 0.720 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (1256 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 0.3%. 83: The balanceable part of the MD step is 58%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.2%. 83: 83: 83: NOTE: 6 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.095 0.052 181.3 83: (ns/day) (hour/ns) 83: Performance: 28.072 0.855 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 0.6%. 83: The balanceable part of the MD step is 54%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.3%. 83: 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.037 0.019 194.6 83: (ns/day) (hour/ns) 83: Performance: 76.525 0.314 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 4. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 4. 83: 83: 83: There were 4 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 5.5%. 83: The balanceable part of the MD step is 36%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 2.0%. 83: 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.063 0.032 198.2 83: (ns/day) (hour/ns) 83: Performance: 46.368 0.518 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 4 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 3.2%. 83: The balanceable part of the MD step is 47%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.5%. 83: 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.071 0.036 198.3 83: (ns/day) (hour/ns) 83: Performance: 40.788 0.588 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 4 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was turned on during the run due to measured imbalance. 83: Average load imbalance: 4.5%. 83: The balanceable part of the MD step is 48%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 2.1%. 83: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 83: 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.081 0.041 198.7 83: (ns/day) (hour/ns) 83: Performance: 35.870 0.669 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 4 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was turned on during the run due to measured imbalance. 83: Average load imbalance: 7.2%. 83: The balanceable part of the MD step is 47%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 3.4%. 83: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 83: 83: 83: NOTE: 22 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.154 0.077 199.0 83: (ns/day) (hour/ns) 83: Performance: 18.994 1.264 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (797 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.7%. 83: The balanceable part of the MD step is 58%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.0%. 83: 83: 83: NOTE: 10 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.178 0.089 199.4 83: (ns/day) (hour/ns) 83: Performance: 16.465 1.458 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.0%. 83: The balanceable part of the MD step is 35%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.7%. 83: 83: 83: NOTE: 14 % of the run time was spent in domain decomposition, 83: 0 % of the run time was spent in pair search, 83: you might want to increase nstlist (this has no effect on accuracy) 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.064 0.032 198.9 83: (ns/day) (hour/ns) 83: Performance: 45.343 0.529 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.9%. 83: The balanceable part of the MD step is 53%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.0%. 83: 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.076 0.038 198.7 83: (ns/day) (hour/ns) 83: Performance: 38.618 0.621 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 0.7%. 83: The balanceable part of the MD step is 51%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.4%. 83: 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.245 0.123 199.7 83: (ns/day) (hour/ns) 83: Performance: 11.983 2.003 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.9%. 83: The balanceable part of the MD step is 50%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.0%. 83: 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.074 0.037 199.0 83: (ns/day) (hour/ns) 83: Performance: 39.551 0.607 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.8%. 83: The balanceable part of the MD step is 51%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.4%. 83: 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.089 0.045 199.1 83: (ns/day) (hour/ns) 83: Performance: 32.742 0.733 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (839 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.1%. 83: The balanceable part of the MD step is 54%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.6%. 83: 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.099 0.063 157.1 83: (ns/day) (hour/ns) 83: Performance: 23.361 1.027 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.1%. 83: The balanceable part of the MD step is 54%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.6%. 83: 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.071 0.036 198.9 83: (ns/day) (hour/ns) 83: Performance: 41.365 0.580 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was turned on during the run due to measured imbalance. 83: Average load imbalance: 16.0%. 83: The balanceable part of the MD step is 46%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 7.4%. 83: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 83: 83: NOTE: 7.4 % of the available CPU time was lost due to load imbalance 83: in the domain decomposition. 83: You can consider manually changing the decomposition (option -dd); 83: e.g. by using fewer domains along the box dimension in which there is 83: considerable inhomogeneity in the simulated system. 83: 83: NOTE: 12 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.127 0.064 199.2 83: (ns/day) (hour/ns) 83: Performance: 22.956 1.045 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was turned on during the run due to measured imbalance. 83: Average load imbalance: 29.7%. 83: The balanceable part of the MD step is 31%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 9.1%. 83: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 83: 83: NOTE: 9.1 % of the available CPU time was lost due to load imbalance 83: in the domain decomposition. 83: You can consider manually changing the decomposition (option -dd); 83: e.g. by using fewer domains along the box dimension in which there is 83: considerable inhomogeneity in the simulated system. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 4.589 2.334 196.6 83: (ns/day) (hour/ns) 83: Performance: 0.629 38.139 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.6%. 83: The balanceable part of the MD step is 45%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.2%. 83: 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.258 0.129 199.5 83: (ns/day) (hour/ns) 83: Performance: 11.351 2.114 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.5%. 83: The balanceable part of the MD step is 46%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.7%. 83: 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.113 0.057 199.2 83: (ns/day) (hour/ns) 83: Performance: 25.965 0.924 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (3173 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 6 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.127 0.064 198.7 83: (ns/day) (hour/ns) 83: Performance: 22.940 1.046 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.055 0.028 196.2 83: (ns/day) (hour/ns) 83: Performance: 52.287 0.459 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.112 0.056 197.9 83: (ns/day) (hour/ns) 83: Performance: 26.062 0.921 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.082 0.041 198.0 83: (ns/day) (hour/ns) 83: Performance: 35.513 0.676 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.088 0.044 198.8 83: (ns/day) (hour/ns) 83: Performance: 33.025 0.727 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.553 0.277 199.8 83: (ns/day) (hour/ns) 83: Performance: 5.309 4.521 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (794 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.088 0.044 198.8 83: (ns/day) (hour/ns) 83: Performance: 33.082 0.725 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 7 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.124 0.062 199.1 83: (ns/day) (hour/ns) 83: Performance: 23.623 1.016 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.113 0.058 196.2 83: (ns/day) (hour/ns) 83: Performance: 25.456 0.943 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.120 0.060 198.8 83: (ns/day) (hour/ns) 83: Performance: 24.373 0.985 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.125 0.063 199.1 83: (ns/day) (hour/ns) 83: Performance: 23.334 1.029 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.105 0.053 199.0 83: (ns/day) (hour/ns) 83: Performance: 27.965 0.858 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (716 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.188 0.094 199.3 83: (ns/day) (hour/ns) 83: Performance: 15.603 1.538 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 1.154 0.578 199.9 83: (ns/day) (hour/ns) 83: Performance: 2.543 9.437 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.704 0.352 199.8 83: (ns/day) (hour/ns) 83: Performance: 4.168 5.759 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.081 0.041 198.6 83: (ns/day) (hour/ns) 83: Performance: 35.922 0.668 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.100 0.051 198.8 83: (ns/day) (hour/ns) 83: Performance: 29.063 0.826 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.096 0.048 198.4 83: (ns/day) (hour/ns) 83: Performance: 30.496 0.787 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (1933 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.084 0.042 198.3 83: (ns/day) (hour/ns) 83: Performance: 34.571 0.694 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.071 0.037 190.6 83: (ns/day) (hour/ns) 83: Performance: 39.535 0.607 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.029 0.015 195.9 83: (ns/day) (hour/ns) 83: Performance: 100.935 0.238 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 33 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.193 0.097 198.8 83: (ns/day) (hour/ns) 83: Performance: 15.124 1.587 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.150 0.075 198.9 83: (ns/day) (hour/ns) 83: Performance: 19.458 1.233 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 1.956 0.978 199.9 83: (ns/day) (hour/ns) 83: Performance: 1.501 15.988 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 (1668 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: MTTK coupling is deprecated and will soon be removed 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: for current Trotter decomposition methods with vv, nsttcouple and 83: nstpcouple must be equal. Both have been reset to 83: min(nsttcouple,nstpcouple) = 2 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 4 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 1.084 0.542 199.9 83: (ns/day) (hour/ns) 83: Performance: 2.710 8.856 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: MTTK coupling is deprecated and will soon be removed 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: for current Trotter decomposition methods with vv, nsttcouple and 83: nstpcouple must be equal. Both have been reset to 83: min(nsttcouple,nstpcouple) = 2 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 4 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 1.791 0.896 199.9 83: (ns/day) (hour/ns) 83: Performance: 1.640 14.634 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: MTTK coupling is deprecated and will soon be removed 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: for current Trotter decomposition methods with vv, nsttcouple and 83: nstpcouple must be equal. Both have been reset to 83: min(nsttcouple,nstpcouple) = 2 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 5 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 2.067 1.034 200.0 83: (ns/day) (hour/ns) 83: Performance: 1.421 16.890 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: MTTK coupling is deprecated and will soon be removed 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: for current Trotter decomposition methods with vv, nsttcouple and 83: nstpcouple must be equal. Both have been reset to 83: min(nsttcouple,nstpcouple) = 2 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 5 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 1.512 0.757 199.7 83: (ns/day) (hour/ns) 83: Performance: 1.941 12.367 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: MTTK coupling is deprecated and will soon be removed 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: for current Trotter decomposition methods with vv, nsttcouple and 83: nstpcouple must be equal. Both have been reset to 83: min(nsttcouple,nstpcouple) = 2 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 5 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.055 0.028 198.4 83: (ns/day) (hour/ns) 83: Performance: 52.909 0.454 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: MTTK coupling is deprecated and will soon be removed 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: for current Trotter decomposition methods with vv, nsttcouple and 83: nstpcouple must be equal. Both have been reset to 83: min(nsttcouple,nstpcouple) = 2 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 5 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.070 0.036 196.1 83: (ns/day) (hour/ns) 83: Performance: 41.278 0.581 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 (3611 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.100 0.052 193.1 83: (ns/day) (hour/ns) 83: Performance: 28.413 0.845 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.136 0.068 199.4 83: (ns/day) (hour/ns) 83: Performance: 21.541 1.114 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.032 0.017 186.8 83: (ns/day) (hour/ns) 83: Performance: 86.434 0.278 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.348 0.174 199.3 83: (ns/day) (hour/ns) 83: Performance: 8.420 2.850 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.353 0.177 199.7 83: (ns/day) (hour/ns) 83: Performance: 8.316 2.886 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.053 0.027 198.1 83: (ns/day) (hour/ns) 83: Performance: 54.549 0.440 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 (768 ms) 83: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest (34459 ms total) 83: 83: [----------] Global test environment tear-down 83: [==========] 25 tests from 1 test suite ran. (34600 ms total) 83: [ PASSED ] 25 tests. 83/90 Test #83: MdrunCoordinationCouplingTests2Ranks ...... Passed 34.63 sec test 84 Start 84: MdrunCoordinationConstraintsTests1Rank 84: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/mdrun-coordination-constraints-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/MdrunCoordinationConstraintsTests1Rank.xml" 84: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests 84: Test timeout computed to be: 1920 84: [==========] Running 13 tests from 1 test suite. 84: [----------] Global test environment set-up. 84: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.020 0.020 99.6 84: (ns/day) (hour/ns) 84: Performance: 72.511 0.331 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.009 0.010 99.0 84: (ns/day) (hour/ns) 84: Performance: 153.405 0.156 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 4. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 4. 84: 84: 84: There were 5 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.010 0.010 99.2 84: (ns/day) (hour/ns) 84: Performance: 146.810 0.163 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 5 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.009 0.009 99.1 84: (ns/day) (hour/ns) 84: Performance: 156.946 0.153 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 5 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.019 0.019 99.6 84: (ns/day) (hour/ns) 84: Performance: 75.832 0.316 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 5 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.082 0.082 99.9 84: (ns/day) (hour/ns) 84: Performance: 17.844 1.345 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (2778 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.011 0.011 99.0 84: (ns/day) (hour/ns) 84: Performance: 138.099 0.174 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.009 0.010 99.2 84: (ns/day) (hour/ns) 84: Performance: 153.413 0.156 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.011 0.011 99.2 84: (ns/day) (hour/ns) 84: Performance: 130.732 0.184 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.012 0.012 99.3 84: (ns/day) (hour/ns) 84: Performance: 117.802 0.204 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.013 0.013 99.4 84: (ns/day) (hour/ns) 84: Performance: 111.042 0.216 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.082 0.082 99.9 84: (ns/day) (hour/ns) 84: Performance: 17.846 1.345 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (2659 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.017 0.017 99.4 84: (ns/day) (hour/ns) 84: Performance: 85.683 0.280 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.012 0.012 99.2 84: (ns/day) (hour/ns) 84: Performance: 124.537 0.193 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.008 0.008 98.1 84: (ns/day) (hour/ns) 84: Performance: 176.901 0.136 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.010 0.010 99.2 84: (ns/day) (hour/ns) 84: Performance: 140.473 0.171 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.222 0.222 100.0 84: (ns/day) (hour/ns) 84: Performance: 6.625 3.622 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.018 0.018 99.5 84: (ns/day) (hour/ns) 84: Performance: 81.147 0.296 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (3333 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.018 0.018 99.5 84: (ns/day) (hour/ns) 84: Performance: 80.531 0.298 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.022 0.022 99.5 84: (ns/day) (hour/ns) 84: Performance: 65.663 0.366 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.461 0.461 100.0 84: (ns/day) (hour/ns) 84: Performance: 3.184 7.537 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.014 0.014 98.9 84: (ns/day) (hour/ns) 84: Performance: 105.861 0.227 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.012 0.012 97.7 84: (ns/day) (hour/ns) 84: Performance: 118.289 0.203 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.186 0.186 99.9 84: (ns/day) (hour/ns) 84: Performance: 7.893 3.041 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (3901 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.026 0.026 99.7 84: (ns/day) (hour/ns) 84: Performance: 56.171 0.427 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.010 0.010 98.4 84: (ns/day) (hour/ns) 84: Performance: 150.468 0.160 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.010 0.010 99.1 84: (ns/day) (hour/ns) 84: Performance: 148.294 0.162 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 1.447 1.447 100.0 84: (ns/day) (hour/ns) 84: Performance: 1.015 23.646 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.878 0.878 100.0 84: (ns/day) (hour/ns) 84: Performance: 1.672 14.350 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 1.055 1.055 100.0 84: (ns/day) (hour/ns) 84: Performance: 1.392 17.241 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (6734 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 1.141 1.141 100.0 84: (ns/day) (hour/ns) 84: Performance: 1.288 18.639 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.012 0.012 99.0 84: (ns/day) (hour/ns) 84: Performance: 124.203 0.193 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.027 0.027 99.5 84: (ns/day) (hour/ns) 84: Performance: 55.074 0.436 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.467 0.467 100.0 84: (ns/day) (hour/ns) 84: Performance: 3.147 7.626 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.027 0.027 99.7 84: (ns/day) (hour/ns) 84: Performance: 54.445 0.441 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.016 0.016 99.5 84: (ns/day) (hour/ns) 84: Performance: 89.945 0.267 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (5132 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.834 0.834 100.0 84: (ns/day) (hour/ns) 84: Performance: 1.761 13.626 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.709 0.709 100.0 84: (ns/day) (hour/ns) 84: Performance: 2.072 11.585 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 4. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 4. 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.308 0.308 100.0 84: (ns/day) (hour/ns) 84: Performance: 4.762 5.040 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.015 0.015 99.5 84: (ns/day) (hour/ns) 84: Performance: 96.626 0.248 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.013 0.013 99.5 84: (ns/day) (hour/ns) 84: Performance: 110.534 0.217 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.014 0.014 99.6 84: (ns/day) (hour/ns) 84: Performance: 102.745 0.234 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (4967 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.014 0.014 99.5 84: (ns/day) (hour/ns) 84: Performance: 102.680 0.234 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.009 0.010 99.0 84: (ns/day) (hour/ns) 84: Performance: 153.926 0.156 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.012 0.012 99.4 84: (ns/day) (hour/ns) 84: Performance: 119.723 0.200 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.016 0.016 99.6 84: (ns/day) (hour/ns) 84: Performance: 89.028 0.270 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.013 0.013 99.4 84: (ns/day) (hour/ns) 84: Performance: 111.573 0.215 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.016 0.016 99.6 84: (ns/day) (hour/ns) 84: Performance: 93.559 0.257 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (2930 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.018 0.018 99.6 84: (ns/day) (hour/ns) 84: Performance: 80.462 0.298 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.014 0.014 99.4 84: (ns/day) (hour/ns) 84: Performance: 101.779 0.236 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.013 0.013 99.1 84: (ns/day) (hour/ns) 84: Performance: 115.733 0.207 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.013 0.013 99.3 84: (ns/day) (hour/ns) 84: Performance: 115.492 0.208 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.016 0.016 99.6 84: (ns/day) (hour/ns) 84: Performance: 91.284 0.263 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.012 0.012 99.3 84: (ns/day) (hour/ns) 84: Performance: 125.175 0.192 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (2711 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.013 0.013 99.6 84: (ns/day) (hour/ns) 84: Performance: 109.072 0.220 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.977 0.977 100.0 84: (ns/day) (hour/ns) 84: Performance: 1.503 15.969 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 4. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 4. 84: 84: 84: There were 5 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.028 0.028 99.8 84: (ns/day) (hour/ns) 84: Performance: 53.069 0.452 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 5 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.847 0.847 100.0 84: (ns/day) (hour/ns) 84: Performance: 1.733 13.848 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 5 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.020 0.020 99.6 84: (ns/day) (hour/ns) 84: Performance: 74.979 0.320 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 5 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.018 0.018 99.7 84: (ns/day) (hour/ns) 84: Performance: 83.484 0.287 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (4736 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.015 0.015 99.6 84: (ns/day) (hour/ns) 84: Performance: 96.040 0.250 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.013 0.014 99.6 84: (ns/day) (hour/ns) 84: Performance: 108.402 0.221 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.015 0.015 99.5 84: (ns/day) (hour/ns) 84: Performance: 99.356 0.242 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.015 0.015 99.6 84: (ns/day) (hour/ns) 84: Performance: 100.797 0.238 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.028 0.028 99.7 84: (ns/day) (hour/ns) 84: Performance: 53.012 0.453 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 1.701 1.701 100.0 84: (ns/day) (hour/ns) 84: Performance: 0.863 27.797 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (4534 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.927 0.927 100.0 84: (ns/day) (hour/ns) 84: Performance: 1.585 15.141 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 1.891 1.891 100.0 84: (ns/day) (hour/ns) 84: Performance: 0.777 30.899 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 1.606 1.606 100.0 84: (ns/day) (hour/ns) 84: Performance: 0.914 26.247 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 1.646 1.646 100.0 84: (ns/day) (hour/ns) 84: Performance: 0.892 26.898 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.013 0.013 99.3 84: (ns/day) (hour/ns) 84: Performance: 112.299 0.214 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.016 0.016 99.6 84: (ns/day) (hour/ns) 84: Performance: 90.942 0.264 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (9657 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.014 0.014 99.3 84: (ns/day) (hour/ns) 84: Performance: 106.494 0.225 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.013 0.013 99.4 84: (ns/day) (hour/ns) 84: Performance: 109.604 0.219 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.016 0.016 99.6 84: (ns/day) (hour/ns) 84: Performance: 92.674 0.259 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.194 0.194 99.9 84: (ns/day) (hour/ns) 84: Performance: 7.580 3.166 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.019 0.020 99.7 84: (ns/day) (hour/ns) 84: Performance: 75.179 0.319 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.299 0.299 100.0 84: (ns/day) (hour/ns) 84: Performance: 4.907 4.891 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (3489 ms) 84: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest (57567 ms total) 84: 84: [----------] Global test environment tear-down 84: [==========] 13 tests from 1 test suite ran. (57662 ms total) 84: [ PASSED ] 13 tests. 84/90 Test #84: MdrunCoordinationConstraintsTests1Rank .... Passed 57.69 sec test 85 Start 85: MdrunCoordinationConstraintsTests2Ranks 85: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/mdrun-coordination-constraints-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/MdrunCoordinationConstraintsTests2Ranks.xml" 85: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests 85: Test timeout computed to be: 1920 85: [==========] Running 13 tests from 1 test suite. 85: [----------] Global test environment set-up. 85: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest 85: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.5%. 85: The balanceable part of the MD step is 37%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.6%. 85: 85: 85: NOTE: 46 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.031 0.015 198.7 85: (ns/day) (hour/ns) 85: Performance: 94.808 0.253 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 5.2%. 85: The balanceable part of the MD step is 23%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.2%. 85: 85: 85: NOTE: 44 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.036 0.018 198.9 85: (ns/day) (hour/ns) 85: Performance: 81.048 0.296 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 4. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 4. 85: 85: 85: There were 5 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 4.8%. 85: The balanceable part of the MD step is 37%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.8%. 85: 85: 85: NOTE: 45 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.019 0.010 186.7 85: (ns/day) (hour/ns) 85: Performance: 148.004 0.162 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 5 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.0%. 85: The balanceable part of the MD step is 10%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.2%. 85: 85: 85: NOTE: 49 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.141 0.071 198.9 85: (ns/day) (hour/ns) 85: Performance: 20.785 1.155 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 5 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB got disabled because it was unsuitable to use. 85: Average load imbalance: 5.6%. 85: The balanceable part of the MD step is 37%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 2.1%. 85: 85: 85: NOTE: 47 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.028 0.014 198.5 85: (ns/day) (hour/ns) 85: Performance: 102.666 0.234 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 5 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.8%. 85: The balanceable part of the MD step is 15%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.4%. 85: 85: 85: NOTE: 47 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.030 0.015 198.4 85: (ns/day) (hour/ns) 85: Performance: 98.407 0.244 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 85: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (3195 ms) 85: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 3.0%. 85: The balanceable part of the MD step is 50%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.5%. 85: 85: 85: NOTE: 48 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.064 0.032 199.1 85: (ns/day) (hour/ns) 85: Performance: 45.977 0.522 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.3%. 85: The balanceable part of the MD step is 44%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.6%. 85: 85: 85: NOTE: 46 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.034 0.017 198.7 85: (ns/day) (hour/ns) 85: Performance: 86.972 0.276 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.6%. 85: The balanceable part of the MD step is 7%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.1%. 85: 85: 85: NOTE: 30 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.041 0.020 198.5 85: (ns/day) (hour/ns) 85: Performance: 71.742 0.335 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 0.7%. 85: The balanceable part of the MD step is 37%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.3%. 85: 85: 85: NOTE: 48 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.041 0.021 198.8 85: (ns/day) (hour/ns) 85: Performance: 71.466 0.336 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB got disabled because it was unsuitable to use. 85: Average load imbalance: 5.2%. 85: The balanceable part of the MD step is 42%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 2.2%. 85: 85: 85: NOTE: 47 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.038 0.019 198.9 85: (ns/day) (hour/ns) 85: Performance: 77.873 0.308 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 0.9%. 85: The balanceable part of the MD step is 11%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.1%. 85: 85: 85: NOTE: 47 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.046 0.023 196.6 85: (ns/day) (hour/ns) 85: Performance: 63.377 0.379 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 85: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (3458 ms) 85: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 0.1%. 85: The balanceable part of the MD step is 55%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.0%. 85: 85: 85: NOTE: 48 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.086 0.043 199.4 85: (ns/day) (hour/ns) 85: Performance: 34.111 0.704 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.0%. 85: The balanceable part of the MD step is 33%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.7%. 85: 85: 85: NOTE: 37 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.057 0.029 198.8 85: (ns/day) (hour/ns) 85: Performance: 51.237 0.468 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.6%. 85: The balanceable part of the MD step is 34%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.5%. 85: 85: 85: NOTE: 48 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.027 0.014 196.5 85: (ns/day) (hour/ns) 85: Performance: 108.688 0.221 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 0.7%. 85: The balanceable part of the MD step is 41%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.3%. 85: 85: 85: NOTE: 47 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.036 0.018 198.4 85: (ns/day) (hour/ns) 85: Performance: 80.537 0.298 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 4.6%. 85: The balanceable part of the MD step is 42%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 2.0%. 85: 85: 85: NOTE: 44 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.032 0.016 198.5 85: (ns/day) (hour/ns) 85: Performance: 92.311 0.260 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 0.5%. 85: The balanceable part of the MD step is 45%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.2%. 85: 85: 85: NOTE: 48 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.029 0.015 197.9 85: (ns/day) (hour/ns) 85: Performance: 98.817 0.243 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 85: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (3242 ms) 85: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 1.898 0.949 199.9 85: (ns/day) (hour/ns) 85: Performance: 1.547 15.511 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.226 0.113 199.6 85: (ns/day) (hour/ns) 85: Performance: 12.958 1.852 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.024 0.012 198.4 85: (ns/day) (hour/ns) 85: Performance: 120.349 0.199 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.035 0.017 198.3 85: (ns/day) (hour/ns) 85: Performance: 84.099 0.285 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.051 0.026 198.8 85: (ns/day) (hour/ns) 85: Performance: 57.319 0.419 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.075 0.038 199.3 85: (ns/day) (hour/ns) 85: Performance: 38.927 0.617 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 85: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (6826 ms) 85: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 9 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.083 0.042 196.9 85: (ns/day) (hour/ns) 85: Performance: 34.653 0.693 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.022 0.011 196.6 85: (ns/day) (hour/ns) 85: Performance: 128.891 0.186 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.023 0.012 184.4 85: (ns/day) (hour/ns) 85: Performance: 119.868 0.200 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 1.385 0.693 200.0 85: (ns/day) (hour/ns) 85: Performance: 2.121 11.318 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 1.277 0.639 199.9 85: (ns/day) (hour/ns) 85: Performance: 2.300 10.436 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.052 0.026 198.8 85: (ns/day) (hour/ns) 85: Performance: 56.513 0.425 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 85: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (5023 ms) 85: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.044 0.022 198.8 85: (ns/day) (hour/ns) 85: Performance: 66.084 0.363 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.475 0.237 199.9 85: (ns/day) (hour/ns) 85: Performance: 6.187 3.879 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.057 0.029 198.9 85: (ns/day) (hour/ns) 85: Performance: 51.116 0.470 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.078 0.039 199.2 85: (ns/day) (hour/ns) 85: Performance: 37.623 0.638 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.071 0.036 199.2 85: (ns/day) (hour/ns) 85: Performance: 41.000 0.585 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.048 0.024 198.3 85: (ns/day) (hour/ns) 85: Performance: 61.313 0.391 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 85: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (5304 ms) 85: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.276 0.138 199.8 85: (ns/day) (hour/ns) 85: Performance: 10.643 2.255 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.039 0.020 198.5 85: (ns/day) (hour/ns) 85: Performance: 74.254 0.323 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 4. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 4. 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.117 0.066 176.4 85: (ns/day) (hour/ns) 85: Performance: 22.240 1.079 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.095 0.047 199.5 85: (ns/day) (hour/ns) 85: Performance: 30.928 0.776 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.050 0.025 198.9 85: (ns/day) (hour/ns) 85: Performance: 57.991 0.414 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.458 0.229 199.8 85: (ns/day) (hour/ns) 85: Performance: 6.413 3.742 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 85: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (6643 ms) 85: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 15 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.249 0.127 195.9 85: (ns/day) (hour/ns) 85: Performance: 11.538 2.080 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.036 0.018 197.6 85: (ns/day) (hour/ns) 85: Performance: 81.579 0.294 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.049 0.025 198.9 85: (ns/day) (hour/ns) 85: Performance: 59.412 0.404 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 1.007 0.506 198.9 85: (ns/day) (hour/ns) 85: Performance: 2.901 8.274 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.040 0.020 198.7 85: (ns/day) (hour/ns) 85: Performance: 73.895 0.325 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.063 0.032 199.1 85: (ns/day) (hour/ns) 85: Performance: 46.179 0.520 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 85: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (7163 ms) 85: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 2.042 1.021 200.0 85: (ns/day) (hour/ns) 85: Performance: 1.439 16.682 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 1.794 0.913 196.5 85: (ns/day) (hour/ns) 85: Performance: 1.609 14.920 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 1.210 0.605 199.9 85: (ns/day) (hour/ns) 85: Performance: 2.426 9.893 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 1.584 0.792 200.0 85: (ns/day) (hour/ns) 85: Performance: 1.855 12.941 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 3.433 1.717 200.0 85: (ns/day) (hour/ns) 85: Performance: 0.856 28.053 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.090 0.045 199.4 85: (ns/day) (hour/ns) 85: Performance: 32.464 0.739 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 85: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (9388 ms) 85: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 0.2%. 85: The balanceable part of the MD step is 23%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.1%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.043 0.022 198.5 85: (ns/day) (hour/ns) 85: Performance: 67.167 0.357 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.0%. 85: The balanceable part of the MD step is 26%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.3%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.085 0.043 199.1 85: (ns/day) (hour/ns) 85: Performance: 34.516 0.695 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 4. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 4. 85: 85: 85: There were 5 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.3%. 85: The balanceable part of the MD step is 24%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.6%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.031 0.016 197.4 85: (ns/day) (hour/ns) 85: Performance: 93.081 0.258 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 5 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 4.4%. 85: The balanceable part of the MD step is 40%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.7%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.031 0.016 193.2 85: (ns/day) (hour/ns) 85: Performance: 92.369 0.260 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 5 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 3.0%. 85: The balanceable part of the MD step is 45%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.3%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.120 0.060 199.5 85: (ns/day) (hour/ns) 85: Performance: 24.511 0.979 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 5 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 3.8%. 85: The balanceable part of the MD step is 40%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.5%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.035 0.018 198.0 85: (ns/day) (hour/ns) 85: Performance: 83.062 0.289 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 85: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (3031 ms) 85: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.3%. 85: The balanceable part of the MD step is 45%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.6%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.041 0.021 197.7 85: (ns/day) (hour/ns) 85: Performance: 70.131 0.342 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.4%. 85: The balanceable part of the MD step is 48%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.1%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.028 0.014 197.4 85: (ns/day) (hour/ns) 85: Performance: 104.825 0.229 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 3.5%. 85: The balanceable part of the MD step is 53%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.9%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.117 0.062 188.8 85: (ns/day) (hour/ns) 85: Performance: 23.628 1.016 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.9%. 85: The balanceable part of the MD step is 30%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.6%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.044 0.022 198.2 85: (ns/day) (hour/ns) 85: Performance: 65.987 0.364 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.7%. 85: The balanceable part of the MD step is 37%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.6%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.046 0.023 198.5 85: (ns/day) (hour/ns) 85: Performance: 63.681 0.377 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.5%. 85: The balanceable part of the MD step is 55%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.8%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.038 0.019 198.2 85: (ns/day) (hour/ns) 85: Performance: 76.048 0.316 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 85: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (2963 ms) 85: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.038 0.019 198.5 85: (ns/day) (hour/ns) 85: Performance: 76.296 0.315 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.028 0.015 191.2 85: (ns/day) (hour/ns) 85: Performance: 101.227 0.237 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.021 0.011 195.3 85: (ns/day) (hour/ns) 85: Performance: 135.274 0.177 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.418 0.209 199.8 85: (ns/day) (hour/ns) 85: Performance: 7.022 3.418 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.034 0.017 197.8 85: (ns/day) (hour/ns) 85: Performance: 86.614 0.277 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.036 0.018 193.9 85: (ns/day) (hour/ns) 85: Performance: 79.615 0.301 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 85: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (3038 ms) 85: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.040 0.020 198.0 85: (ns/day) (hour/ns) 85: Performance: 73.103 0.328 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.056 0.029 189.5 85: (ns/day) (hour/ns) 85: Performance: 50.109 0.479 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.034 0.017 196.5 85: (ns/day) (hour/ns) 85: Performance: 85.035 0.282 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.091 0.046 198.8 85: (ns/day) (hour/ns) 85: Performance: 32.170 0.746 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.034 0.017 197.3 85: (ns/day) (hour/ns) 85: Performance: 85.978 0.279 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.031 0.016 197.0 85: (ns/day) (hour/ns) 85: Performance: 92.223 0.260 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 85: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (3083 ms) 85: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest (62364 ms total) 85: 85: [----------] Global test environment tear-down 85: [==========] 13 tests from 1 test suite ran. (62442 ms total) 85: [ PASSED ] 13 tests. 85/90 Test #85: MdrunCoordinationConstraintsTests2Ranks ... Passed 62.47 sec test 86 Start 86: MdrunFEPTests 86: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/mdrun-fep-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/MdrunFEPTests.xml" 86: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests 86: Test timeout computed to be: 600 86: [==========] Running 14 tests from 2 test suites. 86: [----------] Global test environment set-up. 86: [----------] 2 tests from ExpandedEnsembleTest 86: [ RUN ] ExpandedEnsembleTest.ContinuationPreservesExpandedEnsembleState 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 79.00 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 2 NOTEs 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun '30 atom system in water' 86: 16 steps, 0.0 ps. 86: Generated 2485 of the 2485 non-bonded parameter combinations 86: 86: Generated 2485 of the 2485 1-4 parameter combinations 86: 86: Excluding 3 bonded neighbours molecule type 'nonanol' 86: 86: turning H bonds into constraints... 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: turning H bonds into constraints... 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.045 0.022 199.3 86: (ns/day) (hour/ns) 86: Performance: 65.590 0.366 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Overriding nsteps with value passed on the command line: 8 steps, 0.008 ps 86: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 86: 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun '30 atom system in water' 86: 24 steps, 0.0 ps (continuing from step 16, 0.0 ps). 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.034 0.017 198.1 86: (ns/day) (hour/ns) 86: Performance: 45.368 0.529 86: [ OK ] ExpandedEnsembleTest.ContinuationPreservesExpandedEnsembleState (90 ms) 86: [ RUN ] ExpandedEnsembleTest.WeightEquilibrationReported 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_WeightEquilibrationReported_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 79.00 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_WeightEquilibrationReported_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 2 NOTEs 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_WeightEquilibrationReported.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun '30 atom system in water' 86: 1 steps, 0.0 ps. 86: Generated 2485 of the 2485 non-bonded parameter combinations 86: 86: Generated 2485 of the 2485 1-4 parameter combinations 86: 86: Excluding 3 bonded neighbours molecule type 'nonanol' 86: 86: turning H bonds into constraints... 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: turning H bonds into constraints... 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.177 0.089 199.7 86: (ns/day) (hour/ns) 86: Performance: 1.951 12.303 86: [ OK ] ExpandedEnsembleTest.WeightEquilibrationReported (118 ms) 86: [----------] 2 tests from ExpandedEnsembleTest (209 ms total) 86: 86: [----------] 12 tests from EquivalentToReference/FreeEnergyReferenceTest 86: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_s 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp, line 149]: 86: For proper sampling of the (nearly) decoupled state, stochastic dynamics 86: should be used 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 355.00 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 86: The optimal PME mesh load for parallel simulations is below 0.5 86: and for highly parallel simulations between 0.25 and 0.33, 86: for higher performance, increase the cut-off and the PME grid spacing. 86: 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 86: For free energy simulations, the optimal load limit increases from 0.5 to 86: 0.667 86: 86: 86: 86: There were 3 NOTEs 86: 86: There was 1 WARNING 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_s_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 10 to 100, rlist from 1 to 1 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'AA' 86: 20 steps, 0.0 ps. 86: Setting the LD random seed to -623904004 86: 86: Generated 153 of the 153 non-bonded parameter combinations 86: 86: Generated 153 of the 153 1-4 parameter combinations 86: 86: Excluding 3 bonded neighbours molecule type 'ASN' 86: 86: turning H bonds into constraints... 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: turning H bonds into constraints... 86: 86: Coupling 1 copies of molecule type 'ASN' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/conf.gro' 86: Analysing residue names: 86: There are: 1 Protein residues 86: There are: 56 Water residues 86: Analysing Protein... 86: 86: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 86: 86: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: Calculating fourier grid dimensions for X Y Z 86: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 86: 86: Estimate for the relative computational load of the PME mesh part: 0.94 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.158 0.079 199.7 86: (ns/day) (hour/ns) 86: Performance: 22.967 1.045 86: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_s_energy.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 trr version: GMX_trn_file (single precision) 86: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_s (390 ms) 86: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_s 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp, line 148]: 86: For proper sampling of the (nearly) decoupled state, stochastic dynamics 86: should be used 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 355.00 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 86: The optimal PME mesh load for parallel simulations is below 0.5 86: and for highly parallel simulations between 0.25 and 0.33, 86: for higher performance, increase the cut-off and the PME grid spacing. 86: 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 86: For free energy simulations, the optimal load limit increases from 0.5 to 86: 0.667 86: 86: 86: 86: There were 3 NOTEs 86: 86: There was 1 WARNING 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_s_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 10 to 100, rlist from 1 to 1 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'AA' 86: 20 steps, 0.0 ps. 86: Setting the LD random seed to -167807075 86: 86: Generated 153 of the 153 non-bonded parameter combinations 86: 86: Generated 153 of the 153 1-4 parameter combinations 86: 86: Excluding 3 bonded neighbours molecule type 'ASN' 86: 86: turning H bonds into constraints... 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: turning H bonds into constraints... 86: 86: Coupling 1 copies of molecule type 'ASN' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/conf.gro' 86: Analysing residue names: 86: There are: 1 Protein residues 86: There are: 56 Water residues 86: Analysing Protein... 86: 86: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 86: 86: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: Calculating fourier grid dimensions for X Y Z 86: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 86: 86: Estimate for the relative computational load of the PME mesh part: 0.94 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.119 0.060 199.6 86: (ns/day) (hour/ns) 86: Performance: 30.397 0.790 86: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_s_energy.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_s (230 ms) 86: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_s 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp, line 147]: 86: For proper sampling of the (nearly) decoupled state, stochastic dynamics 86: should be used 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 86: With PME there is a minor soft core effect present at the cut-off, 86: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 86: energy conservation, but usually other effects dominate. With a common 86: sigma value of 0.34 nm the fraction of the particle-particle potential at 86: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 355.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 86: The optimal PME mesh load for parallel simulations is below 0.5 86: and for highly parallel simulations between 0.25 and 0.33, 86: for higher performance, increase the cut-off and the PME grid spacing. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 86: For free energy simulations, the optimal load limit increases from 0.5 to 86: 0.667 86: 86: 86: 86: There were 4 NOTEs 86: 86: There was 1 WARNING 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_s_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 10 to 100, rlist from 1 to 1 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'AA' 86: 20 steps, 0.0 ps. 86: Setting the LD random seed to -22120489 86: 86: Generated 153 of the 153 non-bonded parameter combinations 86: 86: Generated 153 of the 153 1-4 parameter combinations 86: 86: Excluding 3 bonded neighbours molecule type 'ASN' 86: 86: turning H bonds into constraints... 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: turning H bonds into constraints... 86: 86: Coupling 1 copies of molecule type 'ASN' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/conf.gro' 86: Analysing residue names: 86: There are: 1 Protein residues 86: There are: 56 Water residues 86: Analysing Protein... 86: 86: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 86: 86: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: Calculating fourier grid dimensions for X Y Z 86: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 86: 86: Estimate for the relative computational load of the PME mesh part: 0.94 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 1.951 0.975 200.0 86: (ns/day) (hour/ns) 86: Performance: 1.860 12.902 86: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_s_energy.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_s (1193 ms) 86: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_net_charge_s 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp, line 147]: 86: For proper sampling of the (nearly) decoupled state, stochastic dynamics 86: should be used 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 86: With PME there is a minor soft core effect present at the cut-off, 86: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 86: energy conservation, but usually other effects dominate. With a common 86: sigma value of 0.34 nm the fraction of the particle-particle potential at 86: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: 86: NOTE 3 [file topol.top, line 155]: 86: System has non-zero total charge: 1.000000 86: Total charge should normally be an integer. See 86: https://manual.gromacs.org/current/user-guide/floating-point.html 86: for discussion on how close it should be to an integer. 86: 86: 86: 86: 86: WARNING 2 [file topol.top, line 155]: 86: You are using Ewald electrostatics in a system with net charge. This can 86: lead to severe artifacts, such as ions moving into regions with low 86: dielectric, due to the uniform background charge. We suggest to 86: neutralize your system with counter ions, possibly in combination with a 86: physiological salt concentration. 86: 86: Setting the LD random seed to 700447598 86: 86: Generated 171 of the 171 non-bonded parameter combinations 86: 86: Generated 171 of the 171 1-4 parameter combinations 86: 86: Excluding 3 bonded neighbours molecule type 'ASN' 86: 86: turning H bonds into constraints... 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: turning H bonds into constraints... 86: 86: Excluding 1 bonded neighbours molecule type 'NA' 86: 86: turning H bonds into constraints... 86: 86: Coupling 1 copies of molecule type 'ASN' 86: 86: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 86: J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof 86: Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net 86: Charge 86: J. Chem. Theory Comput. (2014) 86: DOI: 10.1021/ct400626b 86: -------- -------- --- Thank You --- -------- -------- 86: 86: Number of degrees of freedom in T-Coupling group System is 358.00 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 86: The optimal PME mesh load for parallel simulations is below 0.5 86: and for highly parallel simulations between 0.25 and 0.33, 86: for higher performance, increase the cut-off and the PME grid spacing. 86: 86: 86: 86: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 86: For free energy simulations, the optimal load limit increases from 0.5 to 86: 0.667 86: 86: 86: 86: There were 5 NOTEs 86: 86: There were 2 WARNINGs 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_net_charge_s_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 10 to 50, rlist from 1.004 to 1.101 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'AA' 86: 20 steps, 0.0 ps. 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/conf.gro' 86: Analysing residue names: 86: There are: 1 Protein residues 86: There are: 56 Water residues 86: There are: 1 Ion residues 86: Analysing Protein... 86: 86: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 86: 86: Determining Verlet buffer for a tolerance of 5e-05 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 1.004 nm, buffer size 0.004 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: Calculating fourier grid dimensions for X Y Z 86: Using a fourier grid of 32x32x32, spacing 0.095 0.095 0.095 86: 86: Estimate for the relative computational load of the PME mesh part: 0.96 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 2.586 1.293 200.0 86: (ns/day) (hour/ns) 86: Performance: 1.403 17.106 86: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_net_charge_s_energy.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_net_charge_s (1605 ms) 86: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_decouple_counter_charge_s 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp, line 147]: 86: For proper sampling of the (nearly) decoupled state, stochastic dynamics 86: should be used 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 86: With PME there is a minor soft core effect present at the cut-off, 86: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 86: energy conservation, but usually other effects dominate. With a common 86: sigma value of 0.34 nm the fraction of the particle-particle potential at 86: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: 86: NOTE 3 [file topol.top, line 165]: 86: System has non-zero total charge: 1.000000 86: Total charge should normally be an integer. See 86: https://manual.gromacs.org/current/user-guide/floating-point.html 86: for discussion on how close it should be to an integer. 86: 86: 86: 86: 86: WARNING 2 [file topol.top, line 165]: 86: You are using Ewald electrostatics in a system with net charge. This can 86: lead to severe artifacts, such as ions moving into regions with low 86: dielectric, due to the uniform background charge. We suggest to 86: neutralize your system with counter ions, possibly in combination with a 86: physiological salt concentration. 86: 86: Setting the LD random seed to -289472946 86: 86: Generated 190 of the 190 non-bonded parameter combinations 86: 86: Generated 190 of the 190 1-4 parameter combinations 86: 86: Excluding 3 bonded neighbours molecule type 'ASN' 86: 86: turning H bonds into constraints... 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: turning H bonds into constraints... 86: 86: Excluding 1 bonded neighbours molecule type 'NA' 86: 86: turning H bonds into constraints... 86: 86: Excluding 1 bonded neighbours molecule type 'CL' 86: 86: turning H bonds into constraints... 86: 86: Coupling 1 copies of molecule type 'CL' 86: 86: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 86: J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof 86: Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net 86: Charge 86: J. Chem. Theory Comput. (2014) 86: DOI: 10.1021/ct400626b 86: -------- -------- --- Thank You --- -------- -------- 86: 86: Number of degrees of freedom in T-Coupling group System is 361.00 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 86: The optimal PME mesh load for parallel simulations is below 0.5 86: and for highly parallel simulations between 0.25 and 0.33, 86: for higher performance, increase the cut-off and the PME grid spacing. 86: 86: 86: 86: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 86: For free energy simulations, the optimal load limit increases from 0.5 to 86: 0.667 86: 86: 86: 86: There were 5 NOTEs 86: 86: There were 2 WARNINGs 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_decouple_counter_charge_s_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 10 to 50, rlist from 1.004 to 1.102 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'AA' 86: 20 steps, 0.0 ps. 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/conf.gro' 86: Analysing residue names: 86: There are: 1 Protein residues 86: There are: 56 Water residues 86: There are: 2 Ion residues 86: Analysing Protein... 86: 86: The largest distance between non-perturbed excluded atoms is 0.331 nm between atom 1 and 9 86: 86: Determining Verlet buffer for a tolerance of 5e-05 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 1.004 nm, buffer size 0.004 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: Calculating fourier grid dimensions for X Y Z 86: Using a fourier grid of 32x32x32, spacing 0.095 0.095 0.095 86: 86: Estimate for the relative computational load of the PME mesh part: 0.96 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 2.648 1.324 200.0 86: (ns/day) (hour/ns) 86: Performance: 1.370 17.514 86: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_decouple_counter_charge_s_energy.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_decouple_counter_charge_s (1361 ms) 86: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_s 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp, line 171]: 86: For proper sampling of the (nearly) decoupled state, stochastic dynamics 86: should be used 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 86: Replacing vdwtype=Shift by the equivalent combination of vdwtype=Cut-off 86: and vdw_modifier=Force-switch 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 355.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 86: The optimal PME mesh load for parallel simulations is below 0.5 86: and for highly parallel simulations between 0.25 and 0.33, 86: for higher performance, increase the cut-off and the PME grid spacing. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 86: For free energy simulations, the optimal load limit increases from 0.5 to 86: 0.667 86: 86: 86: 86: There were 4 NOTEs 86: 86: There was 1 WARNING 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_s_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 10 to 100, rlist from 1 to 1 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'AA' 86: 100 steps, 0.1 ps. 86: Setting the LD random seed to -18939909 86: 86: Generated 153 of the 153 non-bonded parameter combinations 86: 86: Generated 153 of the 153 1-4 parameter combinations 86: 86: Excluding 3 bonded neighbours molecule type 'ASN' 86: 86: turning H bonds into constraints... 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: turning H bonds into constraints... 86: 86: Coupling 1 copies of molecule type 'ASN' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/expanded/conf.gro' 86: Analysing residue names: 86: There are: 1 Protein residues 86: There are: 56 Water residues 86: Analysing Protein... 86: 86: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 86: 86: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: Calculating fourier grid dimensions for X Y Z 86: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 86: 86: Estimate for the relative computational load of the PME mesh part: 0.94 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.497 0.249 199.9 86: (ns/day) (hour/ns) 86: Performance: 35.103 0.684 86: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_s_energy.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Reading energy frame 30 time 0.030 Reading energy frame 40 time 0.040 Reading energy frame 50 time 0.050 Reading energy frame 60 time 0.060 Reading energy frame 70 time 0.070 Reading energy frame 80 time 0.080 Reading energy frame 90 time 0.090 Reading energy frame 100 time 0.100 Last energy frame read 100 time 0.100 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_s (445 ms) 86: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_s 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: 86: WARNING 2 [file topol.top, line 72]: 86: No default Bond types for perturbed atoms in interaction, using normal 86: values. The interaction was 86: '7 8 1'. 86: 86: 86: WARNING 3 [file topol.top, line 73]: 86: No default Bond types for perturbed atoms in interaction, using normal 86: values. The interaction was 86: '7 9 1'. 86: 86: 86: WARNING 4 [file topol.top, line 98]: 86: No default Angle types for perturbed atoms in interaction, using normal 86: values. The interaction was 86: '6 5 7 1'. 86: 86: 86: WARNING 5 [file topol.top, line 99]: 86: No default Angle types for perturbed atoms in interaction, using normal 86: values. The interaction was 86: '5 7 8 1'. 86: 86: 86: WARNING 6 [file topol.top, line 100]: 86: No default Angle types for perturbed atoms in interaction, using normal 86: values. The interaction was 86: '5 7 9 1'. 86: 86: 86: WARNING 7 [file topol.top, line 101]: 86: No default Angle types for perturbed atoms in interaction, using normal 86: values. The interaction was 86: '8 7 9 1'. 86: 86: 86: WARNING 8 [file topol.top, line 111]: 86: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 86: normal values. The interaction was 86: '1 5 7 8 3'. 86: 86: 86: WARNING 9 [file topol.top, line 112]: 86: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 86: normal values. The interaction was 86: '1 5 7 9 3'. 86: 86: 86: WARNING 10 [file topol.top, line 113]: 86: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 86: normal values. The interaction was 86: '6 5 7 8 3'. 86: 86: 86: WARNING 11 [file topol.top, line 114]: 86: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 86: normal values. The interaction was 86: '6 5 7 9 3'. 86: 86: Number of degrees of freedom in T-Coupling group System is 355.00 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 86: The optimal PME mesh load for parallel simulations is below 0.5 86: and for highly parallel simulations between 0.25 and 0.33, 86: for higher performance, increase the cut-off and the PME grid spacing. 86: 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 86: For free energy simulations, the optimal load limit increases from 0.5 to 86: 0.667 86: 86: 86: 86: There were 2 NOTEs 86: 86: There were 11 WARNINGs 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_s_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 10 to 100, rlist from 1 to 1 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'AA' 86: 20 steps, 0.0 ps. 86: Setting the LD random seed to 1055882063 86: 86: Generated 136 of the 136 non-bonded parameter combinations 86: 86: Generated 136 of the 136 1-4 parameter combinations 86: 86: Excluding 3 bonded neighbours molecule type 'ASN' 86: 86: turning H bonds into constraints... 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: turning H bonds into constraints... 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/relative/conf.gro' 86: Analysing residue names: 86: There are: 1 Protein residues 86: There are: 56 Water residues 86: Analysing Protein... 86: 86: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 86: 86: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: Calculating fourier grid dimensions for X Y Z 86: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 86: 86: Estimate for the relative computational load of the PME mesh part: 0.94 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.157 0.078 199.6 86: (ns/day) (hour/ns) 86: Performance: 23.127 1.038 86: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_s_energy.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_s (257 ms) 86: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_s 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: 86: WARNING 2 [file topol.top, line 72]: 86: No default Bond types for perturbed atoms in interaction, using normal 86: values. The interaction was 86: '7 8 1'. 86: 86: 86: WARNING 3 [file topol.top, line 73]: 86: No default Bond types for perturbed atoms in interaction, using normal 86: values. The interaction was 86: '7 9 1'. 86: 86: 86: WARNING 4 [file topol.top, line 98]: 86: No default Angle types for perturbed atoms in interaction, using normal 86: values. The interaction was 86: '6 5 7 1'. 86: 86: 86: WARNING 5 [file topol.top, line 99]: 86: No default Angle types for perturbed atoms in interaction, using normal 86: values. The interaction was 86: '5 7 8 1'. 86: 86: 86: WARNING 6 [file topol.top, line 100]: 86: No default Angle types for perturbed atoms in interaction, using normal 86: values. The interaction was 86: '5 7 9 1'. 86: 86: 86: WARNING 7 [file topol.top, line 101]: 86: No default Angle types for perturbed atoms in interaction, using normal 86: values. The interaction was 86: '8 7 9 1'. 86: 86: 86: WARNING 8 [file topol.top, line 111]: 86: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 86: normal values. The interaction was 86: '1 5 7 8 3'. 86: 86: 86: WARNING 9 [file topol.top, line 112]: 86: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 86: normal values. The interaction was 86: '1 5 7 9 3'. 86: 86: 86: WARNING 10 [file topol.top, line 113]: 86: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 86: normal values. The interaction was 86: '6 5 7 8 3'. 86: 86: 86: WARNING 11 [file topol.top, line 114]: 86: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 86: normal values. The interaction was 86: '6 5 7 9 3'. 86: 86: Number of degrees of freedom in T-Coupling group System is 355.00 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 86: Removing center of mass motion in the presence of position restraints 86: might cause artifacts. When you are using position restraints to 86: equilibrate a macro-molecule, the artifacts are usually negligible. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 86: The optimal PME mesh load for parallel simulations is below 0.5 86: and for highly parallel simulations between 0.25 and 0.33, 86: for higher performance, increase the cut-off and the PME grid spacing. 86: 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 86: For free energy simulations, the optimal load limit increases from 0.5 to 86: 0.667 86: 86: 86: 86: There were 3 NOTEs 86: 86: There were 11 WARNINGs 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_s_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 10 to 100, rlist from 1 to 1 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'AA' 86: 20 steps, 0.0 ps. 86: Setting the LD random seed to 2076884726 86: 86: Generated 136 of the 136 non-bonded parameter combinations 86: 86: Generated 136 of the 136 1-4 parameter combinations 86: 86: Excluding 3 bonded neighbours molecule type 'ASN' 86: 86: turning H bonds into constraints... 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: turning H bonds into constraints... 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/conf.gro' 86: Analysing residue names: 86: There are: 1 Protein residues 86: There are: 56 Water residues 86: Analysing Protein... 86: 86: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 86: 86: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: Calculating fourier grid dimensions for X Y Z 86: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 86: 86: Estimate for the relative computational load of the PME mesh part: 0.94 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.151 0.076 199.6 86: (ns/day) (hour/ns) 86: Performance: 23.957 1.002 86: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_s_energy.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_s (238 ms) 86: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/restraints_s 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 355.00 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 86: The optimal PME mesh load for parallel simulations is below 0.5 86: and for highly parallel simulations between 0.25 and 0.33, 86: for higher performance, increase the cut-off and the PME grid spacing. 86: 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 86: For free energy simulations, the optimal load limit increases from 0.5 to 86: 0.667 86: 86: 86: 86: There were 2 NOTEs 86: 86: There was 1 WARNING 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_s_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 10 to 100, rlist from 1 to 1 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'AA' 86: 20 steps, 0.0 ps. 86: Setting the LD random seed to -2121749 86: 86: Generated 136 of the 136 non-bonded parameter combinations 86: 86: Generated 136 of the 136 1-4 parameter combinations 86: 86: Excluding 3 bonded neighbours molecule type 'ASN' 86: 86: turning H bonds into constraints... 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: turning H bonds into constraints... 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/restraints/conf.gro' 86: Analysing residue names: 86: There are: 1 Protein residues 86: There are: 56 Water residues 86: Analysing Protein... 86: 86: The largest distance between non-perturbed excluded atoms is 0.331 nm between atom 1 and 9 86: 86: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: Calculating fourier grid dimensions for X Y Z 86: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 86: 86: Estimate for the relative computational load of the PME mesh part: 0.88 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.066 0.033 199.3 86: (ns/day) (hour/ns) 86: Performance: 54.575 0.440 86: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_s_energy.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/restraints_s (194 ms) 86: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_s 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/simtemp/grompp.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 355.00 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/simtemp/grompp.mdp]: 86: The optimal PME mesh load for parallel simulations is below 0.5 86: and for highly parallel simulations between 0.25 and 0.33, 86: for higher performance, increase the cut-off and the PME grid spacing. 86: 86: 86: 86: There was 1 NOTE 86: 86: There was 1 WARNING 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_s_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 10 to 100, rlist from 1 to 1 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'AA' 86: 20 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.042 0.021 198.7 86: (ns/day) (hour/ns) 86: Performance: 86.470 0.278 86: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_s_energy.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Setting the LD random seed to 1935583420 86: 86: Generated 136 of the 136 non-bonded parameter combinations 86: 86: Generated 136 of the 136 1-4 parameter combinations 86: 86: Excluding 3 bonded neighbours molecule type 'ASN' 86: 86: turning H bonds into constraints... 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: turning H bonds into constraints... 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/simtemp/conf.gro' 86: Analysing residue names: 86: There are: 1 Protein residues 86: There are: 56 Water residues 86: Analysing Protein... 86: 86: The largest distance between excluded atoms is 0.331 nm between atom 1 and 9 86: 86: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: Calculating fourier grid dimensions for X Y Z 86: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 86: 86: Estimate for the relative computational load of the PME mesh part: 0.88 86: 86: This run will generate roughly 0 Mb of data 86: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_s (193 ms) 86: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_s 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 86: With PME there is a minor soft core effect present at the cut-off, 86: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 86: energy conservation, but usually other effects dominate. With a common 86: sigma value of 0.34 nm the fraction of the particle-particle potential at 86: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 355.00 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 86: The optimal PME mesh load for parallel simulations is below 0.5 86: and for highly parallel simulations between 0.25 and 0.33, 86: for higher performance, increase the cut-off and the PME grid spacing. 86: 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 86: For free energy simulations, the optimal load limit increases from 0.5 to 86: 0.667 86: 86: 86: 86: There were 3 NOTEs 86: 86: There was 1 WARNING 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_s_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 10 to 100, rlist from 1 to 1 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'AA' 86: 20 steps, 0.0 ps. 86: Setting the LD random seed to -537027601 86: 86: Generated 136 of the 136 non-bonded parameter combinations 86: 86: Generated 136 of the 136 1-4 parameter combinations 86: 86: Excluding 3 bonded neighbours molecule type 'ASN' 86: 86: turning H bonds into constraints... 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: turning H bonds into constraints... 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/transformAtoB/conf.gro' 86: Analysing residue names: 86: There are: 1 Protein residues 86: There are: 56 Water residues 86: Analysing Protein... 86: 86: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 86: 86: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: Calculating fourier grid dimensions for X Y Z 86: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 86: 86: Estimate for the relative computational load of the PME mesh part: 0.94 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.142 0.071 199.6 86: (ns/day) (hour/ns) 86: Performance: 25.494 0.941 86: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_s_energy.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_s (244 ms) 86: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/vdwalone_s 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 86: With PME there is a minor soft core effect present at the cut-off, 86: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 86: energy conservation, but usually other effects dominate. With a common 86: sigma value of 0.34 nm the fraction of the particle-particle potential at 86: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 355.00 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 86: The optimal PME mesh load for parallel simulations is below 0.5 86: and for highly parallel simulations between 0.25 and 0.33, 86: for higher performance, increase the cut-off and the PME grid spacing. 86: 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 86: For free energy simulations, the optimal load limit increases from 0.5 to 86: 0.667 86: 86: 86: 86: There were 3 NOTEs 86: 86: There was 1 WARNING 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_s_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 10 to 100, rlist from 1 to 1 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'AA' 86: 20 steps, 0.0 ps. 86: Setting the LD random seed to -34160659 86: 86: Generated 136 of the 136 non-bonded parameter combinations 86: 86: Generated 136 of the 136 1-4 parameter combinations 86: 86: Excluding 3 bonded neighbours molecule type 'ASN' 86: 86: turning H bonds into constraints... 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: turning H bonds into constraints... 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/vdwalone/conf.gro' 86: Analysing residue names: 86: There are: 1 Protein residues 86: There are: 56 Water residues 86: Analysing Protein... 86: 86: The largest distance between non-perturbed excluded atoms is 0.172 nm between atom 8 and 9 86: 86: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: Calculating fourier grid dimensions for X Y Z 86: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 86: 86: Estimate for the relative computational load of the PME mesh part: 0.88 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.090 0.045 199.3 86: (ns/day) (hour/ns) 86: Performance: 39.973 0.600 86: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_s_energy.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/vdwalone_s (214 ms) 86: [----------] 12 tests from EquivalentToReference/FreeEnergyReferenceTest (6570 ms total) 86: 86: [----------] Global test environment tear-down 86: [==========] 14 tests from 2 test suites ran. (6978 ms total) 86: [ PASSED ] 14 tests. 86/90 Test #86: MdrunFEPTests ............................. Passed 7.00 sec test 87 Start 87: MdrunPullTests 87: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/mdrun-pull-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/MdrunPullTests.xml" 87: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests 87: Test timeout computed to be: 600 87: [==========] Running 4 tests from 1 test suite. 87: [----------] Global test environment set-up. 87: [----------] 4 tests from PullTest/PullIntegrationTest 87: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/0 87: Generating 1-4 interactions: fudge = 0.5 87: Pull group 1 'r_1' has 3 atoms 87: Pull group 2 'r_2' has 3 atoms 87: Number of degrees of freedom in T-Coupling group System is 1293.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0_input.mdp]: 87: NVE simulation: will use the initial temperature of 303.122 K for 87: determining the Verlet buffer size 87: 87: Pull group natoms pbc atom distance at start reference at t=0 87: 1 3 2 87: 2 3 5 0.575 nm 0.600 nm 87: 87: There was 1 NOTE 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 1 MPI thread 87: Using 2 OpenMP threads 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 20 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc216.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.055 0.028 199.4 87: (ns/day) (hour/ns) 87: Performance: 65.811 0.365 87: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/0 (515 ms) 87: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/1 87: Generating 1-4 interactions: fudge = 0.5 87: Pull group 1 'r_1' has 3 atoms 87: Pull group 2 'r_2' has 3 atoms 87: Number of degrees of freedom in T-Coupling group System is 1293.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1_input.mdp]: 87: NVE simulation: will use the initial temperature of 303.122 K for 87: determining the Verlet buffer size 87: 87: Pull group natoms pbc atom distance at start reference at t=0 87: 1 3 2 87: 2 3 5 0.301 nm 0.400 nm 87: 87: There was 1 NOTE 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 1 MPI thread 87: Using 2 OpenMP threads 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 20 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc216.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.076 0.038 199.5 87: (ns/day) (hour/ns) 87: Performance: 47.398 0.506 87: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/1 (538 ms) 87: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/2 87: Generating 1-4 interactions: fudge = 0.5 87: Pull group 1 'r_1' has 3 atoms 87: Pull group 2 'r_2' has 3 atoms 87: Pull group 3 'r_3' has 3 atoms 87: Number of degrees of freedom in T-Coupling group System is 1292.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2_input.mdp]: 87: NVE simulation: will use the initial temperature of 303.357 K for 87: determining the Verlet buffer size 87: 87: Pull group natoms pbc atom distance at start reference at t=0 87: 1 3 2 87: 2 3 5 0.575 nm 0.500 nm 87: 1 3 2 87: 3 3 8 0.331 nm 0.400 nm 87: 87: There was 1 NOTE 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 1 MPI thread 87: Using 2 OpenMP threads 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 20 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc216.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.357 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 3.526 1.763 200.0 87: (ns/day) (hour/ns) 87: Performance: 1.029 23.324 87: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/2 (2244 ms) 87: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/3 87: Generating 1-4 interactions: fudge = 0.5 87: Pull group 1 'r_1' has 3 atoms 87: Pull group 2 'r_2' has 3 atoms 87: Number of degrees of freedom in T-Coupling group System is 1293.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3_input.mdp]: 87: NVE simulation: will use the initial temperature of 303.122 K for 87: determining the Verlet buffer size 87: 87: Pull group natoms pbc atom distance at start reference at t=0 87: 1 3 2 87: 2 3 5 0.575 nm 0.000 nm 87: 1 3 2 87: 2 3 5 0.050 nm 0.000 nm 87: 87: There was 1 NOTE 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 1 MPI thread 87: Using 2 OpenMP threads 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 20 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc216.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.123 0.061 199.6 87: (ns/day) (hour/ns) 87: Performance: 29.541 0.812 87: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/3 (517 ms) 87: [----------] 4 tests from PullTest/PullIntegrationTest (3816 ms total) 87: 87: [----------] Global test environment tear-down 87: [==========] 4 tests from 1 test suite ran. (3927 ms total) 87: [ PASSED ] 4 tests. 87/90 Test #87: MdrunPullTests ............................ Passed 3.96 sec test 88 Start 88: MdrunRotationTests 88: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/mdrun-rotation-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/MdrunRotationTests.xml" 88: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests 88: Test timeout computed to be: 600 88: [==========] Running 12 tests from 1 test suite. 88: [----------] Global test environment set-up. 88: [----------] 12 tests from RotationWorks/RotationTest 88: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/0 88: Enforced rotation: Group 0 (iso) normalized rot. vector: 0.267261 0.534522 0.801784 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: Rotation group 0 'system' has 4 atoms 88: Number of degrees of freedom in T-Coupling group rest is 9.00 88: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0_input.mdp]: 88: NVE simulation with an initial temperature of zero: will use a Verlet 88: buffer of 10%. Check your energy drift! 88: 88: Enforced rotation: group 0 has 4 reference positions. 88: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 88: trr version: GMX_trn_file (single precision) 88: 88: There were 2 NOTEs 88: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 88: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 88: 25 steps, 0.1 ps. 88: Setting the LD random seed to -335580461 88: 88: Generated 1 of the 1 non-bonded parameter combinations 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonA' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonB' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonC' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonD' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.036 0.018 199.0 88: (ns/day) (hour/ns) 88: Performance: 245.914 0.098 88: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.edr as single precision energy file 88: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.edr as single precision energy file 88: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 88: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/0 (31 ms) 88: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/1 88: Enforced rotation: Group 0 (iso-pf) normalized rot. vector: 0.267261 0.534522 0.801784 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: Rotation group 0 'system' has 4 atoms 88: Number of degrees of freedom in T-Coupling group rest is 9.00 88: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1_input.mdp]: 88: NVE simulation with an initial temperature of zero: will use a Verlet 88: buffer of 10%. Check your energy drift! 88: 88: Enforced rotation: group 0 has 4 reference positions. 88: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 88: 88: There were 2 NOTEs 88: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 88: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 88: 25 steps, 0.1 ps. 88: Setting the LD random seed to 1869540223 88: 88: Generated 1 of the 1 non-bonded parameter combinations 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonA' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonB' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonC' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonD' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.026 0.013 198.3 88: (ns/day) (hour/ns) 88: Performance: 340.689 0.070 88: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.edr as single precision energy file 88: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.edr as single precision energy file 88: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 88: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/1 (22 ms) 88: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/2 88: Enforced rotation: Group 0 (pm) normalized rot. vector: 0.267261 0.534522 0.801784 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: Rotation group 0 'system' has 4 atoms 88: Number of degrees of freedom in T-Coupling group rest is 9.00 88: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2_input.mdp]: 88: NVE simulation with an initial temperature of zero: will use a Verlet 88: buffer of 10%. Check your energy drift! 88: 88: Enforced rotation: group 0 has 4 reference positions. 88: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 88: 88: There were 2 NOTEs 88: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 88: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 88: 25 steps, 0.1 ps. 88: Setting the LD random seed to -547381263 88: 88: Generated 1 of the 1 non-bonded parameter combinations 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonA' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonB' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonC' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonD' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.026 0.013 198.5 88: (ns/day) (hour/ns) 88: Performance: 343.583 0.070 88: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.edr as single precision energy file 88: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.edr as single precision energy file 88: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 88: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/2 (22 ms) 88: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/3 88: Enforced rotation: Group 0 (pm-pf) normalized rot. vector: 0.267261 0.534522 0.801784 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: Rotation group 0 'system' has 4 atoms 88: Number of degrees of freedom in T-Coupling group rest is 9.00 88: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3_input.mdp]: 88: NVE simulation with an initial temperature of zero: will use a Verlet 88: buffer of 10%. Check your energy drift! 88: 88: Enforced rotation: group 0 has 4 reference positions. 88: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 88: 88: There were 2 NOTEs 88: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 88: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 88: 25 steps, 0.1 ps. 88: Setting the LD random seed to 2147187639 88: 88: Generated 1 of the 1 non-bonded parameter combinations 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonA' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonB' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonC' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonD' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.025 0.012 198.3 88: (ns/day) (hour/ns) 88: Performance: 360.999 0.066 88: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.edr as single precision energy file 88: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.edr as single precision energy file 88: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 88: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/3 (23 ms) 88: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/4 88: Enforced rotation: Group 0 (rm) normalized rot. vector: 0.267261 0.534522 0.801784 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: Rotation group 0 'system' has 4 atoms 88: Number of degrees of freedom in T-Coupling group rest is 9.00 88: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4_input.mdp]: 88: NVE simulation with an initial temperature of zero: will use a Verlet 88: buffer of 10%. Check your energy drift! 88: 88: Enforced rotation: group 0 has 4 reference positions. 88: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 88: 88: There were 2 NOTEs 88: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 88: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 88: 25 steps, 0.1 ps. 88: Setting the LD random seed to -4222100 88: 88: Generated 1 of the 1 non-bonded parameter combinations 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonA' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonB' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonC' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonD' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.024 0.012 198.5 88: (ns/day) (hour/ns) 88: Performance: 369.059 0.065 88: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.edr as single precision energy file 88: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.edr as single precision energy file 88: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 88: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/4 (21 ms) 88: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/5 88: Enforced rotation: Group 0 (rm-pf) normalized rot. vector: 0.267261 0.534522 0.801784 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: Rotation group 0 'system' has 4 atoms 88: Number of degrees of freedom in T-Coupling group rest is 9.00 88: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5_input.mdp]: 88: NVE simulation with an initial temperature of zero: will use a Verlet 88: buffer of 10%. Check your energy drift! 88: 88: Enforced rotation: group 0 has 4 reference positions. 88: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 88: 88: There were 2 NOTEs 88: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 88: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 88: 25 steps, 0.1 ps. 88: Setting the LD random seed to 1325370427 88: 88: Generated 1 of the 1 non-bonded parameter combinations 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonA' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonB' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonC' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonD' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.023 0.012 198.5 88: (ns/day) (hour/ns) 88: Performance: 390.165 0.062 88: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.edr as single precision energy file 88: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.edr as single precision energy file 88: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 88: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/5 (21 ms) 88: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/6 88: Enforced rotation: Group 0 (rm2) normalized rot. vector: 0.267261 0.534522 0.801784 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: Rotation group 0 'system' has 4 atoms 88: Number of degrees of freedom in T-Coupling group rest is 9.00 88: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6_input.mdp]: 88: NVE simulation with an initial temperature of zero: will use a Verlet 88: buffer of 10%. Check your energy drift! 88: 88: Enforced rotation: group 0 has 4 reference positions. 88: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 88: 88: There were 2 NOTEs 88: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 88: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 88: 25 steps, 0.1 ps. 88: Setting the LD random seed to 2147415800 88: 88: Generated 1 of the 1 non-bonded parameter combinations 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonA' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonB' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonC' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonD' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.025 0.013 198.6 88: (ns/day) (hour/ns) 88: Performance: 355.322 0.068 88: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.edr as single precision energy file 88: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.edr as single precision energy file 88: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 88: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/6 (22 ms) 88: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/7 88: Enforced rotation: Group 0 (rm2-pf) normalized rot. vector: 0.267261 0.534522 0.801784 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: Rotation group 0 'system' has 4 atoms 88: Number of degrees of freedom in T-Coupling group rest is 9.00 88: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7_input.mdp]: 88: NVE simulation with an initial temperature of zero: will use a Verlet 88: buffer of 10%. Check your energy drift! 88: 88: Enforced rotation: group 0 has 4 reference positions. 88: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 88: 88: There were 2 NOTEs 88: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 88: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 88: 25 steps, 0.1 ps. 88: Setting the LD random seed to 2076687359 88: 88: Generated 1 of the 1 non-bonded parameter combinations 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonA' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonB' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonC' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonD' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.022 0.011 198.6 88: (ns/day) (hour/ns) 88: Performance: 401.290 0.060 88: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.edr as single precision energy file 88: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.edr as single precision energy file 88: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 88: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/7 (20 ms) 88: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/8 88: Enforced rotation: Group 0 (flex) normalized rot. vector: 0.267261 0.534522 0.801784 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: Rotation group 0 'system' has 4 atoms 88: Number of degrees of freedom in T-Coupling group rest is 9.00 88: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8_input.mdp]: 88: NVE simulation with an initial temperature of zero: will use a Verlet 88: buffer of 10%. Check your energy drift! 88: 88: Enforced rotation: group 0 has 4 reference positions. 88: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 88: 88: There were 2 NOTEs 88: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 88: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 88: 25 steps, 0.1 ps. 88: Setting the LD random seed to -11281477 88: 88: Generated 1 of the 1 non-bonded parameter combinations 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonA' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonB' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonC' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonD' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.050 0.025 199.3 88: (ns/day) (hour/ns) 88: Performance: 178.066 0.135 88: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.edr as single precision energy file 88: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.edr as single precision energy file 88: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 88: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/8 (34 ms) 88: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/9 88: Enforced rotation: Group 0 (flex-t) normalized rot. vector: 0.267261 0.534522 0.801784 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: Rotation group 0 'system' has 4 atoms 88: Number of degrees of freedom in T-Coupling group rest is 9.00 88: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9_input.mdp]: 88: NVE simulation with an initial temperature of zero: will use a Verlet 88: buffer of 10%. Check your energy drift! 88: 88: Enforced rotation: group 0 has 4 reference positions. 88: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 88: 88: There were 2 NOTEs 88: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 88: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 88: 25 steps, 0.1 ps. 88: Setting the LD random seed to 637468153 88: 88: Generated 1 of the 1 non-bonded parameter combinations 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonA' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonB' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonC' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonD' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.030 0.015 198.9 88: (ns/day) (hour/ns) 88: Performance: 301.174 0.080 88: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.edr as single precision energy file 88: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.edr as single precision energy file 88: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 88: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/9 (24 ms) 88: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/10 88: Enforced rotation: Group 0 (flex2) normalized rot. vector: 0.267261 0.534522 0.801784 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: Rotation group 0 'system' has 4 atoms 88: Number of degrees of freedom in T-Coupling group rest is 9.00 88: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10_input.mdp]: 88: NVE simulation with an initial temperature of zero: will use a Verlet 88: buffer of 10%. Check your energy drift! 88: 88: Enforced rotation: group 0 has 4 reference positions. 88: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 88: 88: There were 2 NOTEs 88: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 88: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 88: 25 steps, 0.1 ps. 88: Setting the LD random seed to -278930561 88: 88: Generated 1 of the 1 non-bonded parameter combinations 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonA' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonB' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonC' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonD' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.035 0.018 199.0 88: (ns/day) (hour/ns) 88: Performance: 254.335 0.094 88: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.edr as single precision energy file 88: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.edr as single precision energy file 88: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 88: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/10 (28 ms) 88: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/11 88: Enforced rotation: Group 0 (flex2-t) normalized rot. vector: 0.267261 0.534522 0.801784 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: Rotation group 0 'system' has 4 atoms 88: Number of degrees of freedom in T-Coupling group rest is 9.00 88: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11_input.mdp]: 88: NVE simulation with an initial temperature of zero: will use a Verlet 88: buffer of 10%. Check your energy drift! 88: 88: Enforced rotation: group 0 has 4 reference positions. 88: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 88: 88: There were 2 NOTEs 88: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 88: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 88: 25 steps, 0.1 ps. 88: Setting the LD random seed to -671088655 88: 88: Generated 1 of the 1 non-bonded parameter combinations 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonA' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonB' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonC' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonD' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.031 0.015 198.4 88: (ns/day) (hour/ns) 88: Performance: 291.277 0.082 88: Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.edr as single precision energy file 88: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.edr as single precision energy file 88: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 88: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/11 (27 ms) 88: [----------] 12 tests from RotationWorks/RotationTest (302 ms total) 88: 88: [----------] Global test environment tear-down 88: [==========] 12 tests from 1 test suite ran. (404 ms total) 88: [ PASSED ] 12 tests. 88/90 Test #88: MdrunRotationTests ........................ Passed 0.43 sec test 89 Start 89: MdrunSimulatorComparison 89: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/mdrun-simulator-comparison-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/MdrunSimulatorComparison.xml" 89: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests 89: Test timeout computed to be: 600 89: [==========] Running 0 tests from 0 test suites. 89: [==========] 0 tests from 0 test suites ran. (0 ms total) 89: [ PASSED ] 0 tests. 89: 89: YOU HAVE 82 DISABLED TESTS 89: 89/90 Test #89: MdrunSimulatorComparison .................. Passed 0.02 sec test 90 Start 90: MdrunVirtualSiteTests 90: Test command: /build/reproducible-path/gromacs-2025.0/build/basic/bin/mdrun-vsites-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic/Testing/Temporary/MdrunVirtualSiteTests.xml" 90: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests 90: Test timeout computed to be: 600 90: [==========] Running 37 tests from 2 test suites. 90: [----------] Global test environment set-up. 90: [----------] 1 test from VirtualSiteVelocityTest 90: [ RUN ] VirtualSiteVelocityTest.ReferenceIsCorrect 90: [ OK ] VirtualSiteVelocityTest.ReferenceIsCorrect (0 ms) 90: [----------] 1 test from VirtualSiteVelocityTest (0 ms total) 90: 90: [----------] 36 tests from VelocitiesConformToExpectations/VirtualSiteTest 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/0 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: 90: Dynamic load balancing report: 90: DLB was off during the run due to low measured imbalance. 90: Average load imbalance: 0.1%. 90: The balanceable part of the MD step is 42%, load imbalance is computed from this. 90: Part of the total run time spent waiting due to load imbalance: 0.1%. 90: 90: 90: NOTE: 48 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.031 0.016 198.8 90: (ns/day) (hour/ns) 90: Performance: 50.114 0.479 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: trr version: GMX_trn_file (single precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/0 (27 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/1 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: 90: Dynamic load balancing report: 90: DLB was off during the run due to low measured imbalance. 90: Average load imbalance: 2.8%. 90: The balanceable part of the MD step is 26%, load imbalance is computed from this. 90: Part of the total run time spent waiting due to load imbalance: 0.7%. 90: 90: 90: NOTE: 47 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.029 0.015 198.4 90: (ns/day) (hour/ns) 90: Performance: 52.887 0.454 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/1 (23 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/2 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: 90: Dynamic load balancing report: 90: DLB was off during the run due to low measured imbalance. 90: Average load imbalance: 5.0%. 90: The balanceable part of the MD step is 38%, load imbalance is computed from this. 90: Part of the total run time spent waiting due to load imbalance: 1.9%. 90: 90: 90: NOTE: 46 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.024 0.012 198.1 90: (ns/day) (hour/ns) 90: Performance: 64.879 0.370 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/2 (24 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/3 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 90: There are 6 non-linear virtual site constructions. Their contribution to 90: the energy error is approximated. In most cases this does not affect the 90: error significantly. 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 90: 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 47 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.023 0.012 198.4 90: (ns/day) (hour/ns) 90: Performance: 67.439 0.356 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/3 (30 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/4 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 90: There are 6 non-linear virtual site constructions. Their contribution to 90: the energy error is approximated. In most cases this does not affect the 90: error significantly. 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 90: 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 47 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.026 0.013 198.3 90: (ns/day) (hour/ns) 90: Performance: 58.371 0.411 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/4 (34 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/5 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 90: There are 6 non-linear virtual site constructions. Their contribution to 90: the energy error is approximated. In most cases this does not affect the 90: error significantly. 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 90: 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 45 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.024 0.012 198.0 90: (ns/day) (hour/ns) 90: Performance: 63.439 0.378 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/5 (32 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/6 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 90: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 90: 1 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 90: There are 6 non-linear virtual site constructions. Their contribution to 90: the energy error is approximated. In most cases this does not affect the 90: error significantly. 90: 90: 90: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 5 NOTEs 90: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 90: 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 46 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.022 0.011 197.7 90: (ns/day) (hour/ns) 90: Performance: 70.071 0.343 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/6 (30 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/7 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 90: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 90: 1 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 90: There are 6 non-linear virtual site constructions. Their contribution to 90: the energy error is approximated. In most cases this does not affect the 90: error significantly. 90: 90: 90: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 5 NOTEs 90: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 90: 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 46 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.023 0.012 198.0 90: (ns/day) (hour/ns) 90: Performance: 65.729 0.365 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/7 (31 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/8 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 90: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 90: 1 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 90: There are 6 non-linear virtual site constructions. Their contribution to 90: the energy error is approximated. In most cases this does not affect the 90: error significantly. 90: 90: 90: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 5 NOTEs 90: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 90: 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 46 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.025 0.013 197.7 90: (ns/day) (hour/ns) 90: Performance: 62.105 0.386 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/8 (33 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/9 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: 90: Dynamic load balancing report: 90: DLB was off during the run due to low measured imbalance. 90: Average load imbalance: 0.2%. 90: The balanceable part of the MD step is 38%, load imbalance is computed from this. 90: Part of the total run time spent waiting due to load imbalance: 0.1%. 90: 90: 90: NOTE: 46 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.024 0.012 198.3 90: (ns/day) (hour/ns) 90: Performance: 64.558 0.372 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/9 (22 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/10 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: 90: Dynamic load balancing report: 90: DLB was off during the run due to low measured imbalance. 90: Average load imbalance: 0.3%. 90: The balanceable part of the MD step is 46%, load imbalance is computed from this. 90: Part of the total run time spent waiting due to load imbalance: 0.1%. 90: 90: 90: NOTE: 46 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.027 0.014 197.9 90: (ns/day) (hour/ns) 90: Performance: 56.754 0.423 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/10 (24 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/11 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/11 (0 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/12 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 90: There are 6 non-linear virtual site constructions. Their contribution to 90: the energy error is approximated. In most cases this does not affect the 90: error significantly. 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 90: 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 46 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.025 0.012 197.7 90: (ns/day) (hour/ns) 90: Performance: 62.519 0.384 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/12 (32 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/13 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 90: There are 6 non-linear virtual site constructions. Their contribution to 90: the energy error is approximated. In most cases this does not affect the 90: error significantly. 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 90: 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 46 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.025 0.013 197.6 90: (ns/day) (hour/ns) 90: Performance: 61.603 0.390 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/13 (32 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/14 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/14 (0 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/15 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 90: There are 6 non-linear virtual site constructions. Their contribution to 90: the energy error is approximated. In most cases this does not affect the 90: error significantly. 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 90: 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 46 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.025 0.013 198.1 90: (ns/day) (hour/ns) 90: Performance: 61.447 0.391 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/15 (32 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/16 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 90: There are 6 non-linear virtual site constructions. Their contribution to 90: the energy error is approximated. In most cases this does not affect the 90: error significantly. 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 90: 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 46 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.024 0.012 198.2 90: (ns/day) (hour/ns) 90: Performance: 63.986 0.375 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/16 (32 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/17 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/17 (0 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/18 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 90: There are 6 non-linear virtual site constructions. Their contribution to 90: the energy error is approximated. In most cases this does not affect the 90: error significantly. 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 90: 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 47 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.026 0.013 198.3 90: (ns/day) (hour/ns) 90: Performance: 59.053 0.406 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/18 (34 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/19 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 90: There are 6 non-linear virtual site constructions. Their contribution to 90: the energy error is approximated. In most cases this does not affect the 90: error significantly. 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 90: 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 46 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.028 0.014 198.3 90: (ns/day) (hour/ns) 90: Performance: 55.388 0.433 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/19 (34 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/20 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 90: There are 6 non-linear virtual site constructions. Their contribution to 90: the energy error is approximated. In most cases this does not affect the 90: error significantly. 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 90: 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 47 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.041 0.021 199.1 90: (ns/day) (hour/ns) 90: Performance: 37.774 0.635 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/20 (41 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/21 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/21 (0 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/22 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/22 (0 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/23 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/23 (0 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/24 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/24 (0 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/25 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/25 (0 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/26 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/26 (0 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/27 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 90: There are 6 non-linear virtual site constructions. Their contribution to 90: the energy error is approximated. In most cases this does not affect the 90: error significantly. 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 90: 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 46 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.026 0.013 198.0 90: (ns/day) (hour/ns) 90: Performance: 59.586 0.403 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/27 (42 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/28 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 90: There are 6 non-linear virtual site constructions. Their contribution to 90: the energy error is approximated. In most cases this does not affect the 90: error significantly. 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 90: 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 47 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.029 0.014 198.3 90: (ns/day) (hour/ns) 90: Performance: 54.064 0.444 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/28 (43 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/29 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 90: There are 6 non-linear virtual site constructions. Their contribution to 90: the energy error is approximated. In most cases this does not affect the 90: error significantly. 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 90: 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 46 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.032 0.016 198.4 90: (ns/day) (hour/ns) 90: Performance: 48.342 0.496 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/29 (45 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/30 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/30 (0 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/31 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/31 (0 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/32 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/32 (0 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/33 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/33 (0 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/34 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/34 (0 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/35 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/35 (0 ms) 90: [----------] 36 tests from VelocitiesConformToExpectations/VirtualSiteTest (689 ms total) 90: 90: [----------] Global test environment tear-down 90: [==========] 37 tests from 2 test suites ran. (824 ms total) 90: [ PASSED ] 37 tests. 90/90 Test #90: MdrunVirtualSiteTests ..................... Passed 0.85 sec 100% tests passed, 0 tests failed out of 90 Label Time Summary: GTest = 573.94 sec*proc (88 tests) IntegrationTest = 236.44 sec*proc (28 tests) MpiTest = 422.16 sec*proc (21 tests) QuickGpuTest = 65.27 sec*proc (22 tests) SlowGpuTest = 458.48 sec*proc (14 tests) SlowTest = 322.23 sec*proc (14 tests) UnitTest = 15.27 sec*proc (46 tests) Total Test time (real) = 330.95 sec /usr/bin/make -j20 -C build/basic-dp tests make[1]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.0 -B/build/reproducible-path/gromacs-2025.0/build/basic-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/make -f CMakeFiles/Makefile2 tests make[2]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.0 -B/build/reproducible-path/gromacs-2025.0/build/basic-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.0/build/basic-dp/CMakeFiles 77 /usr/bin/make -f CMakeFiles/Makefile2 CMakeFiles/tests.dir/all make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend /usr/bin/make -f src/external/googletest/googletest/CMakeFiles/gtest.dir/build.make src/external/googletest/googletest/CMakeFiles/gtest.dir/depend /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/external/googletest/googletest /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/external/googletest/googletest/CMakeFiles/gtest.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/selection /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/selection /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/CMakeFiles/release-version-info.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/depend /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs 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'/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake "--color=" /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/external/googletest/googletest && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_CREATE_SHARED_LIBRARY=1 -DGTEST_LANG_CXX11 -Dgtest_EXPORTS 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src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2025.0-Debian_2025.0_2 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2025.0 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.0/build/basic-dp/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2025.0/build/basic-dp/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2025.0-2 -P /build/reproducible-path/gromacs-2025.0/cmake/gmxGenerateVersionInfoWithoutGit.cmake make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' 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'/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build [ 0%] Built target lmfit_objlib /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 0%] Built target scanner [ 0%] Built target release-version-info [ 0%] Built target internal_rpc_xdr /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/options /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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make[4]: Nothing to be done for 'src/gromacs/pulling/CMakeFiles/pulling.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 9%] Built target pulling /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/taskassignment 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'/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 61%] Built target libgromacs /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/depend /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/CMakeFiles/nblib.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/gmxapi 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gmxapi make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/samples/CMakeFiles/methane-water-integration.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make 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CMakeFiles/testutils-test.dir/naming.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/tests/naming.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include 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-Wno-missing-field-initializers -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/trajectorycomparison.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem 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/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator.cpp /usr/bin/make -f src/gromacs/gmxlib/nonbonded/tests/CMakeFiles/nonbonded-fep-test.dir/build.make src/gromacs/gmxlib/nonbonded/tests/CMakeFiles/nonbonded-fep-test.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxlib/nonbonded/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxlib/nonbonded/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxlib/nonbonded/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser 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directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o -MF CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o.d -o CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/calc_verletbuf.cpp /usr/bin/make -f src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/densityfitting/tests/densityfitting.cpp /usr/bin/make -f src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/build.make src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/build /usr/bin/make -f src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/build.make src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem 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/build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/build.make src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/nnpot/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/build.make src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/nnpot/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/nnpot.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/nnpot.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/nnpot.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/tests/nnpot.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testutils-mpi-test.dir/link.d "CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o" "CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o" -o ../../../bin/testutils-mpi-test ../../../lib/libtestutils.a ../../../lib/libtestutils.a ../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 64%] Built target testutils-mpi-test /usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/electricfield.cpp.o -MF 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-std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/qmmm/tests/qmmmtopologypreprocessor.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/bitmask32.cpp.o -MF CMakeFiles/utility-test.dir/bitmask32.cpp.o.d -o CMakeFiles/utility-test.dir/bitmask32.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/bitmask32.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/bitmask64.cpp.o -MF CMakeFiles/utility-test.dir/bitmask64.cpp.o.d -o CMakeFiles/utility-test.dir/bitmask64.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/bitmask64.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/refdata_tests.cpp.o -MF CMakeFiles/testutils-test.dir/refdata_tests.cpp.o.d -o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/tests/refdata_tests.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-mpi-test.dir/link.txt --verbose=1 cd 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 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-fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/bitmask128.cpp.o -MF CMakeFiles/utility-test.dir/bitmask128.cpp.o.d -o CMakeFiles/utility-test.dir/bitmask128.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/bitmask128.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/densityfitting/tests/densityfittingamplitudelookup.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include 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src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/tests/colvarsoptions.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src 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-fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/cstringutil.cpp.o -MF CMakeFiles/utility-test.dir/cstringutil.cpp.o.d -o CMakeFiles/utility-test.dir/cstringutil.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/cstringutil.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/bias.cpp.o -MF CMakeFiles/awh-test.dir/bias.cpp.o.d -o CMakeFiles/awh-test.dir/bias.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/bias.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/utility-mpi-test.dir/link.d "CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o" "CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/utility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 64%] Built target utility-mpi-test /usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/listed_forces/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/bonded.cpp.o -MF CMakeFiles/listed_forces-test.dir/bonded.cpp.o.d -o CMakeFiles/listed_forces-test.dir/bonded.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/tests/bonded.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/nnpotoptions.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/nnpotoptions.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/nnpotoptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/tests/nnpotoptions.cpp /usr/bin/ar qc ../../../../lib/libmdrun_test_infrastructure.a CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o /usr/bin/ranlib ../../../../lib/libmdrun_test_infrastructure.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 66%] Built target mdrun_test_infrastructure /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o -MF CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o.d -o CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/defaultinitializationallocator.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" 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/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include 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-fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constr.cpp.o -MF CMakeFiles/mdlib-test.dir/constr.cpp.o.d -o CMakeFiles/mdlib-test.dir/constr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/constr.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src 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-fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/biasgrid.cpp.o -MF CMakeFiles/awh-test.dir/biasgrid.cpp.o.d -o CMakeFiles/awh-test.dir/biasgrid.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/biasgrid.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include 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/build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/qmmm/tests/qmmmoptions.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem 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/build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o -MF CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o.d -o CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/inmemoryserializer.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include 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src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src 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-I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -MF CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o.d -o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/tests/xvgtest_tests.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o -MF CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o.d -o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/keyvaluetreeserializer.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests && /usr/bin/cmake -P 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-I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/qmmm/tests/qmmmforceprovider.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/applied_forces-test.dir/link.d "CMakeFiles/applied_forces-test.dir/electricfield.cpp.o" "CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/applied_forces-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -lmuparser /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 66%] Built target applied_forces-test /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -MF CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o.d -o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/keyvaluetreetransform.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" 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/usr/bin/ar qc ../../../lib/libnblib_test_infrastructure.a CMakeFiles/nblib_test_infrastructure.dir/testsystems.cpp.o CMakeFiles/nblib_test_infrastructure.dir/__/__/__/src/testutils/unittest_main.cpp.o /usr/bin/ranlib ../../../lib/libnblib_test_infrastructure.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 66%] Built target nblib_test_infrastructure /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp 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-Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -MF CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o.d -o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/nnpot/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/nnpotforceprovider.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/nnpotforceprovider.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/nnpotforceprovider.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/tests/nnpotforceprovider.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/logger.cpp.o -MF CMakeFiles/utility-test.dir/logger.cpp.o.d -o CMakeFiles/utility-test.dir/logger.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/logger.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/qmmm/tests/qmmm.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxlib/nonbonded/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxlib/nonbonded/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxlib/nonbonded/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxlib/nonbonded/tests/CMakeFiles/nonbonded-fep-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nonbonded-fep-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nonbonded-fep-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/tests/colvarspreprocessor.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/biasstate.cpp.o -MF CMakeFiles/awh-test.dir/biasstate.cpp.o.d -o CMakeFiles/awh-test.dir/biasstate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/biasstate.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nbnxm-gpu-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nbnxm-gpu-test.dir/link.d "CMakeFiles/nbnxm-gpu-test.dir/pairlist.cpp.o" "CMakeFiles/nbnxm-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/nbnxm-gpu-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 66%] Built target nbnxm-gpu-test /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include 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/build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/hashedmap.cpp.o -MF CMakeFiles/domdec-test.dir/hashedmap.cpp.o.d -o CMakeFiles/domdec-test.dir/hashedmap.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/tests/hashedmap.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" 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../../../../../bin/nonbonded-fep-test ../../../../../lib/libtestutils.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.10.0.0 -lm ../../../../../lib/libgmock.so.1.13.0 ../../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -lmuparser /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 66%] Built target nonbonded-fep-test /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT 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-I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser 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/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/cmake -P CMakeFiles/onlinehelp-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test-shared.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nnpot_applied_forces-test.dir/link.d "CMakeFiles/nnpot_applied_forces-test.dir/nnpot.cpp.o" "CMakeFiles/nnpot_applied_forces-test.dir/nnpotoptions.cpp.o" "CMakeFiles/nnpot_applied_forces-test.dir/nnpottopologypreprocessor.cpp.o" "CMakeFiles/nnpot_applied_forces-test.dir/nnpotforceprovider.cpp.o" "CMakeFiles/nnpot_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/nnpot_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../../lib/libgmock.so.1.13.0 ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 66%] Built target nnpot_applied_forces-test /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/tests 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-DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/fft/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem 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'/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 66%] Built target onlinehelp-test-shared /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gpu_utils/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o -MF CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/tests/clfftinitializer.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/density_fitting_applied_forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY 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/build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/tests/colvarsforceprovider.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/range.cpp.o -MF CMakeFiles/utility-test.dir/range.cpp.o.d -o CMakeFiles/utility-test.dir/range.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/range.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/qmmm_applied_forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/density_fitting_applied_forces-test.dir/link.d "CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/density_fitting_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.10.0.0 ../../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 66%] Built target density_fitting_applied_forces-test /usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/hardware/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem 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-o CMakeFiles/hardware-test.dir/cpuinfo.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/tests/cpuinfo.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/qmmm_applied_forces-test.dir/link.d "CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/qmmm_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.10.0.0 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-fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/constrtestrunners.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem 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-DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/scope_guard.cpp.o -MF CMakeFiles/utility-test.dir/scope_guard.cpp.o.d -o CMakeFiles/utility-test.dir/scope_guard.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/scope_guard.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/strconvert.cpp.o -MF CMakeFiles/utility-test.dir/strconvert.cpp.o.d -o CMakeFiles/utility-test.dir/strconvert.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/strconvert.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o -MF CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/tests/device_availability.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/friction_metric.cpp.o -MF CMakeFiles/awh-test.dir/friction_metric.cpp.o.d -o CMakeFiles/awh-test.dir/friction_metric.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/friction_metric.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true 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directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 67%] Built target domdec-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include 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/build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o -MF CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/tests/gpueventsynchronizer.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-mpi-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 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/build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/textreader.cpp.o -MF CMakeFiles/utility-test.dir/textreader.cpp.o.d -o CMakeFiles/utility-test.dir/textreader.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/textreader.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/domdec-mpi-test.dir/link.d "CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o" "CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/domdec-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -lmuparser /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 67%] Built target domdec-mpi-test /usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/mdspan/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdspan/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 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"CMakeFiles/awh-test.dir/biasgrid.cpp.o" "CMakeFiles/awh-test.dir/biassharing.cpp.o" "CMakeFiles/awh-test.dir/biasstate.cpp.o" "CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o" "CMakeFiles/awh-test.dir/friction_metric.cpp.o" "CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/awh-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.10.0.0 ../../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 68%] Built target awh-test /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/simd_energy_accumulator.cpp.o -MF CMakeFiles/nbnxm-test.dir/simd_energy_accumulator.cpp.o.d -o CMakeFiles/nbnxm-test.dir/simd_energy_accumulator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/tests/simd_energy_accumulator.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include 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'/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 68%] Built target fft-test /usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/pbcutil/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 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-I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 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-I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/functions.cpp.o -MF CMakeFiles/math-test.dir/functions.cpp.o.d -o CMakeFiles/math-test.dir/functions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/functions.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem 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/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem 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/build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/densityfittingforce.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -MF CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/onlinehelp/tests/helpwritercontext.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/listed_forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -MF CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/tests/pmesplinespreadtest.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/listed_forces-test.dir/link.d "CMakeFiles/listed_forces-test.dir/bonded.cpp.o" "CMakeFiles/listed_forces-test.dir/pairs.cpp.o" "CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o" "CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/listed_forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 71%] Built target listed_forces-test /usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/random/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/random/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/random/tests/CMakeFiles/random-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem 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/build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/invertmatrix.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/langevintestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/langevintestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/langevintestrunners.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/langevintestrunners.cpp /usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/restraint/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/restraint/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/restraint/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY 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/build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/manager.cpp.o -MF CMakeFiles/restraintpotential-test.dir/manager.cpp.o.d -o CMakeFiles/restraintpotential-test.dir/manager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/restraint/tests/manager.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrog.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrog.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrog.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/leapfrog.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pbcutil-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pbcutil-test.dir/link.d "CMakeFiles/pbcutil-test.dir/com.cpp.o" "CMakeFiles/pbcutil-test.dir/mshift.cpp.o" "CMakeFiles/pbcutil-test.dir/pbc.cpp.o" "CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o" "CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pbcutil-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 71%] Built target pbcutil-test /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/tables/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tables/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H 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/build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tables/tests/CMakeFiles/table-test.dir/splinetable.cpp.o -MF CMakeFiles/table-test.dir/splinetable.cpp.o.d -o CMakeFiles/table-test.dir/splinetable.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tables/tests/splinetable.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o -MF CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o.d -o CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/forcebuffers.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/matrix.cpp.o -MF CMakeFiles/math-test.dir/matrix.cpp.o.d -o CMakeFiles/math-test.dir/matrix.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/matrix.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdspan-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/option.cpp.o -MF CMakeFiles/options-test.dir/option.cpp.o.d -o CMakeFiles/options-test.dir/option.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/tests/option.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/device_management.cpp.o -MF CMakeFiles/hardware-test.dir/device_management.cpp.o.d -o CMakeFiles/hardware-test.dir/device_management.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/tests/device_management.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdspan-test.dir/link.d "CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o" "CMakeFiles/mdspan-test.dir/extents.cpp.o" "CMakeFiles/mdspan-test.dir/extensions.cpp.o" "CMakeFiles/mdspan-test.dir/layouts.cpp.o" "CMakeFiles/mdspan-test.dir/mdspan.cpp.o" "CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdspan-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 71%] Built target mdspan-test /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/taskassignment/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/taskassignment/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -MF CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o.d -o CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/tests/usergpuids.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/utility-test.dir/link.d "CMakeFiles/utility-test.dir/alignedallocator.cpp.o" "CMakeFiles/utility-test.dir/arrayref.cpp.o" "CMakeFiles/utility-test.dir/booltype.cpp.o" "CMakeFiles/utility-test.dir/bitmask32.cpp.o" "CMakeFiles/utility-test.dir/bitmask64.cpp.o" "CMakeFiles/utility-test.dir/bitmask128.cpp.o" "CMakeFiles/utility-test.dir/cstringutil.cpp.o" "CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o" "CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o" "CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o" "CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o" "CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o" "CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o" "CMakeFiles/utility-test.dir/listoflists.cpp.o" "CMakeFiles/utility-test.dir/logger.cpp.o" "CMakeFiles/utility-test.dir/message_string_collector.cpp.o" "CMakeFiles/utility-test.dir/path.cpp.o" "CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o" "CMakeFiles/utility-test.dir/range.cpp.o" "CMakeFiles/utility-test.dir/scope_guard.cpp.o" "CMakeFiles/utility-test.dir/strconvert.cpp.o" "CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o" "CMakeFiles/utility-test.dir/stringutil.cpp.o" "CMakeFiles/utility-test.dir/template_mp.cpp.o" "CMakeFiles/utility-test.dir/textreader.cpp.o" "CMakeFiles/utility-test.dir/textwriter.cpp.o" "CMakeFiles/utility-test.dir/typetraits.cpp.o" "CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/utility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 72%] Built target utility-test /usr/bin/make -f src/gromacs/timing/tests/CMakeFiles/timing-test.dir/build.make src/gromacs/timing/tests/CMakeFiles/timing-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/timing/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/timing/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/timing/tests/CMakeFiles/timing-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/timing/tests/CMakeFiles/timing-test.dir/build.make src/gromacs/timing/tests/CMakeFiles/timing-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/timing/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/timing/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/timing/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem 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src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src 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-fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/multidimarray.cpp.o -MF CMakeFiles/math-test.dir/multidimarray.cpp.o.d -o CMakeFiles/math-test.dir/multidimarray.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/multidimarray.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/onlinehelp-test.dir/link.d "CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o" "CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o" "CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o" "CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/onlinehelp-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 72%] Built target onlinehelp-test /usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd 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CMakeFiles/options-test.dir/optionsassigner.cpp.o.d -o CMakeFiles/options-test.dir/optionsassigner.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/tests/optionsassigner.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/repeatingsection.cpp.o -MF CMakeFiles/options-test.dir/repeatingsection.cpp.o.d -o CMakeFiles/options-test.dir/repeatingsection.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/tests/repeatingsection.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/restraint/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/restraintpotential-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include 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/build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o -MF CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o.d -o CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/multipletimestepping.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/leapfrogtestdata.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/restraintpotential-test.dir/link.d "CMakeFiles/restraintpotential-test.dir/manager.cpp.o" "CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/restraintpotential-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 74%] Built target restraintpotential-test cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/neldermead.cpp.o -MF CMakeFiles/math-test.dir/neldermead.cpp.o.d -o CMakeFiles/math-test.dir/neldermead.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/neldermead.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/hardware-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/hardware-test.dir/link.d "CMakeFiles/hardware-test.dir/cpuinfo.cpp.o" "CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o" "CMakeFiles/hardware-test.dir/mockhardwaretopology.cpp.o" "CMakeFiles/hardware-test.dir/device_management.cpp.o" "CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/hardware-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 74%] Built target hardware-test /usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/pulling/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/pulling/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include 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-fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/pull.cpp.o -MF CMakeFiles/pull-test.dir/pull.cpp.o.d -o CMakeFiles/pull-test.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/tests/pull.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/timing/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/timing/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/timing/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/timing/tests/CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/leapfrogtestrunners.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/timing/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/timing-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/optimization.cpp.o -MF CMakeFiles/math-test.dir/optimization.cpp.o.d -o CMakeFiles/math-test.dir/optimization.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/optimization.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/timing-test.dir/link.d "CMakeFiles/timing-test.dir/timing.cpp.o" "CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/timing-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/timeunitmanager.cpp.o -MF CMakeFiles/options-test.dir/timeunitmanager.cpp.o.d -o CMakeFiles/options-test.dir/timeunitmanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/tests/timeunitmanager.cpp [ 74%] Built target timing-test cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/treesupport.cpp.o -MF CMakeFiles/options-test.dir/treesupport.cpp.o.d -o CMakeFiles/options-test.dir/treesupport.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/tests/treesupport.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gpu_utils-test.dir/link.d "CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o" "CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o" "CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o" "CMakeFiles/gpu_utils-test.dir/pinnedmemorychecker.cpp.o" "CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o" "CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o" "CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o" "CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o" "CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o" "CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gpu_utils-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/normaldistribution.cpp.o -MF CMakeFiles/random-test.dir/normaldistribution.cpp.o.d -o CMakeFiles/random-test.dir/normaldistribution.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/random/tests/normaldistribution.cpp [ 75%] Built target gpu_utils-test /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/simd/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/simd/tests/CMakeFiles/simd-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/base.cpp.o -MF CMakeFiles/simd-test.dir/base.cpp.o.d -o CMakeFiles/simd-test.dir/base.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/base.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/taskassignment/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/threefry.cpp.o -MF CMakeFiles/random-test.dir/threefry.cpp.o.d -o CMakeFiles/random-test.dir/threefry.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/random/tests/threefry.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/taskassignment/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/taskassignment-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/taskassignment-test.dir/link.d "CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o" "CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o ../CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o ../CMakeFiles/taskassignment.dir/findallgputasks.cpp.o ../CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o ../CMakeFiles/taskassignment.dir/resourcedivision.cpp.o ../CMakeFiles/taskassignment.dir/taskassignment.cpp.o ../CMakeFiles/taskassignment.dir/usergpuids.cpp.o -o ../../../../bin/taskassignment-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -lmuparser /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 75%] Built target taskassignment-test /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/compat/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/compat/tests/CMakeFiles/compat-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/compat/tests/CMakeFiles/compat-test.dir/mp11.cpp.o -MF CMakeFiles/compat-test.dir/mp11.cpp.o.d -o CMakeFiles/compat-test.dir/mp11.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/tests/mp11.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem 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/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem 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/build/reproducible-path/gromacs-2025.0/src/gromacs/compat/tests/pointers.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/pulling/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -MF CMakeFiles/random-test.dir/uniformintdistribution.cpp.o.d -o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/random/tests/uniformintdistribution.cpp /usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxana/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -MF CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o.d -o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/bootstrap_loadstore.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" 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src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settletestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/settletestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/settletestdata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/settletestdata.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pull-test.dir/link.d "CMakeFiles/pull-test.dir/pull.cpp.o" "CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../CMakeFiles/pulling.dir/output.cpp.o ../CMakeFiles/pulling.dir/pull.cpp.o ../CMakeFiles/pulling.dir/pull_rotation.cpp.o ../CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o ../CMakeFiles/pulling.dir/pullutil.cpp.o ../CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -o ../../../../bin/pull-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lmuparser -lm ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 75%] Built target pull-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/idef.cpp.o -MF CMakeFiles/topology-test.dir/idef.cpp.o.d -o CMakeFiles/topology-test.dir/idef.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/idef.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdtypes-test.dir/link.d "CMakeFiles/mdtypes-test.dir/enerdata.cpp.o" "CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o" "CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o" "CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o" "CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o" "CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdtypes-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 76%] Built target mdtypes-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o -MF CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o.d -o CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -MF CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o.d -o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/random/tests/uniformrealdistribution.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/compat/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/compat-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar.cpp.o -MF CMakeFiles/simd-test.dir/scalar.cpp.o.d -o CMakeFiles/simd-test.dir/scalar.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/scalar.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/tests/gmx_chi.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/compat-test.dir/link.d "CMakeFiles/compat-test.dir/mp11.cpp.o" "CMakeFiles/compat-test.dir/pointers.cpp.o" "CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/compat-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 76%] Built target compat-test cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/tests/gmx_mindist.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/settletestrunners.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tables/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tables/tests/CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o -MF CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o.d -o CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/index.cpp.o -MF CMakeFiles/topology-test.dir/index.cpp.o.d -o CMakeFiles/topology-test.dir/index.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/index.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 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-fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/mtop.cpp.o -MF CMakeFiles/topology-test.dir/mtop.cpp.o.d -o CMakeFiles/topology-test.dir/mtop.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/mtop.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ewald-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tables/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/table-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/symtab.cpp.o -MF CMakeFiles/topology-test.dir/symtab.cpp.o.d -o CMakeFiles/topology-test.dir/symtab.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/symtab.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -MF CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o.d -o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/simulationsignal.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/ewald-test.dir/link.d "CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o" "CMakeFiles/ewald-test.dir/pmegathertest.cpp.o" "CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o" "CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o" "CMakeFiles/ewald-test.dir/pme.cpp.o" "CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o" "CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/ewald-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -lmuparser /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 77%] Built target ewald-test cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/editconf.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/table-test.dir/link.d "CMakeFiles/table-test.dir/splinetable.cpp.o" "CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/table-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/topsort.cpp.o -MF CMakeFiles/topology-test.dir/topsort.cpp.o.d -o CMakeFiles/topology-test.dir/topsort.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/topsort.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 77%] Built target table-test cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/tests/gmx_traj.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=1 -DGROMOS=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem 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/usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/correlationfunctions/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/correlationfunctions/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make 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-I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem 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-Wl,--dependency-file=CMakeFiles/random-test.dir/link.d "CMakeFiles/random-test.dir/exponentialdistribution.cpp.o" "CMakeFiles/random-test.dir/gammadistribution.cpp.o" "CMakeFiles/random-test.dir/normaldistribution.cpp.o" "CMakeFiles/random-test.dir/seed.cpp.o" "CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o" "CMakeFiles/random-test.dir/threefry.cpp.o" "CMakeFiles/random-test.dir/uniformintdistribution.cpp.o" "CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o" "CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/random-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 77%] Built target random-test /usr/bin/make -f 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY 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CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o.d -o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/updategroupscog.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar_util.cpp.o -MF CMakeFiles/simd-test.dir/scalar_util.cpp.o.d -o CMakeFiles/simd-test.dir/scalar_util.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/scalar_util.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar_math.cpp.o -MF CMakeFiles/simd-test.dir/scalar_math.cpp.o.d -o CMakeFiles/simd-test.dir/scalar_math.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/scalar_math.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxana-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmxana-test.dir/link.d "CMakeFiles/gmxana-test.dir/entropy.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o" "CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gmxana-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 77%] Built target gmxana-test /usr/bin/make -f src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build.make src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/coordinateio/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o -MF CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o.d -o CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/constrtestrunners_gpu.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build.make src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 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-I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT 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-I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/genrestr.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/gen_maxwell_velocities.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -MF CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o.d -o CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/tests/mock_datamodule.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H 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/build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/expfit.cpp.o -MF CMakeFiles/correlations-test.dir/expfit.cpp.o.d -o CMakeFiles/correlations-test.dir/expfit.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/correlationfunctions/tests/expfit.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/options-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx1-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/gpp_bond_atomtype.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/topology/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/topology-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/options-test.dir/link.d "CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o" "CMakeFiles/options-test.dir/filenameoption.cpp.o" "CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o" "CMakeFiles/options-test.dir/option.cpp.o" "CMakeFiles/options-test.dir/optionsassigner.cpp.o" "CMakeFiles/options-test.dir/repeatingsection.cpp.o" "CMakeFiles/options-test.dir/timeunitmanager.cpp.o" "CMakeFiles/options-test.dir/treesupport.cpp.o" "CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/options-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 77%] Built target options-test /usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/energyanalysis/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/energyterm.cpp.o -MF CMakeFiles/energyanalysis-test.dir/energyterm.cpp.o.d -o CMakeFiles/energyanalysis-test.dir/energyterm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/energyterm.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o -MF CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o.d -o CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/legacyenergy.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/mdgpugraph.cpp.o -MF CMakeFiles/mdlib-test.dir/mdgpugraph.cpp.o.d -o CMakeFiles/mdlib-test.dir/mdgpugraph.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/mdgpugraph.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd.cpp.o -MF CMakeFiles/simd-test.dir/simd.cpp.o.d -o CMakeFiles/simd-test.dir/simd.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/simd.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pdb2gmx1-test.dir/link.d "CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o" "CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pdb2gmx1-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 79%] Built target pdb2gmx1-test cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/topology-test.dir/link.d "CMakeFiles/topology-test.dir/atoms.cpp.o" "CMakeFiles/topology-test.dir/exclusionblocks.cpp.o" "CMakeFiles/topology-test.dir/idef.cpp.o" "CMakeFiles/topology-test.dir/index.cpp.o" "CMakeFiles/topology-test.dir/mtop.cpp.o" "CMakeFiles/topology-test.dir/symtab.cpp.o" "CMakeFiles/topology-test.dir/topsort.cpp.o" "CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/topology-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 80%] Built target topology-test /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/CMakeFiles/tool-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/dump.cpp.o -MF CMakeFiles/tool-test.dir/dump.cpp.o.d -o CMakeFiles/tool-test.dir/dump.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/tests/dump.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/grompp_directives.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src 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-DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include 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src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/wholemoleculetransform.cpp.o -MF CMakeFiles/mdlib-test.dir/wholemoleculetransform.cpp.o.d -o CMakeFiles/mdlib-test.dir/wholemoleculetransform.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/wholemoleculetransform.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx2-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include 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/build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -MF CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o.d -o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/simd_floatingpoint.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pdb2gmx2-test.dir/link.d "CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o" "CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pdb2gmx2-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 80%] Built target pdb2gmx2-test /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/convert-tpr-with-leaks.cpp.o -MF CMakeFiles/tool-test-with-leaks.dir/convert-tpr-with-leaks.cpp.o.d -o CMakeFiles/tool-test-with-leaks.dir/convert-tpr-with-leaks.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/tests/convert-tpr-with-leaks.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" 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-I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG 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-I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/helpwriting.cpp.o -MF CMakeFiles/tool-test.dir/helpwriting.cpp.o.d -o CMakeFiles/tool-test.dir/helpwriting.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/tests/helpwriting.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include 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src/gromacs/selection/tests/CMakeFiles/selection-test.dir/indexutil.cpp.o -MF CMakeFiles/selection-test.dir/indexutil.cpp.o.d -o CMakeFiles/selection-test.dir/indexutil.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/tests/indexutil.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include 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-fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/readir.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include 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/build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o -MF CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o.d -o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/correlationfunctions/tests/manyautocorrelation.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdlib-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ 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/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/simd_floatingpoint_util.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/solvate.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/topdirs.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdlib-test.dir/link.d "CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o" "CMakeFiles/mdlib-test.dir/calcvir.cpp.o" "CMakeFiles/mdlib-test.dir/constr.cpp.o" 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/build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem 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-I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/correlations-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src 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../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 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-I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/filemd5.cpp.o -MF CMakeFiles/fileio-test.dir/filemd5.cpp.o.d -o CMakeFiles/fileio-test.dir/filemd5.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/filemd5.cpp [ 81%] Built target pdb2gmx3-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o -MF CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/compressed_x_output.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/correlations-test.dir/link.d "CMakeFiles/correlations-test.dir/autocorr.cpp.o" "CMakeFiles/correlations-test.dir/correlationdataset.cpp.o" "CMakeFiles/correlations-test.dir/expfit.cpp.o" "CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o" "CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/correlations-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 81%] Built target correlations-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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/usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 81%] Built target tool-test-with-leaks /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' 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-I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/filetypes.cpp.o -MF CMakeFiles/fileio-test.dir/filetypes.cpp.o.d -o CMakeFiles/fileio-test.dir/filetypes.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/filetypes.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" 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/build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_integer.cpp.o -MF CMakeFiles/simd-test.dir/simd_integer.cpp.o.d -o CMakeFiles/simd-test.dir/simd_integer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/simd_integer.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_math.cpp.o -MF CMakeFiles/simd-test.dir/simd_math.cpp.o.d -o CMakeFiles/simd-test.dir/simd_math.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/simd_math.cpp cd 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-I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/settimestep.cpp.o -MF CMakeFiles/coordinateio-test.dir/settimestep.cpp.o.d -o CMakeFiles/coordinateio-test.dir/settimestep.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/tests/settimestep.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o -MF CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/helpwriting.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmxpreprocess-test.dir/link.d "CMakeFiles/gmxpreprocess-test.dir/convparm.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/massrepartitioning.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gmxpreprocess-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 83%] Built target gmxpreprocess-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build make[4]: Entering directory 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qc ../../../../lib/libanalysisdata-test-shared.a "CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o" "CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o" "CMakeFiles/analysisdata-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o" /usr/bin/ranlib ../../../../lib/libanalysisdata-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 83%] Built target analysisdata-test-shared cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong 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"CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-modules-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 83%] Built target mdrun-modules-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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-I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 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src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd 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src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include 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-I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem 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/build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem 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-fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/normalmodes.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-single-rank-algorithms-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem 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CMakeFiles/mdrun-output-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-single-rank-algorithms-test.dir/link.d "CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/orires.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-single-rank-algorithms-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a 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/build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/simple_mdrun.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-output-test.dir/link.d "CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o" "CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o" "CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o" "CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o" "CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-output-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 84%] Built target mdrun-output-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build make[4]: Entering directory 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4_math.cpp.o -MF CMakeFiles/simd-test.dir/simd4_math.cpp.o.d -o CMakeFiles/simd-test.dir/simd4_math.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/simd4_math.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include 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CMakeFiles/minimize-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/coordinateio-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include 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-fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -MF CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o.d -o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/simd4_vector_operations.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include 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-I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem 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/usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/coordinateio-test.dir/link.d "CMakeFiles/coordinateio-test.dir/builder.cpp.o" "CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o" "CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o" "CMakeFiles/coordinateio-test.dir/register.cpp.o" "CMakeFiles/coordinateio-test.dir/requirements.cpp.o" "CMakeFiles/coordinateio-test.dir/setatoms.cpp.o" "CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o" "CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o" "CMakeFiles/coordinateio-test.dir/settimestep.cpp.o" "CMakeFiles/coordinateio-test.dir/testmodule.cpp.o" "CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/coordinateio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 85%] Built target coordinateio-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/minimize-test.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o -MF CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/multisimtest.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/minimize-test.dir/link.d "CMakeFiles/minimize-test.dir/minimize.cpp.o" "CMakeFiles/minimize-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/minimize-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 85%] Built target minimize-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem 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../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 87%] Built target mdrun-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests 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-DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/simd/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/simd-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileio-test.dir/link.txt --verbose=1 /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions.cpp.o -MF CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions.cpp.o.d -o CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/periodicactions.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o -MF CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/replicaexchange_equivalence.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem 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/build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/simd-test.dir/link.d "CMakeFiles/simd-test.dir/base.cpp.o" "CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o" "CMakeFiles/simd-test.dir/scalar.cpp.o" "CMakeFiles/simd-test.dir/scalar_util.cpp.o" "CMakeFiles/simd-test.dir/scalar_math.cpp.o" "CMakeFiles/simd-test.dir/simd.cpp.o" "CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o" "CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o" "CMakeFiles/simd-test.dir/simd_integer.cpp.o" "CMakeFiles/simd-test.dir/simd_math.cpp.o" "CMakeFiles/simd-test.dir/simd_memory.cpp.o" "CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o" "CMakeFiles/simd-test.dir/simd4.cpp.o" "CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o" "CMakeFiles/simd-test.dir/simd4_math.cpp.o" "CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o" "CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/simd-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 88%] Built target simd-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o -MF CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o.d -o CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/periodicactions.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/fileio-test.dir/link.d "CMakeFiles/fileio-test.dir/checkpoint.cpp.o" "CMakeFiles/fileio-test.dir/confio.cpp.o" "CMakeFiles/fileio-test.dir/filemd5.cpp.o" "CMakeFiles/fileio-test.dir/filetypes.cpp.o" "CMakeFiles/fileio-test.dir/matio.cpp.o" "CMakeFiles/fileio-test.dir/mrcserializer.cpp.o" "CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o" "CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o" "CMakeFiles/fileio-test.dir/readinp.cpp.o" "CMakeFiles/fileio-test.dir/timecontrol.cpp.o" "CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o" "CMakeFiles/fileio-test.dir/tngio.cpp.o" "CMakeFiles/fileio-test.dir/xvgio.cpp.o" "CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/fileio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 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/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include 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/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o -MF CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o.d -o CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/periodicactions_coupling.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-tpi-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/selection/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/selection-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-tpi-test.dir/link.d "CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o" "CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-tpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o -MF CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o.d -o CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/periodicactions_basic.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/depend make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/DependInfo.cmake "--color=" [ 89%] Built target mdrun-tpi-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/expandedensemble.cpp.o -MF CMakeFiles/mdrun-fep-test.dir/expandedensemble.cpp.o.d -o CMakeFiles/mdrun-fep-test.dir/expandedensemble.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/expandedensemble.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/pull.cpp.o -MF CMakeFiles/mdrun-pull-test.dir/pull.cpp.o.d -o CMakeFiles/mdrun-pull-test.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/pull.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 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/build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o -MF CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o.d -o CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/pull_rotation.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o -MF CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o.d -o CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/freeenergy.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/depend /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/selection-test.dir/link.d "CMakeFiles/selection-test.dir/indexutil.cpp.o" "CMakeFiles/selection-test.dir/nbsearch.cpp.o" "CMakeFiles/selection-test.dir/poscalc.cpp.o" "CMakeFiles/selection-test.dir/selectioncollection.cpp.o" "CMakeFiles/selection-test.dir/selectionoption.cpp.o" "CMakeFiles/selection-test.dir/toputils.cpp.o" "CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/selection-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o -MF CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o.d -o CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/simulator.cpp [ 89%] Built target selection-test cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-non-integrator-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-test.dir/link.txt --verbose=1 /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o -MF CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o.d -o CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/virtualsites.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-non-integrator-test.dir/link.d "CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-non-integrator-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-multisim-test.dir/link.d "CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o" "CMakeFiles/mdrun-multisim-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 90%] Built target mdrun-non-integrator-test /usr/bin/make -f api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/build.make api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/DependInfo.cmake "--color=" [ 90%] Built target mdrun-multisim-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/build.make api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/build cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/restraint.cpp.o -MF CMakeFiles/gmxapi-test.dir/restraint.cpp.o.d -o CMakeFiles/gmxapi-test.dir/restraint.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests/restraint.cpp /usr/bin/make -f api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build.make api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/workflow/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/workflow/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build.make api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/workflow/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/workflow.cpp.o -MF CMakeFiles/workflow-details-test.dir/workflow.cpp.o.d -o CMakeFiles/workflow-details-test.dir/workflow.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/workflow/tests/workflow.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-io-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-mpi-test.dir/link.d "CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o" "CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o" "CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 92%] Built target mdrun-mpi-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include 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-Wl,--dependency-file=CMakeFiles/mdrun-io-test.dir/link.d "CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o" "CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o" "CMakeFiles/mdrun-io-test.dir/grompp.cpp.o" "CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o" "CMakeFiles/mdrun-io-test.dir/termination.cpp.o" "CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-io-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 92%] Built target mdrun-io-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-setup-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-setup-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/CMakeFiles/nblib-setup-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-setup-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-setup-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests 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/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-pme-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/runner.cpp.o -MF CMakeFiles/gmxapi-test.dir/runner.cpp.o.d -o CMakeFiles/gmxapi-test.dir/runner.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests/runner.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src 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/build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/status.cpp.o -MF CMakeFiles/gmxapi-test.dir/status.cpp.o.d -o CMakeFiles/gmxapi-test.dir/status.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests/status.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-mpi-pme-test.dir/link.d "CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o" "CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-pme-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 92%] Built target mdrun-mpi-pme-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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/build/reproducible-path/gromacs-2025.0/api/nblib/tests/tpr.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include 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-Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o -MF CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o.d -o CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests/stopsignaler.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/system.cpp.o -MF CMakeFiles/gmxapi-test.dir/system.cpp.o.d -o CMakeFiles/gmxapi-test.dir/system.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests/system.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-replex-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/workflow/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/workflow-details-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && 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-lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 92%] Built target mdrun-multisim-replex-test cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include 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../../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../../lib/libgmock.so.1.13.0 ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 93%] Built target workflow-details-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integration-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/CMakeFiles/nblib-integration-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem 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/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o -MF CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tests/nbkernelsystem.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-coordination-constraints-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/version.cpp.o -MF CMakeFiles/gmxapi-test.dir/version.cpp.o.d -o CMakeFiles/gmxapi-test.dir/version.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests/version.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-coordination-coupling-test.dir/link.d "CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o" "CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o" "CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-coordination-coupling-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 94%] Built target mdrun-coordination-coupling-test /usr/bin/make -f api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build.make api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/listed_forces/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build.make api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/tests/bondtypes.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-coordination-constraints-test.dir/link.d "CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions.cpp.o" "CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions_constraints.cpp.o" "CMakeFiles/mdrun-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-coordination-constraints-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 94%] Built target mdrun-coordination-constraints-test /usr/bin/make -f api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build.make api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/util/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/util/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build.make api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/util/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/util/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/setup.cpp.o -MF CMakeFiles/nblib-util-test.dir/setup.cpp.o.d -o CMakeFiles/nblib-util-test.dir/setup.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/util/tests/setup.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/tests/gmxcalculator.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/include 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api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-coordination-basic-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-coordination-basic-test.dir/link.d "CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions.cpp.o" "CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o" "CMakeFiles/mdrun-coordination-basic-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-coordination-basic-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 94%] Built target mdrun-coordination-basic-test /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && 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-DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/traits.cpp.o -MF CMakeFiles/nblib-util-test.dir/traits.cpp.o.d -o CMakeFiles/nblib-util-test.dir/traits.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/util/tests/traits.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem 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cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/tests/helpers.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/tests/listedtesthelpers.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-rotation-test.dir/link.d "CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o" "CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-rotation-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 94%] Built target mdrun-rotation-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o -MF CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/tests/mdmodulesnotifier.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-simulator-comparison-test.dir/link.d "CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o" "CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-simulator-comparison-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 94%] Built target mdrun-simulator-comparison-test cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/util/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/util/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include 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api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/simstate.cpp.o -MF CMakeFiles/nblib-integration-test.dir/simstate.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/simstate.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tests/simstate.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include 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-Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/tests/kernels.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/tests/typetests.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/particletype.cpp.o -MF CMakeFiles/nblib-setup-test.dir/particletype.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/particletype.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tests/particletype.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-tpr-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" 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/build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -MF CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/tests/threadaffinity.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-tpr-test.dir/link.d "CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o" "CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-tpr-test ../../../lib/libtestutils.a ../../../lib/libmdrun_test_infrastructure.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 ../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 94%] Built target nblib-tpr-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f 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-I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 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/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o -MF CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o.d -o CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/tests/analysisdata.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/util/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-util-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat 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../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 94%] Built target gmxapi-test /usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-vsites-test.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/moduletest.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include 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api/nblib/tests/CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-util-test.dir/link.d "CMakeFiles/nblib-util-test.dir/setup.cpp.o" "CMakeFiles/nblib-util-test.dir/traits.cpp.o" "CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../../bin/nblib-util-test ../../../../lib/libtestutils.a ../../../../lib/libnblib_test_infrastructure.a ../../../../lib/libnblib_gmx.so.0.1.0 ../../../../lib/libtestutils.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 94%] Built target nblib-util-test cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/angle.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-vsites-test.dir/link.d "CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o" "CMakeFiles/mdrun-vsites-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-vsites-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 94%] Built target mdrun-vsites-test cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/tests/calculator.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/link.d "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o" "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-replex-equivalence-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 94%] Built target mdrun-multisim-replex-equivalence-test cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-integrator-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-integrator-test.dir/link.d "CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o" "CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-integrator-test ../../../lib/libtestutils.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 ../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/tests/conversions.cpp [ 94%] Built target nblib-integrator-test cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/tests/shiftforces.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -MF CMakeFiles/analysisdata-test.dir/arraydata.cpp.o.d -o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/tests/arraydata.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o -MF CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tests/pbcholder.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/tests/transformations.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/molecules.cpp.o -MF CMakeFiles/nblib-setup-test.dir/molecules.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/molecules.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tests/molecules.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-integration-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/cmdlinerunner.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-integration-test.dir/link.d "CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o" "CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o" "CMakeFiles/nblib-integration-test.dir/simstate.cpp.o" "CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-integration-test ../../../lib/libtestutils.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 ../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 96%] Built target nblib-integration-test cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-fep-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrunutility-test.dir/link.d "CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o" "CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o" "CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdrunutility-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 96%] Built target mdrunutility-test cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o -MF CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tests/nbnxmsetup.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-fep-test.dir/link.d "CMakeFiles/mdrun-fep-test.dir/expandedensemble.cpp.o" "CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o" "CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-fep-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/tests/cmdlinemodulemanagertest.cpp [ 96%] Built target mdrun-fep-test cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/convert_trj.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-pull-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/topology.cpp.o -MF CMakeFiles/nblib-setup-test.dir/topology.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/topology.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tests/topology.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/virials.cpp.o -MF CMakeFiles/nblib-setup-test.dir/virials.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/virials.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tests/virials.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-pull-test.dir/link.d "CMakeFiles/mdrun-pull-test.dir/pull.cpp.o" "CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-pull-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 96%] Built target mdrun-pull-test cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/distance.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/average.cpp.o -MF CMakeFiles/analysisdata-test.dir/average.cpp.o.d -o CMakeFiles/analysisdata-test.dir/average.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/tests/average.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrunutility-mpi-test.dir/link.d "CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o" "CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdrunutility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 96%] Built target mdrunutility-mpi-test cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/unionfind.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/filenm.cpp.o -MF CMakeFiles/commandline-test.dir/filenm.cpp.o.d -o CMakeFiles/commandline-test.dir/filenm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/tests/filenm.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/pargs.cpp.o -MF CMakeFiles/commandline-test.dir/pargs.cpp.o.d -o CMakeFiles/commandline-test.dir/pargs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/tests/pargs.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/analysisdata-test.dir/link.d "CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o" "CMakeFiles/analysisdata-test.dir/arraydata.cpp.o" "CMakeFiles/analysisdata-test.dir/average.cpp.o" "CMakeFiles/analysisdata-test.dir/histogram.cpp.o" "CMakeFiles/analysisdata-test.dir/lifetime.cpp.o" "CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/analysisdata-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 96%] Built target analysisdata-test cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/commandline-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/commandline-test.dir/link.d "CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o" "CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o" "CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o" "CMakeFiles/commandline-test.dir/filenm.cpp.o" "CMakeFiles/commandline-test.dir/pargs.cpp.o" "CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 97%] Built target commandline-test cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-listed-forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-listed-forces-test.dir/link.d "CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../../bin/nblib-listed-forces-test ../../../../lib/libtestutils.a ../../../../lib/libnblib_test_infrastructure.a ../../../../lib/libnblib_gmx.so.0.1.0 ../../../../lib/libtestutils.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 97%] Built target nblib-listed-forces-test cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryanalysis-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/trajectoryanalysis-test.dir/link.d "CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/dssp.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/gyrate.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/hbond.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/msd.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/scattering.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/trajectoryanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 98%] Built target trajectoryanalysis-test cd /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-setup-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-setup-test.dir/link.d "CMakeFiles/nblib-setup-test.dir/box.cpp.o" "CMakeFiles/nblib-setup-test.dir/interactions.cpp.o" "CMakeFiles/nblib-setup-test.dir/particletype.cpp.o" "CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o" "CMakeFiles/nblib-setup-test.dir/molecules.cpp.o" "CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o" "CMakeFiles/nblib-setup-test.dir/topology.cpp.o" "CMakeFiles/nblib-setup-test.dir/virials.cpp.o" "CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-setup-test ../../../lib/libtestutils.a ../../../lib/libmdrun_test_infrastructure.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 ../../../lib/libgromacs_d.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [100%] Built target nblib-setup-test /usr/bin/make -f api/nblib/CMakeFiles/nblib-tests.dir/build.make api/nblib/CMakeFiles/nblib-tests.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/CMakeFiles/nblib-tests.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f api/nblib/CMakeFiles/nblib-tests.dir/build.make api/nblib/CMakeFiles/nblib-tests.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[4]: Nothing to be done for 'api/nblib/CMakeFiles/nblib-tests.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [100%] Built target nblib-tests /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/CMakeFiles/tests.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [100%] Built target tests make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.0/build/basic-dp/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[1]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' (cd build/basic-dp; LD_LIBRARY_PATH=/build/reproducible-path/gromacs-2025.0/build/basic-dp/lib ctest -V) UpdateCTestConfiguration from :/build/reproducible-path/gromacs-2025.0/build/basic-dp/DartConfiguration.tcl Parse Config file:/build/reproducible-path/gromacs-2025.0/build/basic-dp/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/gromacs-2025.0/build/basic-dp/DartConfiguration.tcl Parse Config file:/build/reproducible-path/gromacs-2025.0/build/basic-dp/DartConfiguration.tcl Test project /build/reproducible-path/gromacs-2025.0/build/basic-dp Constructing a list of tests Done constructing a list of tests Updating test list for fixtures Added 0 tests to meet fixture requirements Checking test dependency graph... Checking test dependency graph end test 1 Start 1: GmxapiExternalInterfaceTests 1: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/gmxapi-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/GmxapiExternalInterfaceTests.xml" 1: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/tests 1: Test timeout computed to be: 600 1: [==========] Running 9 tests from 1 test suite. 1: [----------] Global test environment set-up. 1: [----------] 9 tests from GmxApiTest 1: [ RUN ] GmxApiTest.ApiRunnerRestrainedMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 1: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 1: Changing nstlist from 10 to 25, rlist from 1.062 to 1.197 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to -1275136001 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 2.153 1.077 200.0 1: (ns/day) (hour/ns) 1: Performance: 0.470 51.037 1: [ OK ] GmxApiTest.ApiRunnerRestrainedMD (1806 ms) 1: [ RUN ] GmxApiTest.RunnerBasicMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 1: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 1: Changing nstlist from 10 to 25, rlist from 1.062 to 1.197 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to 1073472441 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 1.025 0.513 200.0 1: (ns/day) (hour/ns) 1: Performance: 0.987 24.304 1: [ OK ] GmxApiTest.RunnerBasicMD (1294 ms) 1: [ RUN ] GmxApiTest.RunnerReinitialize 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 1: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 1: Changing nstlist from 10 to 25, rlist from 1.062 to 1.197 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 20 steps, 0.0 ps. 1: 1: 1: Received the remote INT/TERM signal, stopping within 200 steps 1: 1: Setting the LD random seed to -83895497 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.065 0.033 199.3 1: (ns/day) (hour/ns) 1: Performance: 108.588 0.221 1: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 1: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 1: Changing nstlist from 10 to 25, rlist from 1.062 to 1.197 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 20 steps, 0.0 ps. 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.098 0.049 198.7 1: (ns/day) (hour/ns) 1: Performance: 72.121 0.333 1: [ OK ] GmxApiTest.RunnerReinitialize (1017 ms) 1: [ RUN ] GmxApiTest.RunnerChainedMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 1: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 1: Changing nstlist from 10 to 25, rlist from 1.062 to 1.197 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to -1126183435 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 1.392 0.696 200.0 1: (ns/day) (hour/ns) 1: Performance: 0.727 32.995 1: trr version: GMX_trn_file (double precision) 1: 1: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 1: Setting nsteps to 4 1: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 1: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 1: Changing nstlist from 10 to 25, rlist from 1.062 to 1.197 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 1: Input file: 1: Run start step 0 1: Run start time 0 ps 1: Step to be made during run 2 1: Runtime for the run 0.00390625 ps 1: Run end step 2 1: Run end time 0.00390625 ps 1: 1: 1: Output file: 1: Run start step 0 1: Run start time 0 ps 1: Step to be made during run 4 1: Runtime for the run 0.0078125 ps 1: Run end step 4 1: Run end time 0.0078125 ps 1: 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 1.964 0.982 200.0 1: (ns/day) (hour/ns) 1: Performance: 0.515 46.569 1: 1: [ OK ] GmxApiTest.RunnerChainedMD (2772 ms) 1: [ RUN ] GmxApiTest.Status 1: [ OK ] GmxApiTest.Status (0 ms) 1: [ RUN ] GmxApiTest.ApiRunnerStopSignalClient 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 1: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 1: Changing nstlist from 10 to 1, rlist from 1.062 to 1 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps. 1: Setting the LD random seed to -319063041 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.058 0.029 199.2 1: (ns/day) (hour/ns) 1: Performance: 29.042 0.826 1: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 1: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 1: Overriding nsteps with value passed on the command line: 4 steps, 0.00781 ps 1: Changing nstlist from 10 to 1, rlist from 1.062 to 1 1: 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.132 0.066 199.5 1: (ns/day) (hour/ns) 1: Performance: 5.085 4.720 1: [ OK ] GmxApiTest.ApiRunnerStopSignalClient (950 ms) 1: [ RUN ] GmxApiTest.SystemConstruction 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Setting the LD random seed to -269814785 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: [ OK ] GmxApiTest.SystemConstruction (863 ms) 1: [ RUN ] GmxApiTest.SaneVersionComparisons 1: [ OK ] GmxApiTest.SaneVersionComparisons (0 ms) 1: [ RUN ] GmxApiTest.VersionNamed0_1_Features 1: [ OK ] GmxApiTest.VersionNamed0_1_Features (0 ms) 1: [----------] 9 tests from GmxApiTest (8707 ms total) 1: 1: [----------] Global test environment tear-down 1: [==========] 9 tests from 1 test suite ran. (8803 ms total) 1: [ PASSED ] 9 tests. 1/90 Test #1: GmxapiExternalInterfaceTests .............. Passed 8.86 sec test 2 Start 2: GmxapiInternalInterfaceTests 2: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/workflow-details-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/GmxapiInternalInterfaceTests.xml" 2: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/workflow/tests 2: Test timeout computed to be: 600 2: [==========] Running 2 tests from 1 test suite. 2: [----------] Global test environment set-up. 2: [----------] 2 tests from GmxApiTest 2: [ RUN ] GmxApiTest.BuildApiWorkflowImpl 2: Generating 1-4 interactions: fudge = 0.5 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: Setting the LD random seed to 2109655212 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: [ OK ] GmxApiTest.BuildApiWorkflowImpl (632 ms) 2: [ RUN ] GmxApiTest.CreateApiWorkflow 2: Generating 1-4 interactions: fudge = 0.5 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: Setting the LD random seed to -805441351 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: [ OK ] GmxApiTest.CreateApiWorkflow (678 ms) 2: [----------] 2 tests from GmxApiTest (1310 ms total) 2: 2: [----------] Global test environment tear-down 2: [==========] 2 tests from 1 test suite ran. (1483 ms total) 2: [ PASSED ] 2 tests. 2/90 Test #2: GmxapiInternalInterfaceTests .............. Passed 1.54 sec test 3 Start 3: NbLibListedForcesTests 3: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/nblib-listed-forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/NbLibListedForcesTests.xml" 3: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/listed_forces/tests 3: Test timeout computed to be: 600 3: [==========] Running 44 tests from 22 test suites. 3: [----------] Global test environment set-up. 3: [----------] 8 tests from NBlibTest 3: [ RUN ] NBlibTest.BondTypesOperatorEqualWorks 3: [ OK ] NBlibTest.BondTypesOperatorEqualWorks (0 ms) 3: [ RUN ] NBlibTest.BondTypesLessThanWorks 3: [ OK ] NBlibTest.BondTypesLessThanWorks (0 ms) 3: [ RUN ] NBlibTest.CanSplitListedWork 3: [ OK ] NBlibTest.CanSplitListedWork (0 ms) 3: [ RUN ] NBlibTest.ListedForceBuffer 3: [ OK ] NBlibTest.ListedForceBuffer (0 ms) 3: [ RUN ] NBlibTest.ListedForceCalculatorCanConstruct 3: [ OK ] NBlibTest.ListedForceCalculatorCanConstruct (0 ms) 3: [ RUN ] NBlibTest.GmxToNblibConversionAllTypes 3: [ OK ] NBlibTest.GmxToNblibConversionAllTypes (0 ms) 3: [ RUN ] NBlibTest.EndToEndListedComparison 3: [ OK ] NBlibTest.EndToEndListedComparison (0 ms) 3: [ RUN ] NBlibTest.shiftForcesAreCorrect 3: [ OK ] NBlibTest.shiftForcesAreCorrect (33 ms) 3: [----------] 8 tests from NBlibTest (34 ms total) 3: 3: [----------] 1 test from Kernels 3: [ RUN ] Kernels.HarmonicScalarKernelCanCompute 3: [ OK ] Kernels.HarmonicScalarKernelCanCompute (0 ms) 3: [----------] 1 test from Kernels (0 ms total) 3: 3: [----------] 1 test from FourCenter 3: [ RUN ] FourCenter.ListedForcesProperDihedralTest 3: [ OK ] FourCenter.ListedForcesProperDihedralTest (0 ms) 3: [----------] 1 test from FourCenter (0 ms total) 3: 3: [----------] 7 tests from ThreeCenter 3: [ RUN ] ThreeCenter.ListedForcesG96AngleTest 3: [ OK ] ThreeCenter.ListedForcesG96AngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesHarmonicAngleTest 3: [ OK ] ThreeCenter.ListedForcesHarmonicAngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesLinearAngleTest 3: [ OK ] ThreeCenter.ListedForcesLinearAngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesCrossBondBondTest 3: [ OK ] ThreeCenter.ListedForcesCrossBondBondTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesCrossBondAngleTest 3: [ OK ] ThreeCenter.ListedForcesCrossBondAngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesQuarticAngleTest 3: [ OK ] ThreeCenter.ListedForcesQuarticAngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesRestrictedAngleTest 3: [ OK ] ThreeCenter.ListedForcesRestrictedAngleTest (0 ms) 3: [----------] 7 tests from ThreeCenter (1 ms total) 3: 3: [----------] 5 tests from TwoCenter 3: [ RUN ] TwoCenter.ListedForcesHarmonicBondTest 3: [ OK ] TwoCenter.ListedForcesHarmonicBondTest (0 ms) 3: [ RUN ] TwoCenter.ListedForcesG96BondTest 3: [ OK ] TwoCenter.ListedForcesG96BondTest (0 ms) 3: [ RUN ] TwoCenter.ListedForcesCubicBondTest 3: [ OK ] TwoCenter.ListedForcesCubicBondTest (0 ms) 3: [ RUN ] TwoCenter.ListedForcesMorseBondTest 3: [ OK ] TwoCenter.ListedForcesMorseBondTest (0 ms) 3: [ RUN ] TwoCenter.ListedForcesFeneBondTest 3: [ OK ] TwoCenter.ListedForcesFeneBondTest (0 ms) 3: [----------] 5 tests from TwoCenter (0 ms total) 3: 3: [----------] 5 tests from ListedExampleData 3: [ RUN ] ListedExampleData.ComputeHarmonicBondForces 3: [ OK ] ListedExampleData.ComputeHarmonicBondForces (0 ms) 3: [ RUN ] ListedExampleData.ComputeHarmonicBondEnergies 3: [ OK ] ListedExampleData.ComputeHarmonicBondEnergies (0 ms) 3: [ RUN ] ListedExampleData.ComputeHarmonicAngleForces 3: [ OK ] ListedExampleData.ComputeHarmonicAngleForces (0 ms) 3: [ RUN ] ListedExampleData.CanReduceForces 3: [ OK ] ListedExampleData.CanReduceForces (0 ms) 3: [ RUN ] ListedExampleData.CanReduceEnergies 3: [ OK ] ListedExampleData.CanReduceEnergies (0 ms) 3: [----------] 5 tests from ListedExampleData (0 ms total) 3: 3: [----------] 1 test from LinearChainDataFixture 3: [ RUN ] LinearChainDataFixture.Multithreading 3: [ OK ] LinearChainDataFixture.Multithreading (2 ms) 3: [----------] 1 test from LinearChainDataFixture (2 ms total) 3: 3: [----------] 2 tests from ListedShims 3: [ RUN ] ListedShims.ParameterConversion 3: [ OK ] ListedShims.ParameterConversion (0 ms) 3: [ RUN ] ListedShims.GmxToNblibConversion 3: [ OK ] ListedShims.GmxToNblibConversion (0 ms) 3: [----------] 2 tests from ListedShims (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/0, where TypeParam = nblib::TwoParameterInteraction 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/0.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/0.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/0 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/1, where TypeParam = nblib::G96BondType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/1.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/1.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/1 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/2, where TypeParam = nblib::CubicBondType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/2.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/2.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/2 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/3, where TypeParam = nblib::MorseBondType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/3.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/3.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/3 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/4, where TypeParam = nblib::TwoParameterInteraction 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/4.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/4.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/4 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/5, where TypeParam = nblib::AngleInteractionType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/5.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/5.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/5 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/6, where TypeParam = nblib::CosineParamAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/6.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/6.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/6 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/7, where TypeParam = nblib::CosineParamAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/7.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/7.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/7 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/8, where TypeParam = nblib::TwoParameterInteraction 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/8.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/8.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/8 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/9, where TypeParam = nblib::QuarticAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/9.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/9.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/9 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/10, where TypeParam = nblib::CrossBondBond 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/10.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/10.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/10 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/11, where TypeParam = nblib::CrossBondAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/11.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/11.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/11 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/12, where TypeParam = nblib::ProperDihedral 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/12.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/12.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/12 (0 ms total) 3: 3: [----------] 1 test from ListedTransformations 3: [ RUN ] ListedTransformations.SortInteractionIndices 3: [ OK ] ListedTransformations.SortInteractionIndices (0 ms) 3: [----------] 1 test from ListedTransformations (0 ms total) 3: 3: [----------] Global test environment tear-down 3: [==========] 44 tests from 22 test suites ran. (43 ms total) 3: [ PASSED ] 44 tests. 3/90 Test #3: NbLibListedForcesTests .................... Passed 0.07 sec test 4 Start 4: NbLibSamplesTestArgon 4: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/argon-forces-integration 4: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/samples 4: Test timeout computed to be: 1500 4: initial forces on particle 0: x 0.000000 y 0.000000 z 0.000000 4: final forces on particle 0: x -0.412988 y -1.098243 z -0.113189 4: initial position of particle 0: x 0.794000 y 1.439000 z 0.610000 4: final position of particle 0: x 0.789162 y 1.271508 z 0.819867 4/90 Test #4: NbLibSamplesTestArgon ..................... Passed 0.03 sec test 5 Start 5: NbLibSamplesTestMethaneWater 5: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/methane-water-integration 5: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/samples 5: Test timeout computed to be: 1500 5: initial position of particle 0: x 0.005000 y 0.600000 z 0.244000 5: final position of particle 9: x 77.358372 y 5.325207 z -80.600064 5/90 Test #5: NbLibSamplesTestMethaneWater .............. Passed 0.02 sec test 6 Start 6: NbLibUtilTests 6: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/nblib-util-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/NbLibUtilTests.xml" 6: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/util/tests 6: Test timeout computed to be: 30 6: [==========] Running 16 tests from 2 test suites. 6: [----------] Global test environment set-up. 6: [----------] 6 tests from NBlibTest 6: [ RUN ] NBlibTest.isRealValued 6: [ OK ] NBlibTest.isRealValued (0 ms) 6: [ RUN ] NBlibTest.checkNumericValuesHasNan 6: [ OK ] NBlibTest.checkNumericValuesHasNan (0 ms) 6: [ RUN ] NBlibTest.checkNumericValuesHasInf 6: [ OK ] NBlibTest.checkNumericValuesHasInf (0 ms) 6: [ RUN ] NBlibTest.GeneratedVelocitiesAreCorrect 6: Velocities were taken from a Maxwell distribution at 300 K 6: [ OK ] NBlibTest.GeneratedVelocitiesAreCorrect (0 ms) 6: [ RUN ] NBlibTest.generateVelocitySize 6: Velocities were taken from a Maxwell distribution at 300 K 6: [ OK ] NBlibTest.generateVelocitySize (0 ms) 6: [ RUN ] NBlibTest.generateVelocityCheckNumbers 6: Velocities were taken from a Maxwell distribution at 300 K 6: [ OK ] NBlibTest.generateVelocityCheckNumbers (0 ms) 6: [----------] 6 tests from NBlibTest (0 ms total) 6: 6: [----------] 10 tests from NblibTraitsUtils 6: [ RUN ] NblibTraitsUtils.FuseTwo 6: [ OK ] NblibTraitsUtils.FuseTwo (0 ms) 6: [ RUN ] NblibTraitsUtils.Fuse 6: [ OK ] NblibTraitsUtils.Fuse (0 ms) 6: [ RUN ] NblibTraitsUtils.Repeat 6: [ OK ] NblibTraitsUtils.Repeat (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTuple1 6: [ OK ] NblibTraitsUtils.FindIndexTuple1 (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTuple2 6: [ OK ] NblibTraitsUtils.FindIndexTuple2 (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTypeList1 6: [ OK ] NblibTraitsUtils.FindIndexTypeList1 (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTypeList2 6: [ OK ] NblibTraitsUtils.FindIndexTypeList2 (0 ms) 6: [ RUN ] NblibTraitsUtils.Contains 6: [ OK ] NblibTraitsUtils.Contains (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTupleRepeated 6: [ OK ] NblibTraitsUtils.FindIndexTupleRepeated (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTypeListRepeated 6: [ OK ] NblibTraitsUtils.FindIndexTypeListRepeated (0 ms) 6: [----------] 10 tests from NblibTraitsUtils (0 ms total) 6: 6: [----------] Global test environment tear-down 6: [==========] 16 tests from 2 test suites ran. (0 ms total) 6: [ PASSED ] 16 tests. 6/90 Test #6: NbLibUtilTests ............................ Passed 0.03 sec test 7 Start 7: NbLibSetupTests 7: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/nblib-setup-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/NbLibSetupTests.xml" 7: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests 7: Test timeout computed to be: 600 7: [==========] Running 57 tests from 3 test suites. 7: [----------] Global test environment set-up. 7: [----------] 41 tests from NBlibTest 7: [ RUN ] NBlibTest.CubicBoxCannotHaveNaN 7: [ OK ] NBlibTest.CubicBoxCannotHaveNaN (0 ms) 7: [ RUN ] NBlibTest.CubicBoxCannotHaveInf 7: [ OK ] NBlibTest.CubicBoxCannotHaveInf (0 ms) 7: [ RUN ] NBlibTest.RectangularBoxCannotHaveNaN 7: [ OK ] NBlibTest.RectangularBoxCannotHaveNaN (0 ms) 7: [ RUN ] NBlibTest.RectangularBoxCannotHaveInf 7: [ OK ] NBlibTest.RectangularBoxCannotHaveInf (0 ms) 7: [ RUN ] NBlibTest.CubicBoxWorks 7: [ OK ] NBlibTest.CubicBoxWorks (0 ms) 7: [ RUN ] NBlibTest.BoxEqual 7: [ OK ] NBlibTest.BoxEqual (0 ms) 7: [ RUN ] NBlibTest.NonBondedForceParamsCorrect 7: [ OK ] NBlibTest.NonBondedForceParamsCorrect (0 ms) 7: [ RUN ] NBlibTest.CanMergeInteractions 7: [ OK ] NBlibTest.CanMergeInteractions (0 ms) 7: [ RUN ] NBlibTest.ParticleTypeNameCanBeConstructed 7: [ OK ] NBlibTest.ParticleTypeNameCanBeConstructed (0 ms) 7: [ RUN ] NBlibTest.ParticleTypeMassCanBeConstructed 7: [ OK ] NBlibTest.ParticleTypeMassCanBeConstructed (0 ms) 7: [ RUN ] NBlibTest.PbcHolderWorks 7: [ OK ] NBlibTest.PbcHolderWorks (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName (0 ms) 7: [ RUN ] NBlibTest.CanGetNumParticlesInMolecule 7: [ OK ] NBlibTest.CanGetNumParticlesInMolecule (0 ms) 7: [ RUN ] NBlibTest.CanConstructExclusionListFromNames 7: [ OK ] NBlibTest.CanConstructExclusionListFromNames (0 ms) 7: [ RUN ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed 7: [ OK ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed (0 ms) 7: [ RUN ] NBlibTest.AtWorks 7: [ OK ] NBlibTest.AtWorks (0 ms) 7: [ RUN ] NBlibTest.AtThrows 7: [ OK ] NBlibTest.AtThrows (0 ms) 7: [ RUN ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass 7: [ OK ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass (0 ms) 7: [ RUN ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass 7: [ OK ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass (0 ms) 7: [ RUN ] NBlibTest.MoleculeNoThrowsSameParticleTypeName 7: [ OK ] NBlibTest.MoleculeNoThrowsSameParticleTypeName (0 ms) 7: [ RUN ] NBlibTest.CanAddInteractions 7: [ OK ] NBlibTest.CanAddInteractions (0 ms) 7: [ RUN ] NBlibTest.CanAddUreyBradley 7: [ OK ] NBlibTest.CanAddUreyBradley (0 ms) 7: [ RUN ] NBlibTest.TopologyHasNumParticles 7: [ OK ] NBlibTest.TopologyHasNumParticles (0 ms) 7: [ RUN ] NBlibTest.TopologyHasCharges 7: [ OK ] NBlibTest.TopologyHasCharges (0 ms) 7: [ RUN ] NBlibTest.TopologyHasMasses 7: [ OK ] NBlibTest.TopologyHasMasses (0 ms) 7: [ RUN ] NBlibTest.TopologyHasParticleTypes 7: [ OK ] NBlibTest.TopologyHasParticleTypes (0 ms) 7: [ RUN ] NBlibTest.TopologyHasParticleTypeIds 7: [ OK ] NBlibTest.TopologyHasParticleTypeIds (0 ms) 7: [ RUN ] NBlibTest.TopologyThrowsIdenticalParticleType 7: [ OK ] NBlibTest.TopologyThrowsIdenticalParticleType (0 ms) 7: [ RUN ] NBlibTest.TopologyHasExclusions 7: [ OK ] NBlibTest.TopologyHasExclusions (0 ms) 7: [ RUN ] NBlibTest.TopologyHasSequencing 7: [ OK ] NBlibTest.TopologyHasSequencing (0 ms) 7: [ RUN ] NBlibTest.TopologyCanAggregateBonds 7: [ OK ] NBlibTest.TopologyCanAggregateBonds (0 ms) 7: [ RUN ] NBlibTest.TopologyCanSequencePairIDs 7: [ OK ] NBlibTest.TopologyCanSequencePairIDs (0 ms) 7: [ RUN ] NBlibTest.TopologySequenceIdThrows 7: No particle O-Atom in residue SOL in molecule SOL found 7: [ OK ] NBlibTest.TopologySequenceIdThrows (0 ms) 7: [ RUN ] NBlibTest.TopologyCanEliminateDuplicateBonds 7: [ OK ] NBlibTest.TopologyCanEliminateDuplicateBonds (0 ms) 7: [ RUN ] NBlibTest.TopologyListedInteractions 7: [ OK ] NBlibTest.TopologyListedInteractions (0 ms) 7: [ RUN ] NBlibTest.TopologyListedInteractionsMultipleTypes 7: [ OK ] NBlibTest.TopologyListedInteractionsMultipleTypes (0 ms) 7: [ RUN ] NBlibTest.TopologyInvalidParticleInInteractionThrows 7: No particle Iron in residue SOL in molecule SOL found 7: [ OK ] NBlibTest.TopologyInvalidParticleInInteractionThrows (0 ms) 7: [ RUN ] NBlibTest.toGmxExclusionBlockWorks 7: [ OK ] NBlibTest.toGmxExclusionBlockWorks (0 ms) 7: [----------] 41 tests from NBlibTest (2 ms total) 7: 7: [----------] 15 tests from NbnxmSetupTest 7: [ RUN ] NbnxmSetupTest.findNumEnergyGroups 7: [ OK ] NbnxmSetupTest.findNumEnergyGroups (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnumAuto 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnumAuto (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnumNo 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnumNo (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnum2XM 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnum2XM (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnum4XM 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnum4XM (0 ms) 7: [ RUN ] NbnxmSetupTest.CheckKernelSetupThrowsAuto 7: [ OK ] NbnxmSetupTest.CheckKernelSetupThrowsAuto (0 ms) 7: [ RUN ] NbnxmSetupTest.CheckKernelSetupThrowsCount 7: [ OK ] NbnxmSetupTest.CheckKernelSetupThrowsCount (0 ms) 7: [ RUN ] NbnxmSetupTest.canCreateKernelSetupPlain 7: [ OK ] NbnxmSetupTest.canCreateKernelSetupPlain (0 ms) 7: [ RUN ] NbnxmSetupTest.canCreateParticleInfoAllVdv 7: [ OK ] NbnxmSetupTest.canCreateParticleInfoAllVdv (0 ms) 7: [ RUN ] NbnxmSetupTest.ewaldCoeffWorks 7: [ OK ] NbnxmSetupTest.ewaldCoeffWorks (0 ms) 7: [ RUN ] NbnxmSetupTest.updateForcerecWorks 7: [ OK ] NbnxmSetupTest.updateForcerecWorks (0 ms) 7: [ RUN ] NbnxmSetupTest.canCheckKernelSetup 7: [ OK ] NbnxmSetupTest.canCheckKernelSetup (0 ms) 7: [ RUN ] NbnxmSetupTest.cannotCreateKernelSetupCPU2XM 7: [ OK ] NbnxmSetupTest.cannotCreateKernelSetupCPU2XM (0 ms) 7: [ RUN ] NbnxmSetupTest.cannotCreateKernelSetupCPU4XM 7: [ OK ] NbnxmSetupTest.cannotCreateKernelSetupCPU4XM (0 ms) 7: [ RUN ] NbnxmSetupTest.CanCreateNbnxmCPU 7: [ OK ] NbnxmSetupTest.CanCreateNbnxmCPU (0 ms) 7: [----------] 15 tests from NbnxmSetupTest (0 ms total) 7: 7: [----------] 1 test from VirialsTest 7: [ RUN ] VirialsTest.computeVirialTensorWorks 7: [ OK ] VirialsTest.computeVirialTensorWorks (0 ms) 7: [----------] 1 test from VirialsTest (0 ms total) 7: 7: [----------] Global test environment tear-down 7: [==========] 57 tests from 3 test suites ran. (2 ms total) 7: [ PASSED ] 57 tests. 7/90 Test #7: NbLibSetupTests ........................... Passed 0.14 sec test 8 Start 8: NbLibTprTests 8: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/nblib-tpr-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/NbLibTprTests.xml" 8: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests 8: Test timeout computed to be: 30 8: [==========] Running 4 tests from 1 test suite. 8: [----------] Global test environment set-up. 8: [----------] 4 tests from TprReaderTest 8: [ RUN ] TprReaderTest.SimDBTprIsCreated 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 8: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 8: that with the Verlet scheme, nstlist has no effect on the accuracy of 8: your simulation. 8: 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Number of degrees of freedom in T-Coupling group System is 33.00 8: 8: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 8: NVE simulation: will use the initial temperature of 68.810 K for 8: determining the Verlet buffer size 8: 8: 8: There were 3 NOTEs 8: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 8: Generated 1 of the 1 non-bonded parameter combinations 8: 8: Excluding 1 bonded neighbours molecule type 'Argon' 8: 8: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.SimDBTprIsCreated (36 ms) 8: [ RUN ] TprReaderTest.Spc2Reads 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 8: that with the Verlet scheme, nstlist has no effect on the accuracy of 8: your simulation. 8: 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Generating 1-4 interactions: fudge = 0.5 8: Number of degrees of freedom in T-Coupling group System is 9.00 8: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 8: 8: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: NVE simulation: will use the initial temperature of 2573.591 K for 8: determining the Verlet buffer size 8: 8: 8: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: You are using a plain Coulomb cut-off, which might produce artifacts. 8: You might want to consider using PME electrostatics. 8: 8: 8: 8: There were 4 NOTEs 8: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 8: Generated 3 of the 3 non-bonded parameter combinations 8: 8: Generated 3 of the 3 1-4 parameter combinations 8: 8: Excluding 2 bonded neighbours molecule type 'SOL' 8: 8: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.Spc2Reads (31 ms) 8: [ RUN ] TprReaderTest.ArgonImportedDataIsCorrect 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 8: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 8: that with the Verlet scheme, nstlist has no effect on the accuracy of 8: your simulation. 8: 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Number of degrees of freedom in T-Coupling group System is 33.00 8: 8: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 8: NVE simulation: will use the initial temperature of 68.810 K for 8: determining the Verlet buffer size 8: 8: 8: There were 3 NOTEs 8: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 8: Generated 1 of the 1 non-bonded parameter combinations 8: 8: Excluding 1 bonded neighbours molecule type 'Argon' 8: 8: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.ArgonImportedDataIsCorrect (20 ms) 8: [ RUN ] TprReaderTest.FCfromTprDataWorks 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 8: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 8: that with the Verlet scheme, nstlist has no effect on the accuracy of 8: your simulation. 8: 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Number of degrees of freedom in T-Coupling group System is 33.00 8: 8: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 8: NVE simulation: will use the initial temperature of 68.810 K for 8: determining the Verlet buffer size 8: 8: 8: There were 3 NOTEs 8: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 8: Generated 1 of the 1 non-bonded parameter combinations 8: 8: Excluding 1 bonded neighbours molecule type 'Argon' 8: 8: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.FCfromTprDataWorks (48 ms) 8: [----------] 4 tests from TprReaderTest (136 ms total) 8: 8: [----------] Global test environment tear-down 8: [==========] 4 tests from 1 test suite ran. (262 ms total) 8: [ PASSED ] 4 tests. 8/90 Test #8: NbLibTprTests ............................. Passed 0.29 sec test 9 Start 9: NbLibIntegrationTests 9: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/nblib-integration-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/NbLibIntegrationTests.xml" 9: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests 9: Test timeout computed to be: 600 9: [==========] Running 20 tests from 1 test suite. 9: [----------] Global test environment set-up. 9: [----------] 20 tests from NBlibTest 9: [ RUN ] NBlibTest.GmxForceCalculatorCanCompute 9: [ OK ] NBlibTest.GmxForceCalculatorCanCompute (1 ms) 9: [ RUN ] NBlibTest.ArgonVirialsAreCorrect 9: [ OK ] NBlibTest.ArgonVirialsAreCorrect (0 ms) 9: [ RUN ] NBlibTest.ArgonEnergiesAreCorrect 9: [ OK ] NBlibTest.ArgonEnergiesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.SpcMethanolEnergiesAreCorrect 9: [ OK ] NBlibTest.SpcMethanolEnergiesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.SpcMethanolForcesAreCorrect 9: [ OK ] NBlibTest.SpcMethanolForcesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.ExpectedNumberOfForces 9: [ OK ] NBlibTest.ExpectedNumberOfForces (0 ms) 9: [ RUN ] NBlibTest.CanIntegrateSystem 9: [ OK ] NBlibTest.CanIntegrateSystem (0 ms) 9: [ RUN ] NBlibTest.UpdateChangesForces 9: [ OK ] NBlibTest.UpdateChangesForces (0 ms) 9: [ RUN ] NBlibTest.ArgonOplsaForcesAreCorrect 9: [ OK ] NBlibTest.ArgonOplsaForcesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.ArgonGromos43A1ForcesAreCorrect 9: [ OK ] NBlibTest.ArgonGromos43A1ForcesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.CanConstructSimulationState 9: [ OK ] NBlibTest.CanConstructSimulationState (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateNAN 9: [ OK ] NBlibTest.SimulationStateThrowsCoordinateNAN (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateINF 9: [ OK ] NBlibTest.SimulationStateThrowsCoordinateINF (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsVelocityNAN 9: [ OK ] NBlibTest.SimulationStateThrowsVelocityNAN (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsVelocityINF 9: [ OK ] NBlibTest.SimulationStateThrowsVelocityINF (0 ms) 9: [ RUN ] NBlibTest.SimulationStateCanMove 9: [ OK ] NBlibTest.SimulationStateCanMove (0 ms) 9: [ RUN ] NBlibTest.SimulationStateCanAssign 9: [ OK ] NBlibTest.SimulationStateCanAssign (0 ms) 9: [ RUN ] NBlibTest.SimulationStateHasBox 9: [ OK ] NBlibTest.SimulationStateHasBox (0 ms) 9: [ RUN ] NBlibTest.SimulationStateHasCorrectCoordinates 9: [ OK ] NBlibTest.SimulationStateHasCorrectCoordinates (0 ms) 9: [ RUN ] NBlibTest.SimulationStateHasCorrectVelocities 9: [ OK ] NBlibTest.SimulationStateHasCorrectVelocities (0 ms) 9: [----------] 20 tests from NBlibTest (5 ms total) 9: 9: [----------] Global test environment tear-down 9: [==========] 20 tests from 1 test suite ran. (5 ms total) 9: [ PASSED ] 20 tests. 9/90 Test #9: NbLibIntegrationTests ..................... Passed 0.03 sec test 10 Start 10: NbLibIntegratorTests 10: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/nblib-integrator-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/NbLibIntegratorTests.xml" 10: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/tests 10: Test timeout computed to be: 600 10: [==========] Running 1 test from 1 test suite. 10: [----------] Global test environment set-up. 10: [----------] 1 test from NBlibTest 10: [ RUN ] NBlibTest.IntegratorWorks 10: [ OK ] NBlibTest.IntegratorWorks (0 ms) 10: [----------] 1 test from NBlibTest (0 ms total) 10: 10: [----------] Global test environment tear-down 10: [==========] 1 test from 1 test suite ran. (0 ms total) 10: [ PASSED ] 1 test. 10/90 Test #10: NbLibIntegratorTests ...................... Passed 0.02 sec test 11 Start 11: TestUtilsUnitTests 11: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/testutils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/TestUtilsUnitTests.xml" 11: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/testutils/tests 11: Test timeout computed to be: 30 11: [==========] Running 75 tests from 7 test suites. 11: [----------] Global test environment set-up. 11: [----------] 10 tests from InteractiveTestHelperTest 11: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession 11: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (0 ms) 11: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline 11: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (0 ms) 11: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput 11: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput 11: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput 11: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput 11: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput 11: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput 11: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput 11: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput 11: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (0 ms) 11: [----------] 10 tests from InteractiveTestHelperTest (2 ms total) 11: 11: [----------] 10 tests from NameOfTestFromTupleTest 11: [ RUN ] NameOfTestFromTupleTest.WorksWithEmptyTuple 11: [ OK ] NameOfTestFromTupleTest.WorksWithEmptyTuple (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFunction 11: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFunction (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFunctionOfEnumVariable 11: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFunctionOfEnumVariable (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.RejectsNullptrFormatFunction 11: [ OK ] NameOfTestFromTupleTest.RejectsNullptrFormatFunction (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatLambda 11: [ OK ] NameOfTestFromTupleTest.WorksWithFormatLambda (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.WorksWithUseStringFormat 11: [ OK ] NameOfTestFromTupleTest.WorksWithUseStringFormat (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.WorksWithPrefixFormatter 11: [ OK ] NameOfTestFromTupleTest.WorksWithPrefixFormatter (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFunctor 11: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFunctor (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFromEnumerationArray 11: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFromEnumerationArray (0 ms) 11: [ RUN ] NameOfTestFromTupleTest.WorksWithMixtureOfFormatters 11: [ OK ] NameOfTestFromTupleTest.WorksWithMixtureOfFormatters (0 ms) 11: [----------] 10 tests from NameOfTestFromTupleTest (0 ms total) 11: 11: [----------] 3 tests from RefDataFilenameMakerTest 11: [ RUN ] RefDataFilenameMakerTest.WorksWithFormatFunction 11: [ OK ] RefDataFilenameMakerTest.WorksWithFormatFunction (0 ms) 11: [ RUN ] RefDataFilenameMakerTest.WorksWithMixtureOfFormatters 11: [ OK ] RefDataFilenameMakerTest.WorksWithMixtureOfFormatters (0 ms) 11: [ RUN ] RefDataFilenameMakerTest.WorksWithToEmpty 11: [ OK ] RefDataFilenameMakerTest.WorksWithToEmpty (0 ms) 11: [----------] 3 tests from RefDataFilenameMakerTest (0 ms total) 11: 11: [----------] 37 tests from ReferenceDataTest 11: [ RUN ] ReferenceDataTest.HandlesSimpleData 11: [ OK ] ReferenceDataTest.HandlesSimpleData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesFloatingPointData 11: [ OK ] ReferenceDataTest.HandlesFloatingPointData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesPresenceChecks 11: [ OK ] ReferenceDataTest.HandlesPresenceChecks (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesStringBlockData 11: [ OK ] ReferenceDataTest.HandlesStringBlockData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesVectorData 11: [ OK ] ReferenceDataTest.HandlesVectorData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesSequenceData 11: [ OK ] ReferenceDataTest.HandlesSequenceData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData 11: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (0 ms) 11: [ RUN ] ReferenceDataTest.CheckSequenceArrayRef 11: [ OK ] ReferenceDataTest.CheckSequenceArrayRef (0 ms) 11: [ RUN ] ReferenceDataTest.CheckSequenceArrayRefHandlesIncorrectData 11: [ OK ] ReferenceDataTest.CheckSequenceArrayRefHandlesIncorrectData (0 ms) 11: [ RUN ] ReferenceDataTest.CheckSequenceArrayRefHandlesSequenceOfCustomData 11: [ OK ] ReferenceDataTest.CheckSequenceArrayRefHandlesSequenceOfCustomData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesIncorrectData 11: [ OK ] ReferenceDataTest.HandlesIncorrectData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType 11: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesMissingData 11: [ OK ] ReferenceDataTest.HandlesMissingData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUncheckedData 11: [ OK ] ReferenceDataTest.HandlesUncheckedData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence 11: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound 11: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesAnys 11: [ OK ] ReferenceDataTest.HandlesAnys (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesKeyValueTree 11: [ OK ] ReferenceDataTest.HandlesKeyValueTree (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey 11: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey 11: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectValue 11: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectValue (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectType 11: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectType (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile 11: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings 11: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace 11: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesEmptyStrings 11: [ OK ] ReferenceDataTest.HandlesEmptyStrings (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock 11: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices 11: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData 11: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds 11: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds 11: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesReadingValues 11: [ OK ] ReferenceDataTest.HandlesReadingValues (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges 11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (50 ms) 11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges 11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges 11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges 11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries 11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (0 ms) 11: [----------] 37 tests from ReferenceDataTest (57 ms total) 11: 11: [----------] 7 tests from FloatingPointDifferenceTest 11: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues 11: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues 11: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign 11: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero 11: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences 11: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero 11: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesNaN 11: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms) 11: [----------] 7 tests from FloatingPointDifferenceTest (0 ms total) 11: 11: [----------] 4 tests from FloatingPointToleranceTest 11: [ RUN ] FloatingPointToleranceTest.UlpTolerance 11: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms) 11: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint 11: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms) 11: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp 11: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms) 11: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance 11: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms) 11: [----------] 4 tests from FloatingPointToleranceTest (0 ms total) 11: 11: [----------] 4 tests from XvgTests 11: [ RUN ] XvgTests.CreateFile 11: [ OK ] XvgTests.CreateFile (0 ms) 11: [ RUN ] XvgTests.CheckMissing 11: [ OK ] XvgTests.CheckMissing (0 ms) 11: [ RUN ] XvgTests.CheckExtra 11: [ OK ] XvgTests.CheckExtra (0 ms) 11: [ RUN ] XvgTests.ReadIncorrect 11: [ OK ] XvgTests.ReadIncorrect (0 ms) 11: [----------] 4 tests from XvgTests (1 ms total) 11: 11: [----------] Global test environment tear-down 11: [==========] 75 tests from 7 test suites ran. (62 ms total) 11: [ PASSED ] 75 tests. 11/90 Test #11: TestUtilsUnitTests ........................ Passed 0.08 sec test 12 Start 12: TestUtilsMpiUnitTests 12: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/testutils-mpi-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/TestUtilsMpiUnitTests.xml" 12: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/testutils/tests 12: Test timeout computed to be: 30 12: [==========] Running 1 test from 1 test suite. 12: [----------] Global test environment set-up. 12: [----------] 1 test from MpiSelfTest 12: [ RUN ] MpiSelfTest.Runs 12: [ OK ] MpiSelfTest.Runs (2 ms) 12: [----------] 1 test from MpiSelfTest (2 ms total) 12: 12: [----------] Global test environment tear-down 12: [==========] 1 test from 1 test suite ran. (2 ms total) 12: [ PASSED ] 1 test. 12/90 Test #12: TestUtilsMpiUnitTests ..................... Passed 0.02 sec test 13 Start 13: UtilityUnitTests 13: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/utility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/UtilityUnitTests.xml" 13: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests 13: Test timeout computed to be: 30 13: [==========] Running 420 tests from 65 test suites. 13: [----------] Global test environment set-up. 13: [----------] 6 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 13: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/0.Move 13: [ OK ] AllocatorTest/0.Move (0 ms) 13: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms) 13: [ RUN ] AllocatorTest/0.Comparison 13: [ OK ] AllocatorTest/0.Comparison (0 ms) 13: [----------] 6 tests from AllocatorTest/0 (0 ms total) 13: 13: [----------] 6 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 13: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/1.Move 13: [ OK ] AllocatorTest/1.Move (0 ms) 13: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms) 13: [ RUN ] AllocatorTest/1.Comparison 13: [ OK ] AllocatorTest/1.Comparison (0 ms) 13: [----------] 6 tests from AllocatorTest/1 (0 ms total) 13: 13: [----------] 6 tests from AllocatorTest/2, where TypeParam = gmx::Allocator 13: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/2.Move 13: [ OK ] AllocatorTest/2.Move (0 ms) 13: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms) 13: [ RUN ] AllocatorTest/2.Comparison 13: [ OK ] AllocatorTest/2.Comparison (0 ms) 13: [----------] 6 tests from AllocatorTest/2 (0 ms total) 13: 13: [----------] 6 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 13: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/3.Move 13: [ OK ] AllocatorTest/3.Move (0 ms) 13: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms) 13: [ RUN ] AllocatorTest/3.Comparison 13: [ OK ] AllocatorTest/3.Comparison (0 ms) 13: [----------] 6 tests from AllocatorTest/3 (0 ms total) 13: 13: [----------] 6 tests from AllocatorTest/4, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 13: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/4.Move 13: [ OK ] AllocatorTest/4.Move (0 ms) 13: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms) 13: [ RUN ] AllocatorTest/4.Comparison 13: [ OK ] AllocatorTest/4.Comparison (0 ms) 13: [----------] 6 tests from AllocatorTest/4 (0 ms total) 13: 13: [----------] 6 tests from AllocatorTest/5, where TypeParam = gmx::Allocator, gmx::PageAlignedAllocationPolicy> 13: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/5.Move 13: [ OK ] AllocatorTest/5.Move (0 ms) 13: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms) 13: [ RUN ] AllocatorTest/5.Comparison 13: [ OK ] AllocatorTest/5.Comparison (0 ms) 13: [----------] 6 tests from AllocatorTest/5 (0 ms total) 13: 13: [----------] 1 test from AllocatorUntypedTest 13: [ RUN ] AllocatorUntypedTest.Comparison 13: [ OK ] AllocatorUntypedTest.Comparison (0 ms) 13: [----------] 1 test from AllocatorUntypedTest (0 ms total) 13: 13: [----------] 4 tests from EmptyArrayRefTest 13: [ RUN ] EmptyArrayRefTest.IsEmpty 13: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 13: [ RUN ] EmptyArrayRefTest.ConstructFromNullptrIsEmpty 13: [ OK ] EmptyArrayRefTest.ConstructFromNullptrIsEmpty (0 ms) 13: [ RUN ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForNullptr 13: [ OK ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForNullptr (0 ms) 13: [ RUN ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForSizeNull 13: [ OK ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForSizeNull (0 ms) 13: [----------] 4 tests from EmptyArrayRefTest (0 ms total) 13: 13: [----------] 1 test from EmptyConstArrayRefTest 13: [ RUN ] EmptyConstArrayRefTest.IsEmpty 13: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms) 13: [----------] 1 test from EmptyConstArrayRefTest (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/0 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/1 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/2 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/3 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/4 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/5 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/6 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/7 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/8 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/9 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/10 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/11 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/12 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/13 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/14 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/15 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/16 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/17 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/18 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/19 (0 ms total) 13: 13: [----------] 8 tests from BoolType 13: [ RUN ] BoolType.ImplicitConversion 13: [ OK ] BoolType.ImplicitConversion (0 ms) 13: [ RUN ] BoolType.FalseByDefault 13: [ OK ] BoolType.FalseByDefault (0 ms) 13: [ RUN ] BoolType.Assignment 13: [ OK ] BoolType.Assignment (0 ms) 13: [ RUN ] BoolType.Copy 13: [ OK ] BoolType.Copy (0 ms) 13: [ RUN ] BoolType.ArrayRefCanBeCreated 13: [ OK ] BoolType.ArrayRefCanBeCreated (0 ms) 13: [ RUN ] BoolType.CanBeCastToBool 13: [ OK ] BoolType.CanBeCastToBool (0 ms) 13: [ RUN ] BoolType.HasSizeOfBool 13: [ OK ] BoolType.HasSizeOfBool (0 ms) 13: [ RUN ] BoolType.HasAlignmentOfBool 13: [ OK ] BoolType.HasAlignmentOfBool (0 ms) 13: [----------] 8 tests from BoolType (0 ms total) 13: 13: [----------] 4 tests from ArrayRefFromBoolTypeVector 13: [ RUN ] ArrayRefFromBoolTypeVector.CanConstructEmpty 13: [ OK ] ArrayRefFromBoolTypeVector.CanConstructEmpty (0 ms) 13: [ RUN ] ArrayRefFromBoolTypeVector.Works 13: [ OK ] ArrayRefFromBoolTypeVector.Works (0 ms) 13: [ RUN ] ArrayRefFromBoolTypeVector.CanConstructConstEmpty 13: [ OK ] ArrayRefFromBoolTypeVector.CanConstructConstEmpty (0 ms) 13: [ RUN ] ArrayRefFromBoolTypeVector.ConstWorks 13: [ OK ] ArrayRefFromBoolTypeVector.ConstWorks (0 ms) 13: [----------] 4 tests from ArrayRefFromBoolTypeVector (0 ms total) 13: 13: [----------] 7 tests from CStringUtilityTest 13: [ RUN ] CStringUtilityTest.CaseInsensitiveComparison 13: [ OK ] CStringUtilityTest.CaseInsensitiveComparison (0 ms) 13: [ RUN ] CStringUtilityTest.CaseInsensitiveComparisonInLength 13: [ OK ] CStringUtilityTest.CaseInsensitiveComparisonInLength (0 ms) 13: [ RUN ] CStringUtilityTest.strip_comment 13: [ OK ] CStringUtilityTest.strip_comment (0 ms) 13: [ RUN ] CStringUtilityTest.upstring 13: [ OK ] CStringUtilityTest.upstring (0 ms) 13: [ RUN ] CStringUtilityTest.ltrim 13: [ OK ] CStringUtilityTest.ltrim (0 ms) 13: [ RUN ] CStringUtilityTest.rtrim 13: [ OK ] CStringUtilityTest.rtrim (0 ms) 13: [ RUN ] CStringUtilityTest.trim 13: [ OK ] CStringUtilityTest.trim (0 ms) 13: [----------] 7 tests from CStringUtilityTest (0 ms total) 13: 13: [----------] 2 tests from DefaultInitializationAllocator 13: [ RUN ] DefaultInitializationAllocator.PerformsValueInitialization 13: [ OK ] DefaultInitializationAllocator.PerformsValueInitialization (0 ms) 13: [ RUN ] DefaultInitializationAllocator.PerformsNoInitialization 13: [ OK ] DefaultInitializationAllocator.PerformsNoInitialization (0 ms) 13: [----------] 2 tests from DefaultInitializationAllocator (0 ms total) 13: 13: [----------] 4 tests from EnumerationHelpersTest 13: [ RUN ] EnumerationHelpersTest.EnumerationWrapperWorks 13: [ OK ] EnumerationHelpersTest.EnumerationWrapperWorks (0 ms) 13: [ RUN ] EnumerationHelpersTest.EnumerationArrayWorks 13: [ OK ] EnumerationHelpersTest.EnumerationArrayWorks (0 ms) 13: [ RUN ] EnumerationHelpersTest.EnumerationArrayCountIsSafe 13: [ OK ] EnumerationHelpersTest.EnumerationArrayCountIsSafe (0 ms) 13: [ RUN ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks 13: [ OK ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks (0 ms) 13: [----------] 4 tests from EnumerationHelpersTest (0 ms total) 13: 13: [----------] 1 test from EnumClassSuitsEnumerationArray 13: [ RUN ] EnumClassSuitsEnumerationArray.Works 13: [ OK ] EnumClassSuitsEnumerationArray.Works (0 ms) 13: [----------] 1 test from EnumClassSuitsEnumerationArray (0 ms total) 13: 13: [----------] 18 tests from FixedCapacityVectorTest 13: [ RUN ] FixedCapacityVectorTest.IsEmpty 13: [ OK ] FixedCapacityVectorTest.IsEmpty (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ConstructorWorks 13: [ OK ] FixedCapacityVectorTest.ConstructorWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.PushWorks 13: [ OK ] FixedCapacityVectorTest.PushWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.PopWorks 13: [ OK ] FixedCapacityVectorTest.PopWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ResizeWorks 13: [ OK ] FixedCapacityVectorTest.ResizeWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ClearWorks 13: [ OK ] FixedCapacityVectorTest.ClearWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.EmplaceBackWorks 13: [ OK ] FixedCapacityVectorTest.EmplaceBackWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.AtThrows 13: [ OK ] FixedCapacityVectorTest.AtThrows (0 ms) 13: [ RUN ] FixedCapacityVectorTest.IteratorWorks 13: [ OK ] FixedCapacityVectorTest.IteratorWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ReverseIteratorWorks 13: [ OK ] FixedCapacityVectorTest.ReverseIteratorWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ZeroCapacityWorks 13: [ OK ] FixedCapacityVectorTest.ZeroCapacityWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.CopyConstructorWorks 13: [ OK ] FixedCapacityVectorTest.CopyConstructorWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.CopyAssignmentWorks 13: [ OK ] FixedCapacityVectorTest.CopyAssignmentWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.MoveConstructorWorks 13: [ OK ] FixedCapacityVectorTest.MoveConstructorWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.MoveAssignmentWorks 13: [ OK ] FixedCapacityVectorTest.MoveAssignmentWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ElementAssignmentWorks 13: [ OK ] FixedCapacityVectorTest.ElementAssignmentWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.DataWorks 13: [ OK ] FixedCapacityVectorTest.DataWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ConstMethodsWork 13: [ OK ] FixedCapacityVectorTest.ConstMethodsWork (0 ms) 13: [----------] 18 tests from FixedCapacityVectorTest (0 ms total) 13: 13: [----------] 5 tests from InMemorySerializerTest 13: [ RUN ] InMemorySerializerTest.Roundtrip 13: [ OK ] InMemorySerializerTest.Roundtrip (0 ms) 13: [ RUN ] InMemorySerializerTest.RoundtripWithEndianessSwap 13: [ OK ] InMemorySerializerTest.RoundtripWithEndianessSwap (0 ms) 13: [ RUN ] InMemorySerializerTest.SerializerExplicitEndianessSwap 13: [ OK ] InMemorySerializerTest.SerializerExplicitEndianessSwap (0 ms) 13: [ RUN ] InMemorySerializerTest.DeserializerExplicitEndianessSwap 13: [ OK ] InMemorySerializerTest.DeserializerExplicitEndianessSwap (0 ms) 13: [ RUN ] InMemorySerializerTest.SizeIsCorrect 13: [ OK ] InMemorySerializerTest.SizeIsCorrect (0 ms) 13: [----------] 5 tests from InMemorySerializerTest (0 ms total) 13: 13: [----------] 4 tests from KeyValueTreeSerializerTest 13: [ RUN ] KeyValueTreeSerializerTest.EmptyTree 13: [ OK ] KeyValueTreeSerializerTest.EmptyTree (0 ms) 13: [ RUN ] KeyValueTreeSerializerTest.SimpleObject 13: [ OK ] KeyValueTreeSerializerTest.SimpleObject (0 ms) 13: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays 13: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (0 ms) 13: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects 13: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (0 ms) 13: [----------] 4 tests from KeyValueTreeSerializerTest (0 ms total) 13: 13: [----------] 7 tests from TreeValueTransformTest 13: [ RUN ] TreeValueTransformTest.SimpleTransforms 13: [ OK ] TreeValueTransformTest.SimpleTransforms (0 ms) 13: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive 13: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (0 ms) 13: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject 13: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (0 ms) 13: [ RUN ] TreeValueTransformTest.ObjectFromString 13: [ OK ] TreeValueTransformTest.ObjectFromString (0 ms) 13: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings 13: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (0 ms) 13: [ RUN ] TreeValueTransformTest.ScopedTransformRules 13: [ OK ] TreeValueTransformTest.ScopedTransformRules (0 ms) 13: [ RUN ] TreeValueTransformTest.CanAssignUserMultiValue 13: [ OK ] TreeValueTransformTest.CanAssignUserMultiValue (0 ms) 13: [----------] 7 tests from TreeValueTransformTest (1 ms total) 13: 13: [----------] 1 test from TreeValueTransformErrorTest 13: [ RUN ] TreeValueTransformErrorTest.ConversionError 13: [ OK ] TreeValueTransformErrorTest.ConversionError (0 ms) 13: [----------] 1 test from TreeValueTransformErrorTest (0 ms total) 13: 13: [----------] 9 tests from ListOfLists 13: [ RUN ] ListOfLists.EmptyListOfListsWorks 13: [ OK ] ListOfLists.EmptyListOfListsWorks (0 ms) 13: [ RUN ] ListOfLists.AppendWorks 13: [ OK ] ListOfLists.AppendWorks (0 ms) 13: [ RUN ] ListOfLists.EmptyListWorks 13: [ OK ] ListOfLists.EmptyListWorks (0 ms) 13: [ RUN ] ListOfLists.AppendAccessWorks 13: [ OK ] ListOfLists.AppendAccessWorks (0 ms) 13: [ RUN ] ListOfLists.ClearWorks 13: [ OK ] ListOfLists.ClearWorks (0 ms) 13: [ RUN ] ListOfLists.OutOfRangeAccessThrows 13: [ OK ] ListOfLists.OutOfRangeAccessThrows (0 ms) 13: [ RUN ] ListOfLists.FrontAndBackWork 13: [ OK ] ListOfLists.FrontAndBackWork (0 ms) 13: [ RUN ] ListOfLists.ExtractsAndRestores 13: [ OK ] ListOfLists.ExtractsAndRestores (0 ms) 13: [ RUN ] ListOfLists.AppendsListOfListsWithOffset 13: [ OK ] ListOfLists.AppendsListOfListsWithOffset (0 ms) 13: [----------] 9 tests from ListOfLists (0 ms total) 13: 13: [----------] 7 tests from LoggerTest 13: [ RUN ] LoggerTest.EmptyLoggerWorks 13: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms) 13: [ RUN ] LoggerTest.LogsToStream 13: [ OK ] LoggerTest.LogsToStream (0 ms) 13: [ RUN ] LoggerTest.LogsToFile 13: [ OK ] LoggerTest.LogsToFile (0 ms) 13: [ RUN ] LoggerTest.LevelFilteringWorks 13: [ OK ] LoggerTest.LevelFilteringWorks (0 ms) 13: [ RUN ] LoggerTest.LogsToMultipleStreams 13: [ OK ] LoggerTest.LogsToMultipleStreams (0 ms) 13: [ RUN ] LoggerTest.LogsToMultipleFiles 13: [ OK ] LoggerTest.LogsToMultipleFiles (0 ms) 13: [ RUN ] LoggerTest.LogsToStreamAndFile 13: [ OK ] LoggerTest.LogsToStreamAndFile (0 ms) 13: [----------] 7 tests from LoggerTest (1 ms total) 13: 13: [----------] 7 tests from MessageStringCollectorTest 13: [ RUN ] MessageStringCollectorTest.CanAddAndClearMessagesNoContext 13: [ OK ] MessageStringCollectorTest.CanAddAndClearMessagesNoContext (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanAddAndClearMessagesWithContext 13: [ OK ] MessageStringCollectorTest.CanAddAndClearMessagesWithContext (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanAddStringMessages 13: [ OK ] MessageStringCollectorTest.CanAddStringMessages (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanAddCharMessagesConditionally 13: [ OK ] MessageStringCollectorTest.CanAddCharMessagesConditionally (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanAddStringMessagesConditionally 13: [ OK ] MessageStringCollectorTest.CanAddStringMessagesConditionally (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanMoveConstruct 13: [ OK ] MessageStringCollectorTest.CanMoveConstruct (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanMoveAssign 13: [ OK ] MessageStringCollectorTest.CanMoveAssign (0 ms) 13: [----------] 7 tests from MessageStringCollectorTest (0 ms total) 13: 13: [----------] 1 test from PathTest 13: [ RUN ] PathTest.StripSourcePrefixWorks 13: [ OK ] PathTest.StripSourcePrefixWorks (0 ms) 13: [----------] 1 test from PathTest (0 ms total) 13: 13: [----------] 2 tests from PhysicalNodeCommunicatorTest 13: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 13: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms) 13: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 13: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) 13: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total) 13: 13: [----------] 5 tests from Range 13: [ RUN ] Range.EmptyRangeWorks 13: [ OK ] Range.EmptyRangeWorks (0 ms) 13: [ RUN ] Range.NonEmptyRangeWorks 13: [ OK ] Range.NonEmptyRangeWorks (0 ms) 13: [ RUN ] Range.BeginEnd 13: [ OK ] Range.BeginEnd (0 ms) 13: [ RUN ] Range.IsInRangeWorks 13: [ OK ] Range.IsInRangeWorks (0 ms) 13: [ RUN ] Range.IteratorWorks 13: [ OK ] Range.IteratorWorks (0 ms) 13: [----------] 5 tests from Range (0 ms total) 13: 13: [----------] 3 tests from ScopeGuardTest 13: [ RUN ] ScopeGuardTest.ScopeGuardExecutesCallbackOnExit 13: [ OK ] ScopeGuardTest.ScopeGuardExecutesCallbackOnExit (0 ms) 13: [ RUN ] ScopeGuardTest.ScopeGuardCanFreePointers 13: [ OK ] ScopeGuardTest.ScopeGuardCanFreePointers (0 ms) 13: [ RUN ] ScopeGuardTest.ScopeGuardsCanBeCreatedByHelperFunctions 13: [ OK ] ScopeGuardTest.ScopeGuardsCanBeCreatedByHelperFunctions (0 ms) 13: [----------] 3 tests from ScopeGuardTest (0 ms total) 13: 13: [----------] 7 tests from StringConvert 13: [ RUN ] StringConvert.NoResultFromEptyString 13: [ OK ] StringConvert.NoResultFromEptyString (0 ms) 13: [ RUN ] StringConvert.ThreeFloatsSuccessfully 13: [ OK ] StringConvert.ThreeFloatsSuccessfully (0 ms) 13: [ RUN ] StringConvert.OneIntSucessfully 13: [ OK ] StringConvert.OneIntSucessfully (0 ms) 13: [ RUN ] StringConvert.FloatAsStringToIntArrayThrows 13: [ OK ] StringConvert.FloatAsStringToIntArrayThrows (0 ms) 13: [ RUN ] StringConvert.ThrowsWhenWrongSize 13: [ OK ] StringConvert.ThrowsWhenWrongSize (0 ms) 13: [ RUN ] StringConvert.StringIdentityTransformWithArrayThrows 13: [ OK ] StringConvert.StringIdentityTransformWithArrayThrows (0 ms) 13: [ RUN ] StringConvert.StringIdentityTransformWithArrayOkay 13: [ OK ] StringConvert.StringIdentityTransformWithArrayOkay (0 ms) 13: [----------] 7 tests from StringConvert (0 ms total) 13: 13: [----------] 7 tests from StringToEnumValueConverterTest 13: [ RUN ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithoutStripping 13: [ OK ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithoutStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithoutStripping 13: [ OK ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithoutStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithoutStripping 13: [ OK ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithoutStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithStripping 13: [ OK ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithStripping 13: [ OK ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithStripping 13: [ OK ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.CustomConverterWorks 13: [ OK ] StringToEnumValueConverterTest.CustomConverterWorks (0 ms) 13: [----------] 7 tests from StringToEnumValueConverterTest (0 ms total) 13: 13: [----------] 9 tests from StringUtilityTest 13: [ RUN ] StringUtilityTest.StartsWith 13: [ OK ] StringUtilityTest.StartsWith (0 ms) 13: [ RUN ] StringUtilityTest.EndsWith 13: [ OK ] StringUtilityTest.EndsWith (0 ms) 13: [ RUN ] StringUtilityTest.StripSuffixIfPresent 13: [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms) 13: [ RUN ] StringUtilityTest.StripString 13: [ OK ] StringUtilityTest.StripString (0 ms) 13: [ RUN ] StringUtilityTest.SplitString 13: [ OK ] StringUtilityTest.SplitString (0 ms) 13: [ RUN ] StringUtilityTest.SplitDelimitedString 13: [ OK ] StringUtilityTest.SplitDelimitedString (0 ms) 13: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString 13: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (0 ms) 13: [ RUN ] StringUtilityTest.CanCompareCaseInsensitive 13: [ OK ] StringUtilityTest.CanCompareCaseInsensitive (0 ms) 13: [ RUN ] StringUtilityTest.CanCompareCaseInsensitiveInLength 13: [ OK ] StringUtilityTest.CanCompareCaseInsensitiveInLength (0 ms) 13: [----------] 9 tests from StringUtilityTest (0 ms total) 13: 13: [----------] 2 tests from FormatStringTest 13: [ RUN ] FormatStringTest.HandlesBasicFormatting 13: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms) 13: [ RUN ] FormatStringTest.HandlesLongStrings 13: [ OK ] FormatStringTest.HandlesLongStrings (0 ms) 13: [----------] 2 tests from FormatStringTest (0 ms total) 13: 13: [----------] 1 test from StringFormatterTest 13: [ RUN ] StringFormatterTest.HandlesBasicFormatting 13: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms) 13: [----------] 1 test from StringFormatterTest (0 ms total) 13: 13: [----------] 1 test from formatAndJoinTest 13: [ RUN ] formatAndJoinTest.Works 13: [ OK ] formatAndJoinTest.Works (0 ms) 13: [----------] 1 test from formatAndJoinTest (0 ms total) 13: 13: [----------] 1 test from JoinStringsTest 13: [ RUN ] JoinStringsTest.Works 13: [ OK ] JoinStringsTest.Works (0 ms) 13: [----------] 1 test from JoinStringsTest (0 ms total) 13: 13: [----------] 6 tests from ReplaceAllTest 13: [ RUN ] ReplaceAllTest.HandlesEmptyStrings 13: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms) 13: [ RUN ] ReplaceAllTest.HandlesNoMatches 13: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms) 13: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds 13: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms) 13: [ RUN ] ReplaceAllTest.HandlesMultipleMatches 13: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms) 13: [ RUN ] ReplaceAllTest.HandlesWordBoundaries 13: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms) 13: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches 13: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms) 13: [----------] 6 tests from ReplaceAllTest (0 ms total) 13: 13: [----------] 10 tests from TextLineWrapperTest 13: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings 13: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace 13: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines 13: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms) 13: [ RUN ] TextLineWrapperTest.WrapsCorrectly 13: [ OK ] TextLineWrapperTest.WrapsCorrectly (0 ms) 13: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks 13: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesIndent 13: [ OK ] TextLineWrapperTest.HandlesIndent (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines 13: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesHangingIndent 13: [ OK ] TextLineWrapperTest.HandlesHangingIndent (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter 13: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (0 ms) 13: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace 13: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (0 ms) 13: [----------] 10 tests from TextLineWrapperTest (0 ms total) 13: 13: [----------] 1 test from CompileTimeStringJoin 13: [ RUN ] CompileTimeStringJoin.Works 13: [ OK ] CompileTimeStringJoin.Works (0 ms) 13: [----------] 1 test from CompileTimeStringJoin (0 ms total) 13: 13: [----------] 3 tests from TemplateMPTest 13: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionEnum 13: [ OK ] TemplateMPTest.DispatchTemplatedFunctionEnum (0 ms) 13: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionBool 13: [ OK ] TemplateMPTest.DispatchTemplatedFunctionBool (0 ms) 13: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionEnumBool 13: [ OK ] TemplateMPTest.DispatchTemplatedFunctionEnumBool (0 ms) 13: [----------] 3 tests from TemplateMPTest (0 ms total) 13: 13: [----------] 6 tests from TextWriterTest 13: [ RUN ] TextWriterTest.WritesLines 13: [ OK ] TextWriterTest.WritesLines (0 ms) 13: [ RUN ] TextWriterTest.WritesLinesInParts 13: [ OK ] TextWriterTest.WritesLinesInParts (0 ms) 13: [ RUN ] TextWriterTest.WritesWrappedLines 13: [ OK ] TextWriterTest.WritesWrappedLines (0 ms) 13: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper 13: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (0 ms) 13: [ RUN ] TextWriterTest.TracksNewlines 13: [ OK ] TextWriterTest.TracksNewlines (0 ms) 13: [ RUN ] TextWriterTest.PreservesTrailingWhitespace 13: [ OK ] TextWriterTest.PreservesTrailingWhitespace (0 ms) 13: [----------] 6 tests from TextWriterTest (0 ms total) 13: 13: [----------] 1 test from TypeTraitsTest 13: [ RUN ] TypeTraitsTest.IsIntegralConstant 13: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms) 13: [----------] 1 test from TypeTraitsTest (0 ms total) 13: 13: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms) 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms) 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms) 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms) 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms) 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms) 13: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (0 ms total) 13: 13: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms) 13: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (0 ms total) 13: 13: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms) 13: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (0 ms total) 13: 13: [----------] 11 tests from WithInputPaths/PathSearchTest 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/0 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/0 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/1 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/1 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/2 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/2 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/3 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/3 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/4 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/4 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/5 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/5 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/6 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/6 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/7 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/7 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/8 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/8 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/9 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/9 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/10 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/10 (0 ms) 13: [----------] 11 tests from WithInputPaths/PathSearchTest (0 ms total) 13: 13: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (0 ms) 13: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (0 ms total) 13: 13: [----------] Global test environment tear-down 13: [==========] 420 tests from 65 test suites ran. (11 ms total) 13: [ PASSED ] 420 tests. 13: 13: YOU HAVE 1 DISABLED TEST 13: 13/90 Test #13: UtilityUnitTests .......................... Passed 0.05 sec test 14 Start 14: UtilityMpiUnitTests 14: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/utility-mpi-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/UtilityMpiUnitTests.xml" 14: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/utility/tests 14: Test timeout computed to be: 30 14: [==========] Running 2 tests from 1 test suite. 14: [----------] Global test environment set-up. 14: [----------] 2 tests from PhysicalNodeCommunicatorTest 14: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 14: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (3 ms) 14: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 14: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) 14: [----------] 2 tests from PhysicalNodeCommunicatorTest (4 ms total) 14: 14: [----------] Global test environment tear-down 14: [==========] 2 tests from 1 test suite ran. (4 ms total) 14: [ PASSED ] 2 tests. 14/90 Test #14: UtilityMpiUnitTests ....................... Passed 0.06 sec test 15 Start 15: GmxlibTests 15: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/nonbonded-fep-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/GmxlibTests.xml" 15: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxlib/nonbonded/tests 15: Test timeout computed to be: 30 15: [==========] Running 78 tests from 2 test suites. 15: [----------] Global test environment set-up. 15: [----------] 72 tests from NBInteraction/NonbondedFepTest 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/0 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/0 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/1 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/1 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/2 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/2 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/3 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/3 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/4 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/4 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/5 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/5 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/6 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/6 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/7 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/7 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/8 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/8 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/9 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/9 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/10 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/10 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/11 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/11 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/12 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/12 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/13 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/13 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/14 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/14 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/15 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/15 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/16 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/16 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/17 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/17 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/18 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/18 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/19 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/19 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/20 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/20 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/21 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/21 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/22 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/22 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/23 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/23 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/24 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/24 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/25 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/25 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/26 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/26 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/27 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/27 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/28 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/28 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/29 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/29 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/30 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/30 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/31 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/31 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/32 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/32 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/33 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/33 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/34 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/34 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/35 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/35 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/36 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/36 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/37 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/37 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/38 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/38 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/39 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/39 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/40 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/40 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/41 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/41 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/42 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/42 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/43 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/43 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/44 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/44 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/45 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/45 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/46 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/46 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/47 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/47 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/48 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/48 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/49 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/49 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/50 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/50 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/51 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/51 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/52 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/52 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/53 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/53 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/54 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/54 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/55 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/55 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/56 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/56 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/57 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/57 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/58 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/58 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/59 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/59 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/60 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/60 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/61 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/61 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/62 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/62 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/63 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/63 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/64 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/64 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/65 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/65 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/66 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/66 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/67 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/67 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/68 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/68 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/69 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/69 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/70 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/70 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/71 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/71 (0 ms) 15: [----------] 72 tests from NBInteraction/NonbondedFepTest (9 ms total) 15: 15: [----------] 6 tests from NBInteractionShortDistance/NonbondedFepTest 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/0 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/0 (0 ms) 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/1 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/1 (0 ms) 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/2 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/2 (0 ms) 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/3 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/3 (0 ms) 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/4 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/4 (0 ms) 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/5 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/5 (0 ms) 15: [----------] 6 tests from NBInteractionShortDistance/NonbondedFepTest (0 ms total) 15: 15: [----------] Global test environment tear-down 15: [==========] 78 tests from 2 test suites ran. (9 ms total) 15: [ PASSED ] 78 tests. 15/90 Test #15: GmxlibTests ............................... Passed 0.05 sec test 16 Start 16: MdlibUnitTest 16: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/mdlib-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/MdlibUnitTest.xml" 16: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests 16: Test timeout computed to be: 30 16: [==========] Running 1032 tests from 27 test suites. 16: [----------] Global test environment set-up. 16: [----------] 3 tests from EffectiveAtomDensity 16: [ RUN ] EffectiveAtomDensity.VolumeIndependence 16: [ OK ] EffectiveAtomDensity.VolumeIndependence (0 ms) 16: [ RUN ] EffectiveAtomDensity.WeightingWorks 16: [ OK ] EffectiveAtomDensity.WeightingWorks (0 ms) 16: [ RUN ] EffectiveAtomDensity.LargeValuesHandledWell 16: [ OK ] EffectiveAtomDensity.LargeValuesHandledWell (0 ms) 16: [----------] 3 tests from EffectiveAtomDensity (0 ms total) 16: 16: [----------] 2 tests from AtomNonbondedAndKineticProperties 16: [ RUN ] AtomNonbondedAndKineticProperties.IsAccurate 16: [ OK ] AtomNonbondedAndKineticProperties.IsAccurate (0 ms) 16: [ RUN ] AtomNonbondedAndKineticProperties.ConstraintsWork 16: [ OK ] AtomNonbondedAndKineticProperties.ConstraintsWork (0 ms) 16: [----------] 2 tests from AtomNonbondedAndKineticProperties (0 ms total) 16: 16: [----------] 1 test from VerletBufferConstraintTest 16: [ RUN ] VerletBufferConstraintTest.EqualMasses 16: [ OK ] VerletBufferConstraintTest.EqualMasses (0 ms) 16: [----------] 1 test from VerletBufferConstraintTest (0 ms total) 16: 16: [----------] 1 test from VerletBufferSize 16: [ RUN ] VerletBufferSize.SizeAboveFourIsEquivalent 16: [ OK ] VerletBufferSize.SizeAboveFourIsEquivalent (0 ms) 16: [----------] 1 test from VerletBufferSize (0 ms total) 16: 16: [----------] 6 tests from CalcvirTest 16: [ RUN ] CalcvirTest.CanCalculateVirialAllAtomsInBox 16: [ OK ] CalcvirTest.CanCalculateVirialAllAtomsInBox (0 ms) 16: [ RUN ] CalcvirTest.CanCalculateVirialAllAtomsInBoxScrew 16: [ OK ] CalcvirTest.CanCalculateVirialAllAtomsInBoxScrew (0 ms) 16: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewX 16: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewX (0 ms) 16: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewY 16: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewY (0 ms) 16: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewZ 16: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewZ (0 ms) 16: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewXYZ 16: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewXYZ (0 ms) 16: [----------] 6 tests from CalcvirTest (0 ms total) 16: 16: [----------] 2 tests from PrEbinTest 16: [ RUN ] PrEbinTest.HandlesAverages 16: [ OK ] PrEbinTest.HandlesAverages (0 ms) 16: [ RUN ] PrEbinTest.HandlesEmptyAverages 16: [ OK ] PrEbinTest.HandlesEmptyAverages (0 ms) 16: [----------] 2 tests from PrEbinTest (0 ms total) 16: 16: [----------] 3 tests from EnergyDriftTracker 16: [ RUN ] EnergyDriftTracker.emptyWorks 16: [ OK ] EnergyDriftTracker.emptyWorks (0 ms) 16: [ RUN ] EnergyDriftTracker.onePointWorks 16: [ OK ] EnergyDriftTracker.onePointWorks (0 ms) 16: [ RUN ] EnergyDriftTracker.manyPointsWorks 16: [ OK ] EnergyDriftTracker.manyPointsWorks (0 ms) 16: [----------] 3 tests from EnergyDriftTracker (0 ms total) 16: 16: [----------] 4 tests from ShakeTest 16: [ RUN ] ShakeTest.ConstrainsOneBond 16: [ OK ] ShakeTest.ConstrainsOneBond (0 ms) 16: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds 16: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms) 16: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom 16: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (0 ms) 16: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms 16: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms) 16: [----------] 4 tests from ShakeTest (0 ms total) 16: 16: [----------] 1 test from NullSignalTest 16: [ RUN ] NullSignalTest.NullSignallerWorks 16: [ OK ] NullSignalTest.NullSignallerWorks (0 ms) 16: [----------] 1 test from NullSignalTest (0 ms total) 16: 16: [----------] 7 tests from SignalTest 16: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace 16: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms) 16: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace 16: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms) 16: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace 16: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms) 16: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace 16: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms) 16: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace 16: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms) 16: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace 16: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms) 16: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace 16: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms) 16: [----------] 7 tests from SignalTest (0 ms total) 16: 16: [----------] 13 tests from UpdateGroupsTest 16: [ RUN ] UpdateGroupsTest.WithEthaneUA 16: [ OK ] UpdateGroupsTest.WithEthaneUA (0 ms) 16: [ RUN ] UpdateGroupsTest.WithMethane 16: [ OK ] UpdateGroupsTest.WithMethane (0 ms) 16: [ RUN ] UpdateGroupsTest.WithEthane 16: [ OK ] UpdateGroupsTest.WithEthane (0 ms) 16: [ RUN ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithEthane 16: [ OK ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithEthane (0 ms) 16: [ RUN ] UpdateGroupsTest.WithButaneUALogsThatUnsuitableForUpdateGroups 16: [ OK ] UpdateGroupsTest.WithButaneUALogsThatUnsuitableForUpdateGroups (0 ms) 16: [ RUN ] UpdateGroupsTest.WithWaterThreeSite 16: [ OK ] UpdateGroupsTest.WithWaterThreeSite (0 ms) 16: [ RUN ] UpdateGroupsTest.WithWaterFourSite 16: [ OK ] UpdateGroupsTest.WithWaterFourSite (0 ms) 16: [ RUN ] UpdateGroupsTest.WithFourAtomsWithSettle 16: [ OK ] UpdateGroupsTest.WithFourAtomsWithSettle (0 ms) 16: [ RUN ] UpdateGroupsTest.WithWaterFlexAngle 16: [ OK ] UpdateGroupsTest.WithWaterFlexAngle (0 ms) 16: [ RUN ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithWaterFlexAngle 16: [ OK ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithWaterFlexAngle (0 ms) 16: [ RUN ] UpdateGroupsTest.WithTwoMoltypes 16: [ OK ] UpdateGroupsTest.WithTwoMoltypes (0 ms) 16: [ RUN ] UpdateGroupsTest.LogsWhenSizesAreInvalid 16: [ OK ] UpdateGroupsTest.LogsWhenSizesAreInvalid (0 ms) 16: [ RUN ] UpdateGroupsTest.LogsWhenUpdateGroupsAreNotUseful 16: [ OK ] UpdateGroupsTest.LogsWhenUpdateGroupsAreNotUseful (0 ms) 16: [----------] 13 tests from UpdateGroupsTest (0 ms total) 16: 16: [----------] 1 test from UpdateGroupsCog 16: [ RUN ] UpdateGroupsCog.ComputesCogs 16: [ OK ] UpdateGroupsCog.ComputesCogs (0 ms) 16: [----------] 1 test from UpdateGroupsCog (0 ms total) 16: 16: [----------] 2 tests from WholeMoleculeTransform 16: [ RUN ] WholeMoleculeTransform.MakesMoleculesWhole 16: [ OK ] WholeMoleculeTransform.MakesMoleculesWhole (0 ms) 16: [ RUN ] WholeMoleculeTransform.HandlesReordering 16: [ OK ] WholeMoleculeTransform.HandlesReordering (0 ms) 16: [----------] 2 tests from WholeMoleculeTransform (0 ms total) 16: 16: [----------] 28 tests from WithParameters/ConstraintsTest 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/0 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/0 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/1 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/1 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/2 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/2 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/3 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/3 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/4 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/4 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/5 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/5 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/6 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/6 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/7 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/7 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/8 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/8 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/9 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/9 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/10 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/10 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/11 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/11 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/12 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/12 (8 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/13 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/13 (8 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/0 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/0 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/1 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/1 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/2 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/2 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/3 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/3 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/4 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/4 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/5 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/5 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/6 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/6 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/7 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/7 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/8 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/8 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/9 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/9 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/10 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/10 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/11 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/11 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/12 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/12 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/13 16: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/13 (0 ms) 16: [----------] 28 tests from WithParameters/ConstraintsTest (21 ms total) 16: 16: [----------] 11 tests from WithParameters/EnergyOutputTest 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/0 16: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_0.edr as double precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/0 (75 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/1 16: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_1.edr as double precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/1 (6 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/2 16: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_2.edr as double precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/2 (1 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/3 16: [ OK ] WithParameters/EnergyOutputTest.CheckOutput/3 (0 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/4 16: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_4.edr as double precision energy file 16: Reading energy frame 0 time 10.100 Reading energy frame 1 time 27.500 Reading energy frame 2 time 44.900 Reading energy frame 3 time 62.300 Reading energy frame 4 time 79.700 Reading energy frame 5 time 97.100 Reading energy frame 6 time 114.500 Reading energy frame 7 time 131.900 Reading energy frame 8 time 149.300 Reading energy frame 9 time 166.700 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/4 (7 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/5 16: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_5.edr as double precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/5 (1 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/6 16: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_6.edr as double precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/6 (1 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/7 16: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_7.edr as double precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/7 (1 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/8 16: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_8.edr as double precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/8 (1 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/9 16: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_9.edr as double precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/9 (1 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/10 16: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_10.edr as double precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/10 (1 ms) 16: [----------] 11 tests from WithParameters/EnergyOutputTest (100 ms total) 16: 16: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 (0 ms) 16: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple (0 ms total) 16: 16: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 (0 ms) 16: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression (0 ms total) 16: 16: [----------] 23 tests from WithParameters/FreeEnergyParameterTest 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22 (0 ms) 16: [----------] 23 tests from WithParameters/FreeEnergyParameterTest (0 ms total) 16: 16: [----------] 17 tests from WithParameters/LangevinTest 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/0 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/0 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/1 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/1 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/2 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/2 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/3 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/3 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/4 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/4 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/5 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/5 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/6 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/6 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/7 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/7 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/8 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/8 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/9 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/9 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/10 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/10 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/11 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/11 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/12 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/12 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/13 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/13 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/14 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/14 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/15 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/15 (0 ms) 16: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/16 16: [ OK ] WithParameters/LangevinTest.SimpleIntegration/16 (0 ms) 16: [----------] 17 tests from WithParameters/LangevinTest (2 ms total) 16: 16: [----------] 16 tests from WithParameters/LeapFrogTest 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/0 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/0 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/1 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/1 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/2 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/2 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/3 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/3 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/4 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/4 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/5 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/5 (1 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/6 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/6 (4 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/7 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/7 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/8 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/8 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/9 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/9 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/10 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/10 (1 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/11 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/11 (1 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/12 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/12 (1 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/13 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/13 (1 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/14 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/14 (1 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/15 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/15 (1 ms) 16: [----------] 16 tests from WithParameters/LeapFrogTest (16 ms total) 16: 16: [----------] 140 tests from Cubic/ParrRahmTest 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from Cubic/ParrRahmTest (8 ms total) 16: 16: [----------] 140 tests from Rectilinear/ParrRahmTest 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from Rectilinear/ParrRahmTest (8 ms total) 16: 16: [----------] 140 tests from RhombDodecXYSquare/ParrRahmTest 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from RhombDodecXYSquare/ParrRahmTest (8 ms total) 16: 16: [----------] 140 tests from RhombDodecXYHex/ParrRahmTest 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from RhombDodecXYHex/ParrRahmTest (8 ms total) 16: 16: [----------] 140 tests from TruncOct/ParrRahmTest 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from TruncOct/ParrRahmTest (8 ms total) 16: 16: [----------] 140 tests from Other/ParrRahmTest 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from Other/ParrRahmTest (7 ms total) 16: 16: [----------] 13 tests from WithParameters/SettleTest 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (0 ms) 16: [----------] 13 tests from WithParameters/SettleTest (6 ms total) 16: 16: [----------] Global test environment tear-down 16: [==========] 1032 tests from 27 test suites ran. (201 ms total) 16: [ PASSED ] 1032 tests. 16/90 Test #16: MdlibUnitTest ............................. Passed 0.50 sec test 17 Start 17: AwhTest 17: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/awh-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/AwhTest.xml" 17: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/awh/tests 17: Test timeout computed to be: 30 17: [==========] Running 27 tests from 10 test suites. 17: [----------] Global test environment set-up. 17: [----------] 3 tests from SerializationTest 17: [ RUN ] SerializationTest.CanSerializeDimParams 17: [ OK ] SerializationTest.CanSerializeDimParams (0 ms) 17: [ RUN ] SerializationTest.CanSerializeBiasParams 17: [ OK ] SerializationTest.CanSerializeBiasParams (0 ms) 17: [ RUN ] SerializationTest.CanSerializeAwhParams 17: [ OK ] SerializationTest.CanSerializeAwhParams (0 ms) 17: [----------] 3 tests from SerializationTest (0 ms total) 17: 17: [----------] 1 test from BiasTest 17: [ RUN ] BiasTest.DetectsCovering 17: [ OK ] BiasTest.DetectsCovering (1 ms) 17: [----------] 1 test from BiasTest (1 ms total) 17: 17: [----------] 1 test from biasGridTest 17: [ RUN ] biasGridTest.neighborhood 17: [ OK ] biasGridTest.neighborhood (1 ms) 17: [----------] 1 test from biasGridTest (1 ms total) 17: 17: [----------] 2 tests from BiasSharingTest 17: [ RUN ] BiasSharingTest.SharingWorks 17: [ OK ] BiasSharingTest.SharingWorks (4 ms) 17: [ RUN ] BiasSharingTest.SharingScalingByMetricWorks 17: [ OK ] BiasSharingTest.SharingScalingByMetricWorks (4 ms) 17: [----------] 2 tests from BiasSharingTest (8 ms total) 17: 17: [----------] 2 tests from BiasFepLambdaStateTest 17: [ RUN ] BiasFepLambdaStateTest.DetectsCovering 17: [ OK ] BiasFepLambdaStateTest.DetectsCovering (3 ms) 17: [ RUN ] BiasFepLambdaStateTest.DetectsLargeNegativeForeignEnergy 17: [ OK ] BiasFepLambdaStateTest.DetectsLargeNegativeForeignEnergy (0 ms) 17: [----------] 2 tests from BiasFepLambdaStateTest (3 ms total) 17: 17: [----------] 8 tests from WithParameters/BiasTest 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/0 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/0 (0 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/1 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/1 (0 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/2 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/2 (0 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/3 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/3 (0 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/4 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/4 (0 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/5 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/5 (0 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/6 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/6 (0 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/7 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/7 (0 ms) 17: [----------] 8 tests from WithParameters/BiasTest (4 ms total) 17: 17: [----------] 2 tests from WithParameters/BiasStateTest 17: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0 17: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (0 ms) 17: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1 17: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (0 ms) 17: [----------] 2 tests from WithParameters/BiasStateTest (0 ms total) 17: 17: [----------] 1 test from WithParameters/UserInputTest 17: [ RUN ] WithParameters/UserInputTest.ParsesUser3DInput/0 17: [ OK ] WithParameters/UserInputTest.ParsesUser3DInput/0 (0 ms) 17: [----------] 1 test from WithParameters/UserInputTest (0 ms total) 17: 17: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest 17: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 17: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 (6 ms) 17: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 17: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 (6 ms) 17: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 17: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 (6 ms) 17: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 17: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 (6 ms) 17: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest (28 ms total) 17: 17: [----------] 3 tests from WithParameters/FrictionMetricTest 17: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/0 17: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/0 (0 ms) 17: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/1 17: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/1 (0 ms) 17: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/2 17: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/2 (21 ms) 17: [----------] 3 tests from WithParameters/FrictionMetricTest (24 ms total) 17: 17: [----------] Global test environment tear-down 17: [==========] 27 tests from 10 test suites ran. (73 ms total) 17: [ PASSED ] 27 tests. 17/90 Test #17: AwhTest ................................... Passed 0.10 sec test 18 Start 18: DensityFittingAppliedForcesUnitTest 18: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/density_fitting_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/DensityFittingAppliedForcesUnitTest.xml" 18: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests 18: Test timeout computed to be: 30 18: [==========] Running 18 tests from 4 test suites. 18: [----------] Global test environment set-up. 18: [----------] 2 tests from DensityFittingTest 18: [ RUN ] DensityFittingTest.ForceProviderLackingInputThrows 18: [ OK ] DensityFittingTest.ForceProviderLackingInputThrows (0 ms) 18: [ RUN ] DensityFittingTest.SingleAtom 18: [ OK ] DensityFittingTest.SingleAtom (0 ms) 18: [----------] 2 tests from DensityFittingTest (1 ms total) 18: 18: [----------] 7 tests from DensityFittingAmplitudeLookupTest 18: [ RUN ] DensityFittingAmplitudeLookupTest.Unity 18: [ OK ] DensityFittingAmplitudeLookupTest.Unity (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.Charge 18: [ OK ] DensityFittingAmplitudeLookupTest.Charge (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.Masses 18: [ OK ] DensityFittingAmplitudeLookupTest.Masses (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyAssign 18: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyAssign (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyConstruct 18: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyConstruct (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveAssign 18: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveAssign (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveConstruct 18: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveConstruct (0 ms) 18: [----------] 7 tests from DensityFittingAmplitudeLookupTest (0 ms total) 18: 18: [----------] 1 test from DensityFittingForceProviderState 18: [ RUN ] DensityFittingForceProviderState.RoundTripSaving 18: [ OK ] DensityFittingForceProviderState.RoundTripSaving (0 ms) 18: [----------] 1 test from DensityFittingForceProviderState (0 ms total) 18: 18: [----------] 8 tests from DensityFittingOptionsTest 18: [ RUN ] DensityFittingOptionsTest.DefaultParameters 18: [ OK ] DensityFittingOptionsTest.DefaultParameters (0 ms) 18: [ RUN ] DensityFittingOptionsTest.OptionSetsActive 18: [ OK ] DensityFittingOptionsTest.OptionSetsActive (0 ms) 18: [ RUN ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive 18: [ OK ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 18: [ RUN ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive 18: [ OK ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive (0 ms) 18: [ RUN ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup 18: [ OK ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) 18: [ RUN ] DensityFittingOptionsTest.InternalsToKvt 18: [ OK ] DensityFittingOptionsTest.InternalsToKvt (0 ms) 18: [ RUN ] DensityFittingOptionsTest.KvtToInternal 18: [ OK ] DensityFittingOptionsTest.KvtToInternal (0 ms) 18: [ RUN ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent 18: [ OK ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent (0 ms) 18: [----------] 8 tests from DensityFittingOptionsTest (0 ms total) 18: 18: [----------] Global test environment tear-down 18: [==========] 18 tests from 4 test suites ran. (2 ms total) 18: [ PASSED ] 18 tests. 18/90 Test #18: DensityFittingAppliedForcesUnitTest ....... Passed 0.03 sec test 19 Start 19: QMMMAppliedForcesUnitTest 19: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/qmmm_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/QMMMAppliedForcesUnitTest.xml" 19: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests 19: Test timeout computed to be: 30 19: [==========] Running 21 tests from 5 test suites. 19: [----------] Global test environment set-up. 19: [----------] 3 tests from QMMMInputGeneratorTest 19: [ RUN ] QMMMInputGeneratorTest.CanConstruct 19: [ OK ] QMMMInputGeneratorTest.CanConstruct (0 ms) 19: [ RUN ] QMMMInputGeneratorTest.TwoWatersPBENoLink 19: [ OK ] QMMMInputGeneratorTest.TwoWatersPBENoLink (0 ms) 19: [ RUN ] QMMMInputGeneratorTest.TwoWatersPBEWithLink 19: [ OK ] QMMMInputGeneratorTest.TwoWatersPBEWithLink (0 ms) 19: [----------] 3 tests from QMMMInputGeneratorTest (0 ms total) 19: 19: [----------] 7 tests from QMMMTopologyPreprocessorTest 19: [ RUN ] QMMMTopologyPreprocessorTest.CanConstruct 19: [ OK ] QMMMTopologyPreprocessorTest.CanConstruct (0 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Generating 1-4 interactions: fudge = 0.5 19: Number of degrees of freedom in T-Coupling group rest is 21.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 19: NVE simulation with an initial temperature of zero: will use a Verlet 19: buffer of 10%. Check your energy drift! 19: 19: 19: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 3 NOTEs 19: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 19: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 19: Setting the LD random seed to -285231157 19: 19: Generated 10 of the 10 non-bonded parameter combinations 19: 19: Generated 10 of the 10 1-4 parameter combinations 19: 19: Excluding 2 bonded neighbours molecule type 'SOL' 19: 19: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 19: Analysing residue names: 19: There are: 4 Water residues 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink (8 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Generating 1-4 interactions: fudge = 0.5 19: Number of degrees of freedom in T-Coupling group rest is 21.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 19: NVE simulation with an initial temperature of zero: will use a Verlet 19: buffer of 10%. Check your energy drift! 19: 19: 19: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 3 NOTEs 19: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 19: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 19: Setting the LD random seed to -70681195 19: 19: Generated 10 of the 10 non-bonded parameter combinations 19: 19: Generated 10 of the 10 1-4 parameter combinations 19: 19: Excluding 2 bonded neighbours molecule type 'SOL' 19: 19: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 19: Analysing residue names: 19: There are: 4 Water residues 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink (6 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Generating 1-4 interactions: fudge = 0.5 19: Number of degrees of freedom in T-Coupling group rest is 21.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 19: NVE simulation with an initial temperature of zero: will use a Verlet 19: buffer of 10%. Check your energy drift! 19: 19: 19: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 3 NOTEs 19: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 19: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 19: Setting the LD random seed to -1821460675 19: 19: Generated 10 of the 10 non-bonded parameter combinations 19: 19: Generated 10 of the 10 1-4 parameter combinations 19: 19: Excluding 2 bonded neighbours molecule type 'SOL' 19: 19: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 19: Analysing residue names: 19: There are: 4 Water residues 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink (7 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksNoConstraints 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Generating 1-4 interactions: fudge = 0.5 19: Number of degrees of freedom in T-Coupling group rest is 63.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 19: NVE simulation: will use the initial temperature of 129.093 K for 19: determining the Verlet buffer size 19: 19: 19: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 3 NOTEs 19: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 19: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 19: Setting the LD random seed to -1611074822 19: 19: Generated 2145 of the 2145 non-bonded parameter combinations 19: 19: Generated 2145 of the 2145 1-4 parameter combinations 19: 19: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 19: 19: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 19: Analysing residue names: 19: There are: 3 Protein residues 19: Analysing Protein... 19: 19: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 129.093 K 19: 19: Calculated rlist for 1x1 atom pair-list as 1.021 nm, buffer size 0.021 nm 19: 19: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm 19: 19: Note that mdrun will redetermine rlist based on the actual pair-list setup 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksNoConstraints (22 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksWithConstraints 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Generating 1-4 interactions: fudge = 0.5 19: 19: NOTE 2 [file unknown]: 19: You are using constraints on all bonds, whereas the forcefield has been 19: parametrized only with constraints involving hydrogen atoms. We suggest 19: using constraints = h-bonds instead, this will also improve performance. 19: 19: 19: NOTE 3 [file unknown]: 19: For energy conservation with LINCS, lincs_iter should be 2 or larger. 19: 19: 19: Number of degrees of freedom in T-Coupling group rest is 42.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 19: NVE simulation: will use the initial temperature of 193.640 K for 19: determining the Verlet buffer size 19: 19: 19: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 5 NOTEs 19: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 19: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 19: Setting the LD random seed to -1596229652 19: 19: Generated 2145 of the 2145 non-bonded parameter combinations 19: 19: Generated 2145 of the 2145 1-4 parameter combinations 19: 19: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 19: 19: turning all bonds into constraints... 19: 19: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 19: Analysing residue names: 19: There are: 3 Protein residues 19: Analysing Protein... 19: 19: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 193.64 K 19: 19: Calculated rlist for 1x1 atom pair-list as 1.023 nm, buffer size 0.023 nm 19: 19: Set rlist, assuming 4x4 atom pair-list, to 1.015 nm, buffer size 0.015 nm 19: 19: Note that mdrun will redetermine rlist based on the actual pair-list setup 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksWithConstraints (21 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.RemovingQMVsites 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Number of degrees of freedom in T-Coupling group rest is 45.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 19: NVE simulation with an initial temperature of zero: will use a Verlet 19: buffer of 10%. Check your energy drift! 19: 19: 19: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 3 NOTEs 19: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 19: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 19: Setting the LD random seed to -1104675131 19: 19: Generated 3 of the 6 non-bonded parameter combinations 19: 19: Excluding 3 bonded neighbours molecule type 'VSTEST' 19: 19: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 19: 19: Cleaning up constraints and constant bonded interactions with virtual sites 19: Analysing residue names: 19: There are: 1 Other residues 19: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.RemovingQMVsites (15 ms) 19: [----------] 7 tests from QMMMTopologyPreprocessorTest (82 ms total) 19: 19: [----------] 9 tests from QMMMOptionsTest 19: [ RUN ] QMMMOptionsTest.DefaultParameters 19: [ OK ] QMMMOptionsTest.DefaultParameters (0 ms) 19: [ RUN ] QMMMOptionsTest.OptionSetsActive 19: [ OK ] QMMMOptionsTest.OptionSetsActive (0 ms) 19: [ RUN ] QMMMOptionsTest.OutputNoDefaultValuesWhenInactive 19: [ OK ] QMMMOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 19: [ RUN ] QMMMOptionsTest.OutputDefaultValuesWhenActive 19: [ OK ] QMMMOptionsTest.OutputDefaultValuesWhenActive (0 ms) 19: [ RUN ] QMMMOptionsTest.CanConvertGroupStringToIndexGroup 19: [ OK ] QMMMOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) 19: [ RUN ] QMMMOptionsTest.NoQMGroupConvertGroupStringToIndexGroup 19: [ OK ] QMMMOptionsTest.NoQMGroupConvertGroupStringToIndexGroup (0 ms) 19: [ RUN ] QMMMOptionsTest.EmptyQMGroupConvertGroupStringToIndexGroup 19: [ OK ] QMMMOptionsTest.EmptyQMGroupConvertGroupStringToIndexGroup (0 ms) 19: [ RUN ] QMMMOptionsTest.InternalsToKvtAndBack 19: [ OK ] QMMMOptionsTest.InternalsToKvtAndBack (0 ms) 19: [ RUN ] QMMMOptionsTest.CP2KInputProcessing 19: [ OK ] QMMMOptionsTest.CP2KInputProcessing (0 ms) 19: [----------] 9 tests from QMMMOptionsTest (1 ms total) 19: 19: [----------] 1 test from QMMMForceProviderTest 19: [ RUN ] QMMMForceProviderTest.CanConstructOrNot 19: [ OK ] QMMMForceProviderTest.CanConstructOrNot (0 ms) 19: [----------] 1 test from QMMMForceProviderTest (0 ms total) 19: 19: [----------] 1 test from QMMMTest 19: [ RUN ] QMMMTest.ForceProviderLackingInputThrows 19: [ OK ] QMMMTest.ForceProviderLackingInputThrows (0 ms) 19: [----------] 1 test from QMMMTest (0 ms total) 19: 19: [----------] Global test environment tear-down 19: [==========] 21 tests from 5 test suites ran. (85 ms total) 19: [ PASSED ] 21 tests. 19/90 Test #19: QMMMAppliedForcesUnitTest ................. Passed 0.11 sec test 20 Start 20: ColvarsAppliedForcesUnitTest 20: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/colvars_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/ColvarsAppliedForcesUnitTest.xml" 20: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests 20: Test timeout computed to be: 30 20: [==========] Running 16 tests from 4 test suites. 20: [----------] Global test environment set-up. 20: [----------] 1 test from ColvarsTest 20: [ RUN ] ColvarsTest.ForceProviderLackingInputThrows 20: [ OK ] ColvarsTest.ForceProviderLackingInputThrows (0 ms) 20: [----------] 1 test from ColvarsTest (0 ms total) 20: 20: [----------] 6 tests from ColvarsOptionsTest 20: [ RUN ] ColvarsOptionsTest.OutputNoDefaultValuesWhenInactive 20: [ OK ] ColvarsOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 20: [ RUN ] ColvarsOptionsTest.OutputDefaultValuesWhenActive 20: [ OK ] ColvarsOptionsTest.OutputDefaultValuesWhenActive (0 ms) 20: [ RUN ] ColvarsOptionsTest.OutputValuesWhenActive 20: [ OK ] ColvarsOptionsTest.OutputValuesWhenActive (0 ms) 20: [ RUN ] ColvarsOptionsTest.OptionSetsActive 20: [ OK ] ColvarsOptionsTest.OptionSetsActive (0 ms) 20: [ RUN ] ColvarsOptionsTest.InternalsToKvtAndBack 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 20: Setting the LD random seed to -16777474 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsOptionsTest.InternalsToKvtAndBack (10 ms) 20: [ RUN ] ColvarsOptionsTest.RetrieveEdrFilename 20: [ OK ] ColvarsOptionsTest.RetrieveEdrFilename (0 ms) 20: [----------] 6 tests from ColvarsOptionsTest (11 ms total) 20: 20: [----------] 4 tests from ColvarsPreProcessorTest 20: [ RUN ] ColvarsPreProcessorTest.CanConstructColvarsPreProcess 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 20: Setting the LD random seed to -1746212867 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsPreProcessorTest.CanConstructColvarsPreProcess (6 ms) 20: [ RUN ] ColvarsPreProcessorTest.CheckValuesFourWaters 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 20: Setting the LD random seed to -28835905 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsPreProcessorTest.CheckValuesFourWaters (8 ms) 20: [ RUN ] ColvarsPreProcessorTest.CheckNestedInputFiles 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 20: Setting the LD random seed to -268439553 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsPreProcessorTest.CheckNestedInputFiles (8 ms) 20: [ RUN ] ColvarsPreProcessorTest.WrongColvarsInput 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 20: Setting the LD random seed to -812673285 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsPreProcessorTest.WrongColvarsInput (8 ms) 20: [----------] 4 tests from ColvarsPreProcessorTest (33 ms total) 20: 20: [----------] 5 tests from ColvarsForceProviderTest 20: [ RUN ] ColvarsForceProviderTest.CanConstructOrNot 20: [ OK ] ColvarsForceProviderTest.CanConstructOrNot (0 ms) 20: [ RUN ] ColvarsForceProviderTest.SimpleInputs 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 20: Setting the LD random seed to -408002561 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsForceProviderTest.SimpleInputs (9 ms) 20: [ RUN ] ColvarsForceProviderTest.WrongColvarsInput 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 20: Setting the LD random seed to -10527489 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsForceProviderTest.WrongColvarsInput (9 ms) 20: [ RUN ] ColvarsForceProviderTest.CalculateForces4water 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 20: Setting the LD random seed to -108053 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsForceProviderTest.CalculateForces4water (74 ms) 20: [ RUN ] ColvarsForceProviderTest.CalculateForcesAlanine 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 66.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 20: NVE simulation: will use the initial temperature of 300.368 K for 20: determining the Verlet buffer size 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 20: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 20: Setting the LD random seed to -1630870329 20: 20: Generated 2211 of the 2211 non-bonded parameter combinations 20: 20: Generated 2211 of the 2211 1-4 parameter combinations 20: 20: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 20: 20: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 20: Analysing residue names: 20: There are: 2 Protein residues 20: Analysing Protein... 20: 20: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 20: 20: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 20: 20: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 20: 20: Note that mdrun will redetermine rlist based on the actual pair-list setup 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsForceProviderTest.CalculateForcesAlanine (79 ms) 20: [----------] 5 tests from ColvarsForceProviderTest (174 ms total) 20: 20: [----------] Global test environment tear-down 20: [==========] 16 tests from 4 test suites ran. (219 ms total) 20: [ PASSED ] 16 tests. 20/90 Test #20: ColvarsAppliedForcesUnitTest .............. Passed 0.26 sec test 21 Start 21: NNPotAppliedForcesUnitTest 21: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/nnpot_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/NNPotAppliedForcesUnitTest.xml" 21: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/nnpot/tests 21: Test timeout computed to be: 30 21: [==========] Running 12 tests from 4 test suites. 21: [----------] Global test environment set-up. 21: [----------] 1 test from NNPotTest 21: [ RUN ] NNPotTest.ForceProviderLackingInputThrows 21: [ OK ] NNPotTest.ForceProviderLackingInputThrows (0 ms) 21: [----------] 1 test from NNPotTest (0 ms total) 21: 21: [----------] 5 tests from NNPotOptionsTest 21: [ RUN ] NNPotOptionsTest.DefaultParameters 21: [ OK ] NNPotOptionsTest.DefaultParameters (0 ms) 21: [ RUN ] NNPotOptionsTest.OptionSetsActive 21: [ OK ] NNPotOptionsTest.OptionSetsActive (0 ms) 21: [ RUN ] NNPotOptionsTest.OutputNoDefaultValuesWhenInactive 21: [ OK ] NNPotOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 21: [ RUN ] NNPotOptionsTest.OutputDefaultValuesWhenActive 21: [ OK ] NNPotOptionsTest.OutputDefaultValuesWhenActive (0 ms) 21: [ RUN ] NNPotOptionsTest.InternalsToKvtAndBack 21: [ OK ] NNPotOptionsTest.InternalsToKvtAndBack (0 ms) 21: [----------] 5 tests from NNPotOptionsTest (0 ms total) 21: 21: [----------] 5 tests from NNPotTopologyPreprocessorTest 21: [ RUN ] NNPotTopologyPreprocessorTest.CanConstruct 21: [ OK ] NNPotTopologyPreprocessorTest.CanConstruct (0 ms) 21: [ RUN ] NNPotTopologyPreprocessorTest.FourWatersFirstInQMRegion 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Generating 1-4 interactions: fudge = 0.5 21: Number of degrees of freedom in T-Coupling group rest is 21.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.mdp]: 21: NVE simulation with an initial temperature of zero: will use a Verlet 21: buffer of 10%. Check your energy drift! 21: 21: 21: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.mdp]: 21: You are using a plain Coulomb cut-off, which might produce artifacts. 21: You might want to consider using PME electrostatics. 21: 21: 21: 21: There were 3 NOTEs 21: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 21: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 21: Setting the LD random seed to -1233127682 21: 21: Generated 10 of the 10 non-bonded parameter combinations 21: 21: Generated 10 of the 10 1-4 parameter combinations 21: 21: Excluding 2 bonded neighbours molecule type 'SOL' 21: 21: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 21: Analysing residue names: 21: There are: 4 Water residues 21: 21: This run will generate roughly 0 Mb of data 21: [ OK ] NNPotTopologyPreprocessorTest.FourWatersFirstInQMRegion (5 ms) 21: [ RUN ] NNPotTopologyPreprocessorTest.FourWatersSecondAndFourthInQMRegion 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Generating 1-4 interactions: fudge = 0.5 21: Number of degrees of freedom in T-Coupling group rest is 21.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.mdp]: 21: NVE simulation with an initial temperature of zero: will use a Verlet 21: buffer of 10%. Check your energy drift! 21: 21: 21: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.mdp]: 21: You are using a plain Coulomb cut-off, which might produce artifacts. 21: You might want to consider using PME electrostatics. 21: 21: 21: 21: There were 3 NOTEs 21: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 21: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 21: Setting the LD random seed to 1878904747 21: 21: Generated 10 of the 10 non-bonded parameter combinations 21: 21: Generated 10 of the 10 1-4 parameter combinations 21: 21: Excluding 2 bonded neighbours molecule type 'SOL' 21: 21: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 21: Analysing residue names: 21: There are: 4 Water residues 21: 21: This run will generate roughly 0 Mb of data 21: [ OK ] NNPotTopologyPreprocessorTest.FourWatersSecondAndFourthInQMRegion (125 ms) 21: [ RUN ] NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsNoConstraints 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Generating 1-4 interactions: fudge = 0.5 21: Number of degrees of freedom in T-Coupling group rest is 63.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.mdp]: 21: NVE simulation: will use the initial temperature of 129.093 K for 21: determining the Verlet buffer size 21: 21: 21: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.mdp]: 21: You are using a plain Coulomb cut-off, which might produce artifacts. 21: You might want to consider using PME electrostatics. 21: 21: 21: 21: There were 3 NOTEs 21: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 21: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 21: Setting the LD random seed to 805303263 21: 21: Generated 2145 of the 2145 non-bonded parameter combinations 21: 21: Generated 2145 of the 2145 1-4 parameter combinations 21: 21: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 21: 21: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 21: Analysing residue names: 21: There are: 3 Protein residues 21: Analysing Protein... 21: 21: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 129.093 K 21: 21: Calculated rlist for 1x1 atom pair-list as 1.021 nm, buffer size 0.021 nm 21: 21: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm 21: 21: Note that mdrun will redetermine rlist based on the actual pair-list setup 21: 21: This run will generate roughly 0 Mb of data 21: [ OK ] NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsNoConstraints (20 ms) 21: [ RUN ] NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsWithConstraints 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Generating 1-4 interactions: fudge = 0.5 21: 21: NOTE 2 [file unknown]: 21: You are using constraints on all bonds, whereas the forcefield has been 21: parametrized only with constraints involving hydrogen atoms. We suggest 21: using constraints = h-bonds instead, this will also improve performance. 21: 21: 21: NOTE 3 [file unknown]: 21: For energy conservation with LINCS, lincs_iter should be 2 or larger. 21: 21: 21: Number of degrees of freedom in T-Coupling group rest is 42.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.mdp]: 21: NVE simulation: will use the initial temperature of 193.640 K for 21: determining the Verlet buffer size 21: 21: 21: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.mdp]: 21: You are using a plain Coulomb cut-off, which might produce artifacts. 21: You might want to consider using PME electrostatics. 21: 21: 21: 21: There were 5 NOTEs 21: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 21: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 21: Setting the LD random seed to -548487238 21: 21: Generated 2145 of the 2145 non-bonded parameter combinations 21: 21: Generated 2145 of the 2145 1-4 parameter combinations 21: 21: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 21: 21: turning all bonds into constraints... 21: 21: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 21: Analysing residue names: 21: There are: 3 Protein residues 21: Analysing Protein... 21: 21: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 193.64 K 21: 21: Calculated rlist for 1x1 atom pair-list as 1.023 nm, buffer size 0.023 nm 21: 21: Set rlist, assuming 4x4 atom pair-list, to 1.015 nm, buffer size 0.015 nm 21: 21: Note that mdrun will redetermine rlist based on the actual pair-list setup 21: 21: This run will generate roughly 0 Mb of data 21: [ OK ] NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsWithConstraints (32 ms) 21: [----------] 5 tests from NNPotTopologyPreprocessorTest (183 ms total) 21: 21: [----------] 1 test from NNPotForceProviderTest 21: [ RUN ] NNPotForceProviderTest.CanConstruct 21: [ OK ] NNPotForceProviderTest.CanConstruct (0 ms) 21: [----------] 1 test from NNPotForceProviderTest (0 ms total) 21: 21: [----------] Global test environment tear-down 21: [==========] 12 tests from 4 test suites ran. (184 ms total) 21: [ PASSED ] 12 tests. 21/90 Test #21: NNPotAppliedForcesUnitTest ................ Passed 0.33 sec test 22 Start 22: AppliedForcesUnitTest 22: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/AppliedForcesUnitTest.xml" 22: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/applied_forces/tests 22: Test timeout computed to be: 30 22: [==========] Running 3 tests from 1 test suite. 22: [----------] Global test environment set-up. 22: [----------] 3 tests from ElectricFieldTest 22: [ RUN ] ElectricFieldTest.Static 22: [ OK ] ElectricFieldTest.Static (0 ms) 22: [ RUN ] ElectricFieldTest.Oscillating 22: [ OK ] ElectricFieldTest.Oscillating (0 ms) 22: [ RUN ] ElectricFieldTest.Pulsed 22: [ OK ] ElectricFieldTest.Pulsed (0 ms) 22: [----------] 3 tests from ElectricFieldTest (0 ms total) 22: 22: [----------] Global test environment tear-down 22: [==========] 3 tests from 1 test suite ran. (0 ms total) 22: [ PASSED ] 3 tests. 22/90 Test #22: AppliedForcesUnitTest ..................... Passed 0.02 sec test 23 Start 23: ListedForcesTest 23: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/listed_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/ListedForcesTest.xml" 23: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/listed_forces/tests 23: Test timeout computed to be: 30 23: [==========] Running 132 tests from 9 test suites. 23: [----------] Global test environment set-up. 23: [----------] 24 tests from Bond/ListedForcesTest 23: [ RUN ] Bond/ListedForcesTest.Ifunc/0 23: [ OK ] Bond/ListedForcesTest.Ifunc/0 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/1 23: [ OK ] Bond/ListedForcesTest.Ifunc/1 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/2 23: [ OK ] Bond/ListedForcesTest.Ifunc/2 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/3 23: [ OK ] Bond/ListedForcesTest.Ifunc/3 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/4 23: [ OK ] Bond/ListedForcesTest.Ifunc/4 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/5 23: [ OK ] Bond/ListedForcesTest.Ifunc/5 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/6 23: [ OK ] Bond/ListedForcesTest.Ifunc/6 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/7 23: [ OK ] Bond/ListedForcesTest.Ifunc/7 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/8 23: [ OK ] Bond/ListedForcesTest.Ifunc/8 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/9 23: [ OK ] Bond/ListedForcesTest.Ifunc/9 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/10 23: [ OK ] Bond/ListedForcesTest.Ifunc/10 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/11 23: [ OK ] Bond/ListedForcesTest.Ifunc/11 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/12 23: [ OK ] Bond/ListedForcesTest.Ifunc/12 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/13 23: [ OK ] Bond/ListedForcesTest.Ifunc/13 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/14 23: [ OK ] Bond/ListedForcesTest.Ifunc/14 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/15 23: [ OK ] Bond/ListedForcesTest.Ifunc/15 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/16 23: [ OK ] Bond/ListedForcesTest.Ifunc/16 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/17 23: [ OK ] Bond/ListedForcesTest.Ifunc/17 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/18 23: [ OK ] Bond/ListedForcesTest.Ifunc/18 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/19 23: [ OK ] Bond/ListedForcesTest.Ifunc/19 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/20 23: [ OK ] Bond/ListedForcesTest.Ifunc/20 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/21 23: [ OK ] Bond/ListedForcesTest.Ifunc/21 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/22 23: [ OK ] Bond/ListedForcesTest.Ifunc/22 (0 ms) 23: [ RUN ] Bond/ListedForcesTest.Ifunc/23 23: [ OK ] Bond/ListedForcesTest.Ifunc/23 (0 ms) 23: [----------] 24 tests from Bond/ListedForcesTest (4 ms total) 23: 23: [----------] 33 tests from Angle/ListedForcesTest 23: [ RUN ] Angle/ListedForcesTest.Ifunc/0 23: [ OK ] Angle/ListedForcesTest.Ifunc/0 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/1 23: [ OK ] Angle/ListedForcesTest.Ifunc/1 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/2 23: [ OK ] Angle/ListedForcesTest.Ifunc/2 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/3 23: [ OK ] Angle/ListedForcesTest.Ifunc/3 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/4 23: [ OK ] Angle/ListedForcesTest.Ifunc/4 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/5 23: [ OK ] Angle/ListedForcesTest.Ifunc/5 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/6 23: [ OK ] Angle/ListedForcesTest.Ifunc/6 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/7 23: [ OK ] Angle/ListedForcesTest.Ifunc/7 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/8 23: [ OK ] Angle/ListedForcesTest.Ifunc/8 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/9 23: [ OK ] Angle/ListedForcesTest.Ifunc/9 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/10 23: [ OK ] Angle/ListedForcesTest.Ifunc/10 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/11 23: [ OK ] Angle/ListedForcesTest.Ifunc/11 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/12 23: [ OK ] Angle/ListedForcesTest.Ifunc/12 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/13 23: [ OK ] Angle/ListedForcesTest.Ifunc/13 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/14 23: [ OK ] Angle/ListedForcesTest.Ifunc/14 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/15 23: [ OK ] Angle/ListedForcesTest.Ifunc/15 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/16 23: [ OK ] Angle/ListedForcesTest.Ifunc/16 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/17 23: [ OK ] Angle/ListedForcesTest.Ifunc/17 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/18 23: [ OK ] Angle/ListedForcesTest.Ifunc/18 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/19 23: [ OK ] Angle/ListedForcesTest.Ifunc/19 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/20 23: [ OK ] Angle/ListedForcesTest.Ifunc/20 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/21 23: [ OK ] Angle/ListedForcesTest.Ifunc/21 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/22 23: [ OK ] Angle/ListedForcesTest.Ifunc/22 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/23 23: [ OK ] Angle/ListedForcesTest.Ifunc/23 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/24 23: [ OK ] Angle/ListedForcesTest.Ifunc/24 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/25 23: [ OK ] Angle/ListedForcesTest.Ifunc/25 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/26 23: [ OK ] Angle/ListedForcesTest.Ifunc/26 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/27 23: [ OK ] Angle/ListedForcesTest.Ifunc/27 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/28 23: [ OK ] Angle/ListedForcesTest.Ifunc/28 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/29 23: [ OK ] Angle/ListedForcesTest.Ifunc/29 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/30 23: [ OK ] Angle/ListedForcesTest.Ifunc/30 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/31 23: [ OK ] Angle/ListedForcesTest.Ifunc/31 (0 ms) 23: [ RUN ] Angle/ListedForcesTest.Ifunc/32 23: [ OK ] Angle/ListedForcesTest.Ifunc/32 (0 ms) 23: [----------] 33 tests from Angle/ListedForcesTest (6 ms total) 23: 23: [----------] 18 tests from Dihedral/ListedForcesTest 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/0 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/0 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/1 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/1 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/2 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/2 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/3 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/3 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/4 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/4 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/5 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/5 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/6 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/6 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/7 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/7 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/8 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/8 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/9 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/9 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/10 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/10 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/11 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/11 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/12 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/12 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/13 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/13 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/14 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/14 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/15 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/15 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/16 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/16 (0 ms) 23: [ RUN ] Dihedral/ListedForcesTest.Ifunc/17 23: [ OK ] Dihedral/ListedForcesTest.Ifunc/17 (0 ms) 23: [----------] 18 tests from Dihedral/ListedForcesTest (4 ms total) 23: 23: [----------] 12 tests from Polarize/ListedForcesTest 23: [ RUN ] Polarize/ListedForcesTest.Ifunc/0 23: [ OK ] Polarize/ListedForcesTest.Ifunc/0 (0 ms) 23: [ RUN ] Polarize/ListedForcesTest.Ifunc/1 23: [ OK ] Polarize/ListedForcesTest.Ifunc/1 (0 ms) 23: [ RUN ] Polarize/ListedForcesTest.Ifunc/2 23: [ OK ] Polarize/ListedForcesTest.Ifunc/2 (0 ms) 23: [ RUN ] Polarize/ListedForcesTest.Ifunc/3 23: [ OK ] Polarize/ListedForcesTest.Ifunc/3 (0 ms) 23: [ RUN ] Polarize/ListedForcesTest.Ifunc/4 23: [ OK ] Polarize/ListedForcesTest.Ifunc/4 (0 ms) 23: [ RUN ] Polarize/ListedForcesTest.Ifunc/5 23: [ OK ] Polarize/ListedForcesTest.Ifunc/5 (0 ms) 23: [ RUN ] Polarize/ListedForcesTest.Ifunc/6 23: [ OK ] Polarize/ListedForcesTest.Ifunc/6 (0 ms) 23: [ RUN ] Polarize/ListedForcesTest.Ifunc/7 23: [ OK ] Polarize/ListedForcesTest.Ifunc/7 (0 ms) 23: [ RUN ] Polarize/ListedForcesTest.Ifunc/8 23: [ OK ] Polarize/ListedForcesTest.Ifunc/8 (0 ms) 23: [ RUN ] Polarize/ListedForcesTest.Ifunc/9 23: [ OK ] Polarize/ListedForcesTest.Ifunc/9 (0 ms) 23: [ RUN ] Polarize/ListedForcesTest.Ifunc/10 23: [ OK ] Polarize/ListedForcesTest.Ifunc/10 (0 ms) 23: [ RUN ] Polarize/ListedForcesTest.Ifunc/11 23: [ OK ] Polarize/ListedForcesTest.Ifunc/11 (0 ms) 23: [----------] 12 tests from Polarize/ListedForcesTest (1 ms total) 23: 23: [----------] 18 tests from Restraints/ListedForcesTest 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/0 23: [ OK ] Restraints/ListedForcesTest.Ifunc/0 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/1 23: [ OK ] Restraints/ListedForcesTest.Ifunc/1 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/2 23: [ OK ] Restraints/ListedForcesTest.Ifunc/2 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/3 23: [ OK ] Restraints/ListedForcesTest.Ifunc/3 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/4 23: [ OK ] Restraints/ListedForcesTest.Ifunc/4 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/5 23: [ OK ] Restraints/ListedForcesTest.Ifunc/5 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/6 23: [ OK ] Restraints/ListedForcesTest.Ifunc/6 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/7 23: [ OK ] Restraints/ListedForcesTest.Ifunc/7 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/8 23: [ OK ] Restraints/ListedForcesTest.Ifunc/8 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/9 23: [ OK ] Restraints/ListedForcesTest.Ifunc/9 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/10 23: [ OK ] Restraints/ListedForcesTest.Ifunc/10 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/11 23: [ OK ] Restraints/ListedForcesTest.Ifunc/11 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/12 23: [ OK ] Restraints/ListedForcesTest.Ifunc/12 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/13 23: [ OK ] Restraints/ListedForcesTest.Ifunc/13 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/14 23: [ OK ] Restraints/ListedForcesTest.Ifunc/14 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/15 23: [ OK ] Restraints/ListedForcesTest.Ifunc/15 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/16 23: [ OK ] Restraints/ListedForcesTest.Ifunc/16 (0 ms) 23: [ RUN ] Restraints/ListedForcesTest.Ifunc/17 23: [ OK ] Restraints/ListedForcesTest.Ifunc/17 (0 ms) 23: [----------] 18 tests from Restraints/ListedForcesTest (3 ms total) 23: 23: [----------] 3 tests from BondZeroLength/ListedForcesTest 23: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/0 23: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/0 (0 ms) 23: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/1 23: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/1 (0 ms) 23: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/2 23: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/2 (0 ms) 23: [----------] 3 tests from BondZeroLength/ListedForcesTest (0 ms total) 23: 23: [----------] 3 tests from AngleZero/ListedForcesTest 23: [ RUN ] AngleZero/ListedForcesTest.Ifunc/0 23: [ OK ] AngleZero/ListedForcesTest.Ifunc/0 (0 ms) 23: [ RUN ] AngleZero/ListedForcesTest.Ifunc/1 23: [ OK ] AngleZero/ListedForcesTest.Ifunc/1 (0 ms) 23: [ RUN ] AngleZero/ListedForcesTest.Ifunc/2 23: [ OK ] AngleZero/ListedForcesTest.Ifunc/2 (0 ms) 23: [----------] 3 tests from AngleZero/ListedForcesTest (0 ms total) 23: 23: [----------] 12 tests from 14Interaction/ListedForcesPairsTest 23: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/0 23: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/0 (0 ms) 23: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/1 23: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/1 (0 ms) 23: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/2 23: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/2 (0 ms) 23: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/3 23: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/3 (0 ms) 23: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/4 23: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/4 (0 ms) 23: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/5 23: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/5 (0 ms) 23: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/6 23: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/6 (0 ms) 23: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/7 23: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/7 (0 ms) 23: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/8 23: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/8 (0 ms) 23: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/9 23: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/9 (0 ms) 23: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/10 23: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/10 (0 ms) 23: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/11 23: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/11 (0 ms) 23: [----------] 12 tests from 14Interaction/ListedForcesPairsTest (2 ms total) 23: 23: [----------] 9 tests from PosResBasicTest/PositionRestraintsTest 23: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/0 23: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/0 (0 ms) 23: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/1 23: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/1 (0 ms) 23: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/2 23: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/2 (0 ms) 23: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/3 23: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/3 (0 ms) 23: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/4 23: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/4 (0 ms) 23: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/5 23: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/5 (0 ms) 23: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/6 23: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/6 (0 ms) 23: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/7 23: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/7 (0 ms) 23: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/8 23: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/8 (0 ms) 23: [----------] 9 tests from PosResBasicTest/PositionRestraintsTest (1 ms total) 23: 23: [----------] Global test environment tear-down 23: [==========] 132 tests from 9 test suites ran. (24 ms total) 23: [ PASSED ] 132 tests. 23/90 Test #23: ListedForcesTest .......................... Passed 0.06 sec test 24 Start 24: NbnxmTests 24: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/nbnxm-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/NbnxmTests.xml" 24: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/nbnxm/tests 24: Test timeout computed to be: 30 24: [==========] Running 383 tests from 4 test suites. 24: [----------] Global test environment set-up. 24: [----------] 18 tests from KernelSetupTest 24: [ RUN ] KernelSetupTest.getCoulombKernelTypeRF 24: [ OK ] KernelSetupTest.getCoulombKernelTypeRF (0 ms) 24: [ RUN ] KernelSetupTest.getCoulombKernelTypeCut 24: [ OK ] KernelSetupTest.getCoulombKernelTypeCut (0 ms) 24: [ RUN ] KernelSetupTest.getCoulombKernelTypeTable 24: [ OK ] KernelSetupTest.getCoulombKernelTypeTable (0 ms) 24: [ RUN ] KernelSetupTest.getCoulombKernelTypeTableTwin 24: [ OK ] KernelSetupTest.getCoulombKernelTypeTableTwin (0 ms) 24: [ RUN ] KernelSetupTest.getCoulombKernelTypeEwald 24: [ OK ] KernelSetupTest.getCoulombKernelTypeEwald (0 ms) 24: [ RUN ] KernelSetupTest.getCoulombKernelTypeEwaldTwin 24: [ OK ] KernelSetupTest.getCoulombKernelTypeEwaldTwin (0 ms) 24: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomNone 24: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomNone (0 ms) 24: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomPotShift 24: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomPotShift (0 ms) 24: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombLBNone 24: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombLBNone (0 ms) 24: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombLBPotShift 24: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombLBPotShift (0 ms) 24: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombNoneNone 24: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombNoneNone (0 ms) 24: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombNonePotShift 24: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombNonePotShift (0 ms) 24: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutThrows 24: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutThrows (0 ms) 24: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutForceSwitch 24: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutForceSwitch (0 ms) 24: [ RUN ] KernelSetupTest.getVdwKernelTypePmeGeom 24: [ OK ] KernelSetupTest.getVdwKernelTypePmeGeom (0 ms) 24: [ RUN ] KernelSetupTest.getVdwKernelTypePmeNone 24: [ OK ] KernelSetupTest.getVdwKernelTypePmeNone (0 ms) 24: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutPotSwitch 24: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutPotSwitch (0 ms) 24: [ RUN ] KernelSetupTest.getVdwKernelTypeAllCountThrows 24: [ OK ] KernelSetupTest.getVdwKernelTypeAllCountThrows (0 ms) 24: [----------] 18 tests from KernelSetupTest (0 ms total) 24: 24: [----------] 2 tests from SimdEnergyAccumulatorTest 24: [ RUN ] SimdEnergyAccumulatorTest.SingleEnergyGroupSimd4xM 24: [ OK ] SimdEnergyAccumulatorTest.SingleEnergyGroupSimd4xM (0 ms) 24: [ RUN ] SimdEnergyAccumulatorTest.EnergyGroupsSimd4xM 24: [ OK ] SimdEnergyAccumulatorTest.EnergyGroupsSimd4xM (0 ms) 24: [----------] 2 tests from SimdEnergyAccumulatorTest (0 ms total) 24: 24: [----------] 3 tests from WithParameters/CpuListDiagonalExclusionsTest 24: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/0 24: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/0 (0 ms) 24: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/1 24: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/1 (0 ms) 24: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/2 24: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/2 (0 ms) 24: [----------] 3 tests from WithParameters/CpuListDiagonalExclusionsTest (0 ms total) 24: 24: [----------] 360 tests from Combinations/NbnxmKernelTest 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (5 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombNone (5 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (5 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwForceSwitch (5 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (5 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwPotSwitch (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (5 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (5 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (5 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (5 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (5 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombNone (5 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (5 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (5 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwForceSwitch (5 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (5 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (5 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwPotSwitch (5 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (5 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (5 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (5 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (6 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (5 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (5 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (5 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (5 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (5 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (5 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (5 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (5 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (5 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (5 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (5 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombNone (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwForceSwitch (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwPotSwitch (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 24: Analytical Ewald is not implemented for the plain-C kernel, skip this test 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombNone (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwForceSwitch (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwPotSwitch (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (6 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (5 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (5 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 24: There are no combination rule versions of the plain-C kernel 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (5 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (5 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (5 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (5 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombLB 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombLB (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombNone (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwForceSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwPotSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombGeom (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombLB 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombLB (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombNone (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwForceSwitch (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwPotSwitch (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombGeom (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (4 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombLB 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombLB (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombNone (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwForceSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwPotSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (3 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 24: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 24: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 24: Cannot test or generate data for 2xNN kernels without suitable SIMD support 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 24: [----------] 360 tests from Combinations/NbnxmKernelTest (691 ms total) 24: 24: [----------] Global test environment tear-down 24: [==========] 383 tests from 4 test suites ran. (692 ms total) 24: [ PASSED ] 185 tests. 24: [ SKIPPED ] 198 tests, listed below: 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 24: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 24/90 Test #24: NbnxmTests ................................ Passed 0.81 sec test 25 Start 25: NbnxmGpuTests 25: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/nbnxm-gpu-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/NbnxmGpuTests.xml" 25: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/nbnxm/tests 25: Test timeout computed to be: 30 25: [==========] Running 0 tests from 0 test suites. 25: [==========] 0 tests from 0 test suites ran. (0 ms total) 25: [ PASSED ] 0 tests. 25/90 Test #25: NbnxmGpuTests ............................. Passed 0.41 sec test 26 Start 26: CommandLineUnitTests 26: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/commandline-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/CommandLineUnitTests.xml" 26: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/commandline/tests 26: Test timeout computed to be: 30 26: [==========] Running 60 tests from 7 test suites. 26: [----------] Global test environment set-up. 26: [----------] 3 tests from CommandLineHelpModuleTest 26: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp 26: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (0 ms) 26: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic 26: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (0 ms) 26: [ RUN ] CommandLineHelpModuleTest.ExportsHelp 26: [ OK ] CommandLineHelpModuleTest.ExportsHelp (0 ms) 26: [----------] 3 tests from CommandLineHelpModuleTest (1 ms total) 26: 26: [----------] 7 tests from CommandLineHelpWriterTest 26: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes 26: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (0 ms) 26: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables 26: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (0 ms) 26: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions 26: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (0 ms) 26: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions 26: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (0 ms) 26: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups 26: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (0 ms) 26: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText 26: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (0 ms) 26: [ RUN ] CommandLineHelpWriterTest.HandlesKnownIssues 26: [ OK ] CommandLineHelpWriterTest.HandlesKnownIssues (0 ms) 26: [----------] 7 tests from CommandLineHelpWriterTest (1 ms total) 26: 26: [----------] 6 tests from CommandLineModuleManagerTest 26: [ RUN ] CommandLineModuleManagerTest.RunsModule 26: [ OK ] CommandLineModuleManagerTest.RunsModule (0 ms) 26: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp 26: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (0 ms) 26: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet 26: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (0 ms) 26: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH 26: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (0 ms) 26: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule 26: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (0 ms) 26: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames 26: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (0 ms) 26: [----------] 6 tests from CommandLineModuleManagerTest (0 ms total) 26: 26: [----------] 13 tests from CommandLineParserTest 26: [ RUN ] CommandLineParserTest.HandlesSingleValues 26: [ OK ] CommandLineParserTest.HandlesSingleValues (0 ms) 26: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument 26: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms) 26: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument 26: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms) 26: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument 26: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (0 ms) 26: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers 26: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (0 ms) 26: [ RUN ] CommandLineParserTest.HandlesString 26: [ OK ] CommandLineParserTest.HandlesString (0 ms) 26: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues 26: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (0 ms) 26: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix 26: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms) 26: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers 26: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms) 26: [ RUN ] CommandLineParserTest.HandlesSkipUnknown 26: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms) 26: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault 26: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms) 26: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments 26: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms) 26: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions 26: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (0 ms) 26: [----------] 13 tests from CommandLineParserTest (0 ms total) 26: 26: [----------] 6 tests from CommandLineProgramContextTest 26: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath 26: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (0 ms) 26: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath 26: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms) 26: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath 26: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (0 ms) 26: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory 26: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms) 26: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink 26: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (0 ms) 26: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink 26: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (0 ms) 26: [----------] 6 tests from CommandLineProgramContextTest (0 ms total) 26: 26: [----------] 3 tests from OutputNamesTest 26: [ RUN ] OutputNamesTest.CanBeSuffixed 26: [ OK ] OutputNamesTest.CanBeSuffixed (0 ms) 26: [ RUN ] OutputNamesTest.HasSuffixFromNoAppend 26: [ OK ] OutputNamesTest.HasSuffixFromNoAppend (0 ms) 26: [ RUN ] OutputNamesTest.CanHavePartNumberAdded 26: [ OK ] OutputNamesTest.CanHavePartNumberAdded (0 ms) 26: [----------] 3 tests from OutputNamesTest (0 ms total) 26: 26: [----------] 22 tests from ParseCommonArgsTest 26: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs 26: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesInt64Args 26: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesRealArgs 26: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesStringArgs 26: [ OK ] ParseCommonArgsTest.ParsesStringArgs (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs 26: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgsToValuesOfSuitableEnum 26: [ OK ] ParseCommonArgsTest.ParsesBooleanArgsToValuesOfSuitableEnum (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs 26: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs 26: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit 26: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs 26: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesFileArgs 26: [ OK ] ParseCommonArgsTest.ParsesFileArgs (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults 26: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName 26: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension 26: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms) 26: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles 26: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (0 ms) 26: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles 26: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (0 ms) 26: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified 26: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (0 ms) 26: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles 26: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (0 ms) 26: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension 26: Value is /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary/ParseCommonArgsTest_AcceptsUnknownTrajectoryExtension.foo 26: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (0 ms) 26: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile 26: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (0 ms) 26: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName 26: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (207 ms) 26: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs 26: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (0 ms) 26: [----------] 22 tests from ParseCommonArgsTest (210 ms total) 26: 26: [----------] Global test environment tear-down 26: [==========] 60 tests from 7 test suites ran. (214 ms total) 26: [ PASSED ] 60 tests. 26/90 Test #26: CommandLineUnitTests ...................... Passed 0.23 sec test 27 Start 27: DomDecTests 27: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/domdec-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/DomDecTests.xml" 27: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/domdec/tests 27: Test timeout computed to be: 30 27: [==========] Running 9 tests from 2 test suites. 27: [----------] Global test environment set-up. 27: [----------] 7 tests from HashedMap 27: [ RUN ] HashedMap.InsertsFinds 27: [ OK ] HashedMap.InsertsFinds (0 ms) 27: [ RUN ] HashedMap.NegativeKeysWork 27: [ OK ] HashedMap.NegativeKeysWork (0 ms) 27: [ RUN ] HashedMap.InsertsErases 27: [ OK ] HashedMap.InsertsErases (0 ms) 27: [ RUN ] HashedMap.InsertsOrAssigns 27: [ OK ] HashedMap.InsertsOrAssigns (0 ms) 27: [ RUN ] HashedMap.Clears 27: [ OK ] HashedMap.Clears (0 ms) 27: [ RUN ] HashedMap.LinkedEntries 27: [ OK ] HashedMap.LinkedEntries (0 ms) 27: [ RUN ] HashedMap.ResizesTable 27: [ OK ] HashedMap.ResizesTable (0 ms) 27: [----------] 7 tests from HashedMap (0 ms total) 27: 27: [----------] 2 tests from LocalAtomSetManager 27: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet 27: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms) 27: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices 27: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms) 27: [----------] 2 tests from LocalAtomSetManager (0 ms total) 27: 27: [----------] Global test environment tear-down 27: [==========] 9 tests from 2 test suites ran. (0 ms total) 27: [ PASSED ] 9 tests. 27/90 Test #27: DomDecTests ............................... Passed 0.06 sec test 28 Start 28: DomDecMpiTests 28: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/domdec-mpi-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/DomDecMpiTests.xml" 28: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/domdec/tests 28: Test timeout computed to be: 30 28: [==========] Running 4 tests from 1 test suite. 28: [----------] Global test environment set-up. 28: [----------] 4 tests from HaloExchangeTest 28: [ RUN ] HaloExchangeTest.Coordinates1dHaloWith1Pulse 28: [ OK ] HaloExchangeTest.Coordinates1dHaloWith1Pulse (4 ms) 28: [ RUN ] HaloExchangeTest.Coordinates1dHaloWith2Pulses 28: [ OK ] HaloExchangeTest.Coordinates1dHaloWith2Pulses (0 ms) 28: [ RUN ] HaloExchangeTest.Coordinates2dHaloWith1PulseInEachDim 28: [ OK ] HaloExchangeTest.Coordinates2dHaloWith1PulseInEachDim (0 ms) 28: [ RUN ] HaloExchangeTest.Coordinates2dHaloWith2PulsesInDim1 28: [ OK ] HaloExchangeTest.Coordinates2dHaloWith2PulsesInDim1 (13 ms) 28: [----------] 4 tests from HaloExchangeTest (19 ms total) 28: 28: [----------] Global test environment tear-down 28: [==========] 4 tests from 1 test suite ran. (19 ms total) 28: [ PASSED ] 4 tests. 28/90 Test #28: DomDecMpiTests ............................ Passed 0.11 sec test 29 Start 29: EwaldUnitTests 29: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/ewald-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/EwaldUnitTests.xml" 29: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/ewald/tests 29: Test timeout computed to be: 30 29: [==========] Running 407 tests from 9 test suites. 29: [----------] Global test environment set-up. 29: [----------] 6 tests from SeparatePmeRanksPermittedTest 29: [ RUN ] SeparatePmeRanksPermittedTest.ZeroPmeDisableReasons 29: [ OK ] SeparatePmeRanksPermittedTest.ZeroPmeDisableReasons (0 ms) 29: [ RUN ] SeparatePmeRanksPermittedTest.CanBeDisabled 29: [ OK ] SeparatePmeRanksPermittedTest.CanBeDisabled (0 ms) 29: [ RUN ] SeparatePmeRanksPermittedTest.OneDisableReasonFlag 29: [ OK ] SeparatePmeRanksPermittedTest.OneDisableReasonFlag (0 ms) 29: [ RUN ] SeparatePmeRanksPermittedTest.OneDisableReasonText 29: [ OK ] SeparatePmeRanksPermittedTest.OneDisableReasonText (0 ms) 29: [ RUN ] SeparatePmeRanksPermittedTest.TwoDisableReasonText 29: [ OK ] SeparatePmeRanksPermittedTest.TwoDisableReasonText (0 ms) 29: [ RUN ] SeparatePmeRanksPermittedTest.EmptyDisableReasonText 29: [ OK ] SeparatePmeRanksPermittedTest.EmptyDisableReasonText (0 ms) 29: [----------] 6 tests from SeparatePmeRanksPermittedTest (0 ms total) 29: 29: [----------] 108 tests from Pme_SplineAndSpreadTest 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spline (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spline (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spline (2 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spline (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_fused spline and spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spline (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spline (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spread (2 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_fused spline and spread (2 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spline (2 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spread (2 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_fused spline and spread (3 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spline (2 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spread (2 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_fused spline and spread (3 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spread (2 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spline (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_fused spline and spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spline (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spline (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_fused spline and spread (2 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spline (2 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spread (2 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_fused spline and spread (2 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spline (2 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spread (2 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_fused spline and spread (2 ms) 29: [----------] 108 tests from Pme_SplineAndSpreadTest (125 ms total) 29: 29: [----------] 64 tests from Pme_SolveTest 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (1 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [----------] 64 tests from Pme_SolveTest (16 ms total) 29: 29: [----------] 32 tests from PmeDiffEwaldQ_SolveTest 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [----------] 32 tests from PmeDiffEwaldQ_SolveTest (5 ms total) 29: 29: [----------] 32 tests from PmeDiffEwaldLJ_SolveTest 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 29: [----------] 32 tests from PmeDiffEwaldLJ_SolveTest (9 ms total) 29: 29: [----------] 64 tests from PmeDiffEps_SolveTest 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [----------] 64 tests from PmeDiffEps_SolveTest (15 ms total) 29: 29: [----------] 72 tests from Pme_GatherTest 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 29: [----------] 72 tests from Pme_GatherTest (16 ms total) 29: 29: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest 29: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 29: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (0 ms) 29: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 29: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms) 29: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 29: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (0 ms) 29: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 29: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (3 ms) 29: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 29: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (0 ms) 29: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (3 ms total) 29: 29: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (4 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (4 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (3 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (3 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (4 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (4 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (4 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (4 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (4 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (5 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (5 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (4 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (7 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (4 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (3 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (4 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (4 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (4 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (4 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (4 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (3 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (4 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (3 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (2 ms) 29: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (110 ms total) 29: 29: [----------] Global test environment tear-down 29: [==========] 407 tests from 9 test suites ran. (304 ms total) 29: [ PASSED ] 311 tests. 29: [ SKIPPED ] 96 tests, listed below: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29/90 Test #29: EwaldUnitTests ............................ Passed 0.45 sec test 30 Start 30: FFTUnitTests 30: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/fft-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/FFTUnitTests.xml" 30: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/fft/tests 30: Test timeout computed to be: 1920 30: [==========] Running 15 tests from 4 test suites. 30: [----------] Global test environment set-up. 30: [----------] 2 tests from ManyFFTTest 30: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test 30: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (7 ms) 30: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test 30: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (15 ms) 30: [----------] 2 tests from ManyFFTTest (23 ms total) 30: 30: [----------] 1 test from FFTTest 30: [ RUN ] FFTTest.Real2DLength18_15Test 30: [ OK ] FFTTest.Real2DLength18_15Test (4 ms) 30: [----------] 1 test from FFTTest (5 ms total) 30: 30: [----------] 10 tests from 7_8_25_36_60/FFTTest1D 30: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0 30: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (0 ms) 30: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1 30: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (0 ms) 30: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2 30: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (1 ms) 30: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3 30: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (2 ms) 30: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4 30: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (2 ms) 30: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0 30: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (0 ms) 30: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1 30: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (0 ms) 30: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2 30: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (0 ms) 30: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3 30: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (9 ms) 30: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4 30: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (12 ms) 30: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (31 ms total) 30: 30: [----------] 2 tests from Works/ParameterizedFFTTest3D 30: [ RUN ] Works/ParameterizedFFTTest3D.RunsOnHost/5_6_9 30: [ OK ] Works/ParameterizedFFTTest3D.RunsOnHost/5_6_9 (1 ms) 30: [ RUN ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 30: [ OK ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 (1 ms) 30: [----------] 2 tests from Works/ParameterizedFFTTest3D (2 ms total) 30: 30: [----------] Global test environment tear-down 30: [==========] 15 tests from 4 test suites ran. (63 ms total) 30: [ PASSED ] 15 tests. 30/90 Test #30: FFTUnitTests .............................. Passed 0.18 sec test 31 Start 31: GpuUtilsUnitTests 31: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/gpu_utils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/GpuUtilsUnitTests.xml" 31: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gpu_utils/tests 31: Test timeout computed to be: 30 31: [==========] Running 67 tests from 22 test suites. 31: [----------] Global test environment set-up. 31: [----------] 2 tests from ClfftInitializer 31: [ RUN ] ClfftInitializer.SingleInitializationWorks 31: [ OK ] ClfftInitializer.SingleInitializationWorks (0 ms) 31: [ RUN ] ClfftInitializer.TwoInitializationsWork 31: [ OK ] ClfftInitializer.TwoInitializationsWork (0 ms) 31: [----------] 2 tests from ClfftInitializer (0 ms total) 31: 31: [----------] 1 test from DevicesAvailable 31: [ RUN ] DevicesAvailable.ShouldBeAbleToRunOnDevice 31: [ OK ] DevicesAvailable.ShouldBeAbleToRunOnDevice (0 ms) 31: [----------] 1 test from DevicesAvailable (0 ms total) 31: 31: [----------] 1 test from DeviceStreamManagerTest 31: [ RUN ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice 31: [ OK ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice (0 ms) 31: [----------] 1 test from DeviceStreamManagerTest (0 ms total) 31: 31: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int 31: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks 31: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms) 31: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory 31: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms) 31: [----------] 2 tests from HostAllocatorTest/0 (0 ms total) 31: 31: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = double 31: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks 31: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms) 31: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory 31: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms) 31: [----------] 2 tests from HostAllocatorTest/1 (0 ms total) 31: 31: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector 31: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks 31: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms) 31: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory 31: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms) 31: [----------] 2 tests from HostAllocatorTest/2 (0 ms total) 31: 31: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly 31: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks 31: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms) 31: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory 31: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms) 31: [----------] 2 tests from HostAllocatorTest/3 (0 ms total) 31: 31: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int 31: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks 31: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 31: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork 31: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms) 31: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve 31: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms) 31: [----------] 3 tests from HostAllocatorTestCopyable/0 (0 ms total) 31: 31: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = double 31: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks 31: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 31: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork 31: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms) 31: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve 31: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms) 31: [----------] 3 tests from HostAllocatorTestCopyable/1 (0 ms total) 31: 31: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector 31: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks 31: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 31: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork 31: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms) 31: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve 31: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms) 31: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total) 31: 31: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int 31: [ RUN ] HostAllocatorTestNoMem/0.CreateVector 31: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment 31: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction 31: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/0.Swap 31: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/0.Comparison 31: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms) 31: [----------] 5 tests from HostAllocatorTestNoMem/0 (0 ms total) 31: 31: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = double 31: [ RUN ] HostAllocatorTestNoMem/1.CreateVector 31: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment 31: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction 31: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/1.Swap 31: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/1.Comparison 31: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms) 31: [----------] 5 tests from HostAllocatorTestNoMem/1 (0 ms total) 31: 31: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector 31: [ RUN ] HostAllocatorTestNoMem/2.CreateVector 31: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment 31: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction 31: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/2.Swap 31: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/2.Comparison 31: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms) 31: [----------] 5 tests from HostAllocatorTestNoMem/2 (0 ms total) 31: 31: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly 31: [ RUN ] HostAllocatorTestNoMem/3.CreateVector 31: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment 31: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction 31: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/3.Swap 31: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/3.Comparison 31: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms) 31: [----------] 5 tests from HostAllocatorTestNoMem/3 (0 ms total) 31: 31: [----------] 3 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int 31: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment 31: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms) 31: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction 31: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms) 31: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator 31: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator (0 ms) 31: [----------] 3 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total) 31: 31: [----------] 3 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = double 31: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment 31: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms) 31: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction 31: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms) 31: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator 31: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator (0 ms) 31: [----------] 3 tests from HostAllocatorTestNoMemCopyable/1 (0 ms total) 31: 31: [----------] 3 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector 31: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment 31: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms) 31: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction 31: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms) 31: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator 31: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator (0 ms) 31: [----------] 3 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total) 31: 31: [----------] 1 test from HostAllocatorUntypedTest 31: [ RUN ] HostAllocatorUntypedTest.Comparison 31: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms) 31: [----------] 1 test from HostAllocatorUntypedTest (0 ms total) 31: 31: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 31: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 31: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 31: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 31: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/0.Move 31: [ OK ] AllocatorTest/0.Move (0 ms) 31: [----------] 4 tests from AllocatorTest/0 (0 ms total) 31: 31: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 31: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 31: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 31: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 31: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/1.Move 31: [ OK ] AllocatorTest/1.Move (0 ms) 31: [----------] 4 tests from AllocatorTest/1 (0 ms total) 31: 31: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator, gmx::HostAllocationPolicy> 31: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 31: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 31: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 31: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/2.Move 31: [ OK ] AllocatorTest/2.Move (0 ms) 31: [----------] 4 tests from AllocatorTest/2 (0 ms total) 31: 31: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 31: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 31: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 31: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 31: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/3.Move 31: [ OK ] AllocatorTest/3.Move (0 ms) 31: [----------] 4 tests from AllocatorTest/3 (0 ms total) 31: 31: [----------] Global test environment tear-down 31: [==========] 67 tests from 22 test suites ran. (1 ms total) 31: [ PASSED ] 67 tests. 31/90 Test #31: GpuUtilsUnitTests ......................... Passed 0.17 sec test 32 Start 32: HardwareUnitTests 32: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/hardware-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/HardwareUnitTests.xml" 32: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/hardware/tests 32: Test timeout computed to be: 30 32: [==========] Running 22 tests from 10 test suites. 32: [----------] Global test environment set-up. 32: [----------] 1 test from CpuInfoTest 32: [ RUN ] CpuInfoTest.SupportLevel 32: [ OK ] CpuInfoTest.SupportLevel (17 ms) 32: [----------] 1 test from CpuInfoTest (17 ms total) 32: 32: [----------] 4 tests from HardwareTopologyTest 32: [ RUN ] HardwareTopologyTest.Execute 32: [ OK ] HardwareTopologyTest.Execute (31 ms) 32: [ RUN ] HardwareTopologyTest.HwlocExecute 32: [ OK ] HardwareTopologyTest.HwlocExecute (27 ms) 32: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency 32: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (31 ms) 32: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency 32: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (39 ms) 32: [----------] 4 tests from HardwareTopologyTest (130 ms total) 32: 32: [----------] 1 test from DevicesManagerTest 32: [ RUN ] DevicesManagerTest.Serialization 32: [ OK ] DevicesManagerTest.Serialization (0 ms) 32: [ DISABLED ] DevicesManagerTest.DISABLED_DetectsUuid 32: [----------] 1 test from DevicesManagerTest (0 ms total) 32: 32: [----------] 1 test from UuidStringTest 32: [ RUN ] UuidStringTest.Works 32: [ OK ] UuidStringTest.Works (0 ms) 32: [----------] 1 test from UuidStringTest (0 ms total) 32: 32: [----------] 5 tests from XeonE52620/MockHardwareTopologyTest 32: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/0 32: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/0 (1 ms) 32: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/1 32: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/1 (0 ms) 32: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/2 32: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/2 (0 ms) 32: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/3 32: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/3 (0 ms) 32: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/4 32: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/4 (0 ms) 32: [----------] 5 tests from XeonE52620/MockHardwareTopologyTest (3 ms total) 32: 32: [----------] 5 tests from Xeon4116/MockHardwareTopologyTest 32: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/0 32: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/0 (1 ms) 32: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/1 32: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/1 (0 ms) 32: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/2 32: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/2 (0 ms) 32: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/3 32: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/3 (0 ms) 32: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/4 32: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/4 (0 ms) 32: [----------] 5 tests from Xeon4116/MockHardwareTopologyTest (3 ms total) 32: 32: [----------] 2 tests from Core12900K/MockHardwareTopologyTest 32: [ RUN ] Core12900K/MockHardwareTopologyTest.DetectsHardware/0 32: [ OK ] Core12900K/MockHardwareTopologyTest.DetectsHardware/0 (0 ms) 32: [ RUN ] Core12900K/MockHardwareTopologyTest.DetectsHardware/1 32: [ OK ] Core12900K/MockHardwareTopologyTest.DetectsHardware/1 (0 ms) 32: [----------] 2 tests from Core12900K/MockHardwareTopologyTest (1 ms total) 32: 32: [----------] 1 test from Core12900K/MockHardwareTopologySpecialSystemTest 32: [ RUN ] Core12900K/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 32: [ OK ] Core12900K/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (1 ms) 32: [----------] 1 test from Core12900K/MockHardwareTopologySpecialSystemTest (1 ms total) 32: 32: [----------] 1 test from Power9/MockHardwareTopologySpecialSystemTest 32: [ RUN ] Power9/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 32: [ OK ] Power9/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (1 ms) 32: [----------] 1 test from Power9/MockHardwareTopologySpecialSystemTest (1 ms total) 32: 32: [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest 32: [ RUN ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 32: [ OK ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (2 ms) 32: [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest (2 ms total) 32: 32: [----------] Global test environment tear-down 32: [==========] 22 tests from 10 test suites ran. (161 ms total) 32: [ PASSED ] 22 tests. 32: 32: YOU HAVE 1 DISABLED TEST 32: 32/90 Test #32: HardwareUnitTests ......................... Passed 0.23 sec test 33 Start 33: MathUnitTests 33: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/math-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/MathUnitTests.xml" 33: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/math/tests 33: Test timeout computed to be: 30 33: [==========] Running 328 tests from 41 test suites. 33: [----------] Global test environment set-up. 33: [----------] 1 test from EmptyArrayRefWithPaddingTest 33: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty 33: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms) 33: [----------] 1 test from EmptyArrayRefWithPaddingTest (0 ms total) 33: 33: [----------] 1 test from EmptyConstArrayRefWithPaddingTest 33: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty 33: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms) 33: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total) 33: 33: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding 33: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks 33: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms) 33: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks 33: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms) 33: [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total) 33: 33: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding 33: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks 33: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms) 33: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks 33: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms) 33: [----------] 2 tests from ArrayRefWithPaddingTest/1 (0 ms total) 33: 33: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding 33: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks 33: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms) 33: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks 33: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms) 33: [----------] 2 tests from ArrayRefWithPaddingTest/2 (0 ms total) 33: 33: [----------] 2 tests from InvertBoxMatrixTest 33: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent 33: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms) 33: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace 33: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms) 33: [----------] 2 tests from InvertBoxMatrixTest (0 ms total) 33: 33: [----------] 8 tests from ComplexNumberTest 33: [ RUN ] ComplexNumberTest.RealComplexMultiply 33: [ OK ] ComplexNumberTest.RealComplexMultiply (0 ms) 33: [ RUN ] ComplexNumberTest.RealComplexExp 33: [ OK ] ComplexNumberTest.RealComplexExp (0 ms) 33: [ RUN ] ComplexNumberTest.ComplexAdd 33: [ OK ] ComplexNumberTest.ComplexAdd (0 ms) 33: [ RUN ] ComplexNumberTest.ComplexSubtract 33: [ OK ] ComplexNumberTest.ComplexSubtract (0 ms) 33: [ RUN ] ComplexNumberTest.ComplexMultiply 33: [ OK ] ComplexNumberTest.ComplexMultiply (0 ms) 33: [ RUN ] ComplexNumberTest.ComplexDivision 33: [ OK ] ComplexNumberTest.ComplexDivision (0 ms) 33: [ RUN ] ComplexNumberTest.ComplexConjugate 33: [ OK ] ComplexNumberTest.ComplexConjugate (0 ms) 33: [ RUN ] ComplexNumberTest.ComplexAbs2 33: [ OK ] ComplexNumberTest.ComplexAbs2 (0 ms) 33: [----------] 8 tests from ComplexNumberTest (0 ms total) 33: 33: [----------] 11 tests from TranslateAndScaleTest 33: [ RUN ] TranslateAndScaleTest.identityTransformation 33: [ OK ] TranslateAndScaleTest.identityTransformation (0 ms) 33: [ RUN ] TranslateAndScaleTest.translationWithIdentityScaling 33: [ OK ] TranslateAndScaleTest.translationWithIdentityScaling (0 ms) 33: [ RUN ] TranslateAndScaleTest.scalingWithZeroTranslation 33: [ OK ] TranslateAndScaleTest.scalingWithZeroTranslation (0 ms) 33: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivial 33: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivial (0 ms) 33: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector 33: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector (0 ms) 33: [ RUN ] TranslateAndScaleTest.scalingIdentity 33: [ OK ] TranslateAndScaleTest.scalingIdentity (0 ms) 33: [ RUN ] TranslateAndScaleTest.scalingNonTrivial 33: [ OK ] TranslateAndScaleTest.scalingNonTrivial (0 ms) 33: [ RUN ] TranslateAndScaleTest.scalingNonTrivialSingleVector 33: [ OK ] TranslateAndScaleTest.scalingNonTrivialSingleVector (0 ms) 33: [ RUN ] TranslateAndScaleTest.scalingInverseNoZero 33: [ OK ] TranslateAndScaleTest.scalingInverseNoZero (0 ms) 33: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero 33: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero (0 ms) 33: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector 33: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector (0 ms) 33: [----------] 11 tests from TranslateAndScaleTest (0 ms total) 33: 33: [----------] 3 tests from AffineTransformationTest 33: [ RUN ] AffineTransformationTest.identityTransformYieldsSameVectors 33: [ OK ] AffineTransformationTest.identityTransformYieldsSameVectors (0 ms) 33: [ RUN ] AffineTransformationTest.applyTransformationToVectors 33: [ OK ] AffineTransformationTest.applyTransformationToVectors (0 ms) 33: [ RUN ] AffineTransformationTest.retrieveGradient 33: [ OK ] AffineTransformationTest.retrieveGradient (0 ms) 33: [----------] 3 tests from AffineTransformationTest (0 ms total) 33: 33: [----------] 14 tests from DensitySimilarityTest 33: [ RUN ] DensitySimilarityTest.InnerProductIsCorrect 33: [ OK ] DensitySimilarityTest.InnerProductIsCorrect (0 ms) 33: [ RUN ] DensitySimilarityTest.InnerProductGradientIsCorrect 33: [ OK ] DensitySimilarityTest.InnerProductGradientIsCorrect (0 ms) 33: [ RUN ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch 33: [ OK ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch (0 ms) 33: [ RUN ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch 33: [ OK ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch (0 ms) 33: [ RUN ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect 33: [ OK ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect (0 ms) 33: [ RUN ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero 33: [ OK ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero (0 ms) 33: [ RUN ] DensitySimilarityTest.RelativeEntropyIsCorrect 33: [ OK ] DensitySimilarityTest.RelativeEntropyIsCorrect (0 ms) 33: [ RUN ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect 33: [ OK ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect (0 ms) 33: [ RUN ] DensitySimilarityTest.CrossCorrelationIsOne 33: [ OK ] DensitySimilarityTest.CrossCorrelationIsOne (29 ms) 33: [ RUN ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated 33: [ OK ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated (30 ms) 33: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated 33: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated (1 ms) 33: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect 33: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect (0 ms) 33: [ RUN ] DensitySimilarityTest.NormalizationCorrect 33: [ OK ] DensitySimilarityTest.NormalizationCorrect (0 ms) 33: [ RUN ] DensitySimilarityTest.NormalizationAllNonPositive 33: [ OK ] DensitySimilarityTest.NormalizationAllNonPositive (0 ms) 33: [----------] 14 tests from DensitySimilarityTest (63 ms total) 33: 33: [----------] 6 tests from StructureSimilarityTest 33: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD 33: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms) 33: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho 33: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms) 33: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD 33: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms) 33: [ RUN ] StructureSimilarityTest.YieldsCorrectRho 33: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms) 33: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex 33: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms) 33: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex 33: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms) 33: [----------] 6 tests from StructureSimilarityTest (0 ms total) 33: 33: [----------] 8 tests from ExponentialMovingAverage 33: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero 33: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero (0 ms) 33: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative 33: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative (0 ms) 33: [ RUN ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue 33: [ OK ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue (0 ms) 33: [ RUN ] ExponentialMovingAverage.YieldsCorrectValue 33: [ OK ] ExponentialMovingAverage.YieldsCorrectValue (0 ms) 33: [ RUN ] ExponentialMovingAverage.SetAverageCorrectly 33: [ OK ] ExponentialMovingAverage.SetAverageCorrectly (0 ms) 33: [ RUN ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing 33: [ OK ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing (0 ms) 33: [ RUN ] ExponentialMovingAverage.InverseLagTimeCorrect 33: [ OK ] ExponentialMovingAverage.InverseLagTimeCorrect (0 ms) 33: [ RUN ] ExponentialMovingAverage.RoundTripAsKeyValueTree 33: [ OK ] ExponentialMovingAverage.RoundTripAsKeyValueTree (0 ms) 33: [----------] 8 tests from ExponentialMovingAverage (0 ms total) 33: 33: [----------] 21 tests from FunctionTest 33: [ RUN ] FunctionTest.StaticLog2 33: [ OK ] FunctionTest.StaticLog2 (0 ms) 33: [ RUN ] FunctionTest.Log2I32Bit 33: [ OK ] FunctionTest.Log2I32Bit (0 ms) 33: [ RUN ] FunctionTest.Log2I64Bit 33: [ OK ] FunctionTest.Log2I64Bit (0 ms) 33: [ RUN ] FunctionTest.GreatestCommonDivisor 33: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms) 33: [ RUN ] FunctionTest.InvsqrtFloat 33: [ OK ] FunctionTest.InvsqrtFloat (0 ms) 33: [ RUN ] FunctionTest.InvsqrtDouble 33: [ OK ] FunctionTest.InvsqrtDouble (0 ms) 33: [ RUN ] FunctionTest.InvsqrtInteger 33: [ OK ] FunctionTest.InvsqrtInteger (0 ms) 33: [ RUN ] FunctionTest.InvcbrtFloat 33: [ OK ] FunctionTest.InvcbrtFloat (0 ms) 33: [ RUN ] FunctionTest.InvcbrtDouble 33: [ OK ] FunctionTest.InvcbrtDouble (0 ms) 33: [ RUN ] FunctionTest.InvcbrtInteger 33: [ OK ] FunctionTest.InvcbrtInteger (0 ms) 33: [ RUN ] FunctionTest.SixthrootFloat 33: [ OK ] FunctionTest.SixthrootFloat (0 ms) 33: [ RUN ] FunctionTest.SixthrootDouble 33: [ OK ] FunctionTest.SixthrootDouble (0 ms) 33: [ RUN ] FunctionTest.SixthrootInteger 33: [ OK ] FunctionTest.SixthrootInteger (0 ms) 33: [ RUN ] FunctionTest.InvsixthrootFloat 33: [ OK ] FunctionTest.InvsixthrootFloat (0 ms) 33: [ RUN ] FunctionTest.InvsixthrootDouble 33: [ OK ] FunctionTest.InvsixthrootDouble (0 ms) 33: [ RUN ] FunctionTest.InvsixthrootInteger 33: [ OK ] FunctionTest.InvsixthrootInteger (0 ms) 33: [ RUN ] FunctionTest.Powers 33: [ OK ] FunctionTest.Powers (0 ms) 33: [ RUN ] FunctionTest.ErfInvFloat 33: [ OK ] FunctionTest.ErfInvFloat (0 ms) 33: [ RUN ] FunctionTest.ErfInvDouble 33: [ OK ] FunctionTest.ErfInvDouble (0 ms) 33: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat 33: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (0 ms) 33: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble 33: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (0 ms) 33: [----------] 21 tests from FunctionTest (1 ms total) 33: 33: [----------] 2 tests from FunctionTestIntegerTypes/0, where TypeParam = signed char 33: [ RUN ] FunctionTestIntegerTypes/0.IsPowerOfTwo 33: [ OK ] FunctionTestIntegerTypes/0.IsPowerOfTwo (0 ms) 33: [ RUN ] FunctionTestIntegerTypes/0.DivideRoundUp 33: [ OK ] FunctionTestIntegerTypes/0.DivideRoundUp (0 ms) 33: [----------] 2 tests from FunctionTestIntegerTypes/0 (0 ms total) 33: 33: [----------] 2 tests from FunctionTestIntegerTypes/1, where TypeParam = unsigned char 33: [ RUN ] FunctionTestIntegerTypes/1.IsPowerOfTwo 33: [ OK ] FunctionTestIntegerTypes/1.IsPowerOfTwo (0 ms) 33: [ RUN ] FunctionTestIntegerTypes/1.DivideRoundUp 33: [ OK ] FunctionTestIntegerTypes/1.DivideRoundUp (0 ms) 33: [----------] 2 tests from FunctionTestIntegerTypes/1 (0 ms total) 33: 33: [----------] 2 tests from FunctionTestIntegerTypes/2, where TypeParam = short 33: [ RUN ] FunctionTestIntegerTypes/2.IsPowerOfTwo 33: [ OK ] FunctionTestIntegerTypes/2.IsPowerOfTwo (0 ms) 33: [ RUN ] FunctionTestIntegerTypes/2.DivideRoundUp 33: [ OK ] FunctionTestIntegerTypes/2.DivideRoundUp (0 ms) 33: [----------] 2 tests from FunctionTestIntegerTypes/2 (0 ms total) 33: 33: [----------] 2 tests from FunctionTestIntegerTypes/3, where TypeParam = unsigned short 33: [ RUN ] FunctionTestIntegerTypes/3.IsPowerOfTwo 33: [ OK ] FunctionTestIntegerTypes/3.IsPowerOfTwo (0 ms) 33: [ RUN ] FunctionTestIntegerTypes/3.DivideRoundUp 33: [ OK ] FunctionTestIntegerTypes/3.DivideRoundUp (0 ms) 33: [----------] 2 tests from FunctionTestIntegerTypes/3 (0 ms total) 33: 33: [----------] 2 tests from FunctionTestIntegerTypes/4, where TypeParam = int 33: [ RUN ] FunctionTestIntegerTypes/4.IsPowerOfTwo 33: [ OK ] FunctionTestIntegerTypes/4.IsPowerOfTwo (0 ms) 33: [ RUN ] FunctionTestIntegerTypes/4.DivideRoundUp 33: [ OK ] FunctionTestIntegerTypes/4.DivideRoundUp (0 ms) 33: [----------] 2 tests from FunctionTestIntegerTypes/4 (0 ms total) 33: 33: [----------] 2 tests from FunctionTestIntegerTypes/5, where TypeParam = unsigned int 33: [ RUN ] FunctionTestIntegerTypes/5.IsPowerOfTwo 33: [ OK ] FunctionTestIntegerTypes/5.IsPowerOfTwo (0 ms) 33: [ RUN ] FunctionTestIntegerTypes/5.DivideRoundUp 33: [ OK ] FunctionTestIntegerTypes/5.DivideRoundUp (0 ms) 33: [----------] 2 tests from FunctionTestIntegerTypes/5 (0 ms total) 33: 33: [----------] 2 tests from FunctionTestIntegerTypes/6, where TypeParam = long 33: [ RUN ] FunctionTestIntegerTypes/6.IsPowerOfTwo 33: [ OK ] FunctionTestIntegerTypes/6.IsPowerOfTwo (0 ms) 33: [ RUN ] FunctionTestIntegerTypes/6.DivideRoundUp 33: [ OK ] FunctionTestIntegerTypes/6.DivideRoundUp (0 ms) 33: [----------] 2 tests from FunctionTestIntegerTypes/6 (0 ms total) 33: 33: [----------] 2 tests from FunctionTestIntegerTypes/7, where TypeParam = unsigned long 33: [ RUN ] FunctionTestIntegerTypes/7.IsPowerOfTwo 33: [ OK ] FunctionTestIntegerTypes/7.IsPowerOfTwo (0 ms) 33: [ RUN ] FunctionTestIntegerTypes/7.DivideRoundUp 33: [ OK ] FunctionTestIntegerTypes/7.DivideRoundUp (0 ms) 33: [----------] 2 tests from FunctionTestIntegerTypes/7 (0 ms total) 33: 33: [----------] 4 tests from GaussianOn1DLattice 33: [ RUN ] GaussianOn1DLattice.sumsCloseToOne 33: [ OK ] GaussianOn1DLattice.sumsCloseToOne (0 ms) 33: [ RUN ] GaussianOn1DLattice.isCorrect 33: [ OK ] GaussianOn1DLattice.isCorrect (0 ms) 33: [ RUN ] GaussianOn1DLattice.complementaryAmplitudesSumToZero 33: [ OK ] GaussianOn1DLattice.complementaryAmplitudesSumToZero (0 ms) 33: [ RUN ] GaussianOn1DLattice.doesNotOverflowForLargeRange 33: [ OK ] GaussianOn1DLattice.doesNotOverflowForLargeRange (0 ms) 33: [----------] 4 tests from GaussianOn1DLattice (0 ms total) 33: 33: [----------] 9 tests from GaussTransformTest 33: [ RUN ] GaussTransformTest.isZeroUponConstruction 33: [ OK ] GaussTransformTest.isZeroUponConstruction (0 ms) 33: [ RUN ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss 33: [ OK ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss (0 ms) 33: [ RUN ] GaussTransformTest.isZeroAfterSettingZero 33: [ OK ] GaussTransformTest.isZeroAfterSettingZero (0 ms) 33: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinX 33: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinX (0 ms) 33: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinY 33: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinY (0 ms) 33: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinZ 33: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinZ (0 ms) 33: [ RUN ] GaussTransformTest.complementaryGaussAddToZero 33: [ OK ] GaussTransformTest.complementaryGaussAddToZero (0 ms) 33: [ RUN ] GaussTransformTest.centerGaussianInCubeHasExpectedValues 33: [ OK ] GaussTransformTest.centerGaussianInCubeHasExpectedValues (0 ms) 33: [ RUN ] GaussTransformTest.view 33: [ OK ] GaussTransformTest.view (0 ms) 33: [----------] 9 tests from GaussTransformTest (0 ms total) 33: 33: [----------] 3 tests from DensityFittingForce 33: [ RUN ] DensityFittingForce.isZeroWhenMatchingDensity 33: [ OK ] DensityFittingForce.isZeroWhenMatchingDensity (0 ms) 33: [ RUN ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections 33: [ OK ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections (0 ms) 33: [ RUN ] DensityFittingForce.pullsTowardsDerivative 33: [ OK ] DensityFittingForce.pullsTowardsDerivative (0 ms) 33: [----------] 3 tests from DensityFittingForce (0 ms total) 33: 33: [----------] 2 tests from InvertMatrixTest 33: [ RUN ] InvertMatrixTest.IdentityIsImpotent 33: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms) 33: [ RUN ] InvertMatrixTest.ComputesInverse 33: [ OK ] InvertMatrixTest.ComputesInverse (0 ms) 33: [----------] 2 tests from InvertMatrixTest (0 ms total) 33: 33: [----------] 22 tests from MatrixTest 33: [ RUN ] MatrixTest.canSetFromArray 33: [ OK ] MatrixTest.canSetFromArray (0 ms) 33: [ RUN ] MatrixTest.canSetStaticallyFromList 33: [ OK ] MatrixTest.canSetStaticallyFromList (0 ms) 33: [ RUN ] MatrixTest.canConstructAndFill 33: [ OK ] MatrixTest.canConstructAndFill (0 ms) 33: [ RUN ] MatrixTest.canSetValues 33: [ OK ] MatrixTest.canSetValues (0 ms) 33: [ RUN ] MatrixTest.canCopyAssign 33: [ OK ] MatrixTest.canCopyAssign (0 ms) 33: [ RUN ] MatrixTest.canSwap 33: [ OK ] MatrixTest.canSwap (0 ms) 33: [ RUN ] MatrixTest.staticMultiDimArrayExtent 33: [ OK ] MatrixTest.staticMultiDimArrayExtent (0 ms) 33: [ RUN ] MatrixTest.canAddMatrix 33: [ OK ] MatrixTest.canAddMatrix (0 ms) 33: [ RUN ] MatrixTest.canSubstractMatrix 33: [ OK ] MatrixTest.canSubstractMatrix (0 ms) 33: [ RUN ] MatrixTest.canNegateMatrix 33: [ OK ] MatrixTest.canNegateMatrix (0 ms) 33: [ RUN ] MatrixTest.determinantWorks 33: [ OK ] MatrixTest.determinantWorks (0 ms) 33: [ RUN ] MatrixTest.noninvertableDeterminantIsZero 33: [ OK ] MatrixTest.noninvertableDeterminantIsZero (0 ms) 33: [ RUN ] MatrixTest.determinantOfDiagonalMatrix 33: [ OK ] MatrixTest.determinantOfDiagonalMatrix (0 ms) 33: [ RUN ] MatrixTest.traceWorks 33: [ OK ] MatrixTest.traceWorks (0 ms) 33: [ RUN ] MatrixTest.transposeWorks 33: [ OK ] MatrixTest.transposeWorks (0 ms) 33: [ RUN ] MatrixTest.transposeOfSymmetricMatrix 33: [ OK ] MatrixTest.transposeOfSymmetricMatrix (0 ms) 33: [ RUN ] MatrixTest.canCreateFromLegacyMatrix 33: [ OK ] MatrixTest.canCreateFromLegacyMatrix (0 ms) 33: [ RUN ] MatrixTest.canFillLegacyMatrix 33: [ OK ] MatrixTest.canFillLegacyMatrix (0 ms) 33: [ RUN ] MatrixTest.IdentityMatrix 33: [ OK ] MatrixTest.IdentityMatrix (0 ms) 33: [ RUN ] MatrixTest.MatrixMatrixInnerProduct 33: [ OK ] MatrixTest.MatrixMatrixInnerProduct (0 ms) 33: [ RUN ] MatrixTest.MatrixMatrixMultiplication 33: [ OK ] MatrixTest.MatrixMatrixMultiplication (0 ms) 33: [ RUN ] MatrixTest.MatrixVectorMultiplication 33: [ OK ] MatrixTest.MatrixVectorMultiplication (0 ms) 33: [----------] 22 tests from MatrixTest (0 ms total) 33: 33: [----------] 25 tests from MultiDimArrayTest 33: [ RUN ] MultiDimArrayTest.canConstructAndFillStatic 33: [ OK ] MultiDimArrayTest.canConstructAndFillStatic (0 ms) 33: [ RUN ] MultiDimArrayTest.canConstructAndFillDynamic 33: [ OK ] MultiDimArrayTest.canConstructAndFillDynamic (0 ms) 33: [ RUN ] MultiDimArrayTest.canSetValuesInStatic 33: [ OK ] MultiDimArrayTest.canSetValuesInStatic (0 ms) 33: [ RUN ] MultiDimArrayTest.canSetValuesInDynamic 33: [ OK ] MultiDimArrayTest.canSetValuesInDynamic (0 ms) 33: [ RUN ] MultiDimArrayTest.canMoveConstructStatic 33: [ OK ] MultiDimArrayTest.canMoveConstructStatic (0 ms) 33: [ RUN ] MultiDimArrayTest.canMoveConstructDynamic 33: [ OK ] MultiDimArrayTest.canMoveConstructDynamic (0 ms) 33: [ RUN ] MultiDimArrayTest.canMoveAssignStatic 33: [ OK ] MultiDimArrayTest.canMoveAssignStatic (0 ms) 33: [ RUN ] MultiDimArrayTest.canMoveAssignDynamic 33: [ OK ] MultiDimArrayTest.canMoveAssignDynamic (0 ms) 33: [ RUN ] MultiDimArrayTest.canCopyConstructStatic 33: [ OK ] MultiDimArrayTest.canCopyConstructStatic (0 ms) 33: [ RUN ] MultiDimArrayTest.canCopyConstructDynamic 33: [ OK ] MultiDimArrayTest.canCopyConstructDynamic (0 ms) 33: [ RUN ] MultiDimArrayTest.canCopyAssignStatic 33: [ OK ] MultiDimArrayTest.canCopyAssignStatic (0 ms) 33: [ RUN ] MultiDimArrayTest.canCopyAssignDynamic 33: [ OK ] MultiDimArrayTest.canCopyAssignDynamic (0 ms) 33: [ RUN ] MultiDimArrayTest.canSwapStatic 33: [ OK ] MultiDimArrayTest.canSwapStatic (0 ms) 33: [ RUN ] MultiDimArrayTest.canSwapDynamic 33: [ OK ] MultiDimArrayTest.canSwapDynamic (0 ms) 33: [ RUN ] MultiDimArrayTest.staticMultiDimArrayExtent 33: [ OK ] MultiDimArrayTest.staticMultiDimArrayExtent (0 ms) 33: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayExtent 33: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayExtent (0 ms) 33: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent 33: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent (0 ms) 33: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue 33: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue (0 ms) 33: [ RUN ] MultiDimArrayTest.staticMultiDimArrayFromArray 33: [ OK ] MultiDimArrayTest.staticMultiDimArrayFromArray (0 ms) 33: [ RUN ] MultiDimArrayTest.conversionToView 33: [ OK ] MultiDimArrayTest.conversionToView (0 ms) 33: [ RUN ] MultiDimArrayTest.conversionToConstView 33: [ OK ] MultiDimArrayTest.conversionToConstView (0 ms) 33: [ RUN ] MultiDimArrayTest.viewBegin 33: [ OK ] MultiDimArrayTest.viewBegin (0 ms) 33: [ RUN ] MultiDimArrayTest.viewEnd 33: [ OK ] MultiDimArrayTest.viewEnd (0 ms) 33: [ RUN ] MultiDimArrayTest.constViewConstBegin 33: [ OK ] MultiDimArrayTest.constViewConstBegin (0 ms) 33: [ RUN ] MultiDimArrayTest.constViewConstEnd 33: [ OK ] MultiDimArrayTest.constViewConstEnd (0 ms) 33: [----------] 25 tests from MultiDimArrayTest (0 ms total) 33: 33: [----------] 4 tests from MultiDimArrayToMdSpanTest 33: [ RUN ] MultiDimArrayToMdSpanTest.convertsToMdSpan 33: [ OK ] MultiDimArrayToMdSpanTest.convertsToMdSpan (0 ms) 33: [ RUN ] MultiDimArrayToMdSpanTest.constArrayToMdSpan 33: [ OK ] MultiDimArrayToMdSpanTest.constArrayToMdSpan (0 ms) 33: [ RUN ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan 33: [ OK ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan (0 ms) 33: [ RUN ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan 33: [ OK ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan (0 ms) 33: [----------] 4 tests from MultiDimArrayToMdSpanTest (0 ms total) 33: 33: [----------] 9 tests from NelderMeadSimplexTest 33: [ RUN ] NelderMeadSimplexTest.BestVertex 33: [ OK ] NelderMeadSimplexTest.BestVertex (0 ms) 33: [ RUN ] NelderMeadSimplexTest.WorstVertex 33: [ OK ] NelderMeadSimplexTest.WorstVertex (0 ms) 33: [ RUN ] NelderMeadSimplexTest.SecondWorstValue 33: [ OK ] NelderMeadSimplexTest.SecondWorstValue (0 ms) 33: [ RUN ] NelderMeadSimplexTest.ReflectionPoint 33: [ OK ] NelderMeadSimplexTest.ReflectionPoint (0 ms) 33: [ RUN ] NelderMeadSimplexTest.EvaluateExpansionPoint 33: [ OK ] NelderMeadSimplexTest.EvaluateExpansionPoint (0 ms) 33: [ RUN ] NelderMeadSimplexTest.EvaluateContractionPoint 33: [ OK ] NelderMeadSimplexTest.EvaluateContractionPoint (0 ms) 33: [ RUN ] NelderMeadSimplexTest.SwapOutWorst 33: [ OK ] NelderMeadSimplexTest.SwapOutWorst (0 ms) 33: [ RUN ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest 33: [ OK ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest (0 ms) 33: [ RUN ] NelderMeadSimplexTest.OrientedLength 33: [ OK ] NelderMeadSimplexTest.OrientedLength (0 ms) 33: [----------] 9 tests from NelderMeadSimplexTest (0 ms total) 33: 33: [----------] 2 tests from NelderMead 33: [ RUN ] NelderMead.Optimizes2DFunctionCorrectly 33: [ OK ] NelderMead.Optimizes2DFunctionCorrectly (0 ms) 33: [ RUN ] NelderMead.Optimizes3DFunctorCorrectly 33: [ OK ] NelderMead.Optimizes3DFunctorCorrectly (0 ms) 33: [----------] 2 tests from NelderMead (0 ms total) 33: 33: [----------] 11 tests from PaddedVectorTest/0, where TypeParam = std::allocator 33: [ RUN ] PaddedVectorTest/0.DefaultConstructorWorks 33: [ OK ] PaddedVectorTest/0.DefaultConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/0.ResizeWorks 33: [ OK ] PaddedVectorTest/0.ResizeWorks (0 ms) 33: [ RUN ] PaddedVectorTest/0.ReserveWorks 33: [ OK ] PaddedVectorTest/0.ReserveWorks (0 ms) 33: [ RUN ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve 33: [ OK ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve (0 ms) 33: [ RUN ] PaddedVectorTest/0.MoveConstructorWorks 33: [ OK ] PaddedVectorTest/0.MoveConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks 33: [ OK ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/0.MoveAssignmentWorks 33: [ OK ] PaddedVectorTest/0.MoveAssignmentWorks (0 ms) 33: [ RUN ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical 33: [ OK ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical (0 ms) 33: [ RUN ] PaddedVectorTest/0.CanCopyAssign 33: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms) 33: [ RUN ] PaddedVectorTest/0.CanMoveAssign 33: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms) 33: [ RUN ] PaddedVectorTest/0.CanSwap 33: [ OK ] PaddedVectorTest/0.CanSwap (0 ms) 33: [----------] 11 tests from PaddedVectorTest/0 (0 ms total) 33: 33: [----------] 11 tests from PaddedVectorTest/1, where TypeParam = std::allocator 33: [ RUN ] PaddedVectorTest/1.DefaultConstructorWorks 33: [ OK ] PaddedVectorTest/1.DefaultConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/1.ResizeWorks 33: [ OK ] PaddedVectorTest/1.ResizeWorks (0 ms) 33: [ RUN ] PaddedVectorTest/1.ReserveWorks 33: [ OK ] PaddedVectorTest/1.ReserveWorks (0 ms) 33: [ RUN ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve 33: [ OK ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve (0 ms) 33: [ RUN ] PaddedVectorTest/1.MoveConstructorWorks 33: [ OK ] PaddedVectorTest/1.MoveConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks 33: [ OK ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/1.MoveAssignmentWorks 33: [ OK ] PaddedVectorTest/1.MoveAssignmentWorks (0 ms) 33: [ RUN ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical 33: [ OK ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical (0 ms) 33: [ RUN ] PaddedVectorTest/1.CanCopyAssign 33: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms) 33: [ RUN ] PaddedVectorTest/1.CanMoveAssign 33: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms) 33: [ RUN ] PaddedVectorTest/1.CanSwap 33: [ OK ] PaddedVectorTest/1.CanSwap (0 ms) 33: [----------] 11 tests from PaddedVectorTest/1 (0 ms total) 33: 33: [----------] 11 tests from PaddedVectorTest/2, where TypeParam = std::allocator 33: [ RUN ] PaddedVectorTest/2.DefaultConstructorWorks 33: [ OK ] PaddedVectorTest/2.DefaultConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/2.ResizeWorks 33: [ OK ] PaddedVectorTest/2.ResizeWorks (0 ms) 33: [ RUN ] PaddedVectorTest/2.ReserveWorks 33: [ OK ] PaddedVectorTest/2.ReserveWorks (0 ms) 33: [ RUN ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve 33: [ OK ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve (0 ms) 33: [ RUN ] PaddedVectorTest/2.MoveConstructorWorks 33: [ OK ] PaddedVectorTest/2.MoveConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks 33: [ OK ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/2.MoveAssignmentWorks 33: [ OK ] PaddedVectorTest/2.MoveAssignmentWorks (0 ms) 33: [ RUN ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical 33: [ OK ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical (0 ms) 33: [ RUN ] PaddedVectorTest/2.CanCopyAssign 33: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms) 33: [ RUN ] PaddedVectorTest/2.CanMoveAssign 33: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms) 33: [ RUN ] PaddedVectorTest/2.CanSwap 33: [ OK ] PaddedVectorTest/2.CanSwap (0 ms) 33: [----------] 11 tests from PaddedVectorTest/2 (0 ms total) 33: 33: [----------] 11 tests from PaddedVectorTest/3, where TypeParam = std::allocator > 33: [ RUN ] PaddedVectorTest/3.DefaultConstructorWorks 33: [ OK ] PaddedVectorTest/3.DefaultConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/3.ResizeWorks 33: [ OK ] PaddedVectorTest/3.ResizeWorks (0 ms) 33: [ RUN ] PaddedVectorTest/3.ReserveWorks 33: [ OK ] PaddedVectorTest/3.ReserveWorks (0 ms) 33: [ RUN ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve 33: [ OK ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve (0 ms) 33: [ RUN ] PaddedVectorTest/3.MoveConstructorWorks 33: [ OK ] PaddedVectorTest/3.MoveConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks 33: [ OK ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/3.MoveAssignmentWorks 33: [ OK ] PaddedVectorTest/3.MoveAssignmentWorks (0 ms) 33: [ RUN ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical 33: [ OK ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical (0 ms) 33: [ RUN ] PaddedVectorTest/3.CanCopyAssign 33: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms) 33: [ RUN ] PaddedVectorTest/3.CanMoveAssign 33: [ OK ] PaddedVectorTest/3.CanMoveAssign (0 ms) 33: [ RUN ] PaddedVectorTest/3.CanSwap 33: [ OK ] PaddedVectorTest/3.CanSwap (0 ms) 33: [----------] 11 tests from PaddedVectorTest/3 (0 ms total) 33: 33: [----------] 11 tests from PaddedVectorTest/4, where TypeParam = std::allocator > 33: [ RUN ] PaddedVectorTest/4.DefaultConstructorWorks 33: [ OK ] PaddedVectorTest/4.DefaultConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/4.ResizeWorks 33: [ OK ] PaddedVectorTest/4.ResizeWorks (0 ms) 33: [ RUN ] PaddedVectorTest/4.ReserveWorks 33: [ OK ] PaddedVectorTest/4.ReserveWorks (0 ms) 33: [ RUN ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve 33: [ OK ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve (0 ms) 33: [ RUN ] PaddedVectorTest/4.MoveConstructorWorks 33: [ OK ] PaddedVectorTest/4.MoveConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks 33: [ OK ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/4.MoveAssignmentWorks 33: [ OK ] PaddedVectorTest/4.MoveAssignmentWorks (0 ms) 33: [ RUN ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical 33: [ OK ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical (0 ms) 33: [ RUN ] PaddedVectorTest/4.CanCopyAssign 33: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms) 33: [ RUN ] PaddedVectorTest/4.CanMoveAssign 33: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms) 33: [ RUN ] PaddedVectorTest/4.CanSwap 33: [ OK ] PaddedVectorTest/4.CanSwap (0 ms) 33: [----------] 11 tests from PaddedVectorTest/4 (0 ms total) 33: 33: [----------] 11 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator 33: [ RUN ] PaddedVectorTest/5.DefaultConstructorWorks 33: [ OK ] PaddedVectorTest/5.DefaultConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/5.ResizeWorks 33: [ OK ] PaddedVectorTest/5.ResizeWorks (0 ms) 33: [ RUN ] PaddedVectorTest/5.ReserveWorks 33: [ OK ] PaddedVectorTest/5.ReserveWorks (0 ms) 33: [ RUN ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve 33: [ OK ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve (0 ms) 33: [ RUN ] PaddedVectorTest/5.MoveConstructorWorks 33: [ OK ] PaddedVectorTest/5.MoveConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks 33: [ OK ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/5.MoveAssignmentWorks 33: [ OK ] PaddedVectorTest/5.MoveAssignmentWorks (0 ms) 33: [ RUN ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical 33: [ OK ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical (0 ms) 33: [ RUN ] PaddedVectorTest/5.CanCopyAssign 33: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms) 33: [ RUN ] PaddedVectorTest/5.CanMoveAssign 33: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms) 33: [ RUN ] PaddedVectorTest/5.CanSwap 33: [ OK ] PaddedVectorTest/5.CanSwap (0 ms) 33: [----------] 11 tests from PaddedVectorTest/5 (0 ms total) 33: 33: [----------] 11 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator 33: [ RUN ] PaddedVectorTest/6.DefaultConstructorWorks 33: [ OK ] PaddedVectorTest/6.DefaultConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/6.ResizeWorks 33: [ OK ] PaddedVectorTest/6.ResizeWorks (0 ms) 33: [ RUN ] PaddedVectorTest/6.ReserveWorks 33: [ OK ] PaddedVectorTest/6.ReserveWorks (0 ms) 33: [ RUN ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve 33: [ OK ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve (0 ms) 33: [ RUN ] PaddedVectorTest/6.MoveConstructorWorks 33: [ OK ] PaddedVectorTest/6.MoveConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks 33: [ OK ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/6.MoveAssignmentWorks 33: [ OK ] PaddedVectorTest/6.MoveAssignmentWorks (0 ms) 33: [ RUN ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical 33: [ OK ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical (0 ms) 33: [ RUN ] PaddedVectorTest/6.CanCopyAssign 33: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms) 33: [ RUN ] PaddedVectorTest/6.CanMoveAssign 33: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms) 33: [ RUN ] PaddedVectorTest/6.CanSwap 33: [ OK ] PaddedVectorTest/6.CanSwap (0 ms) 33: [----------] 11 tests from PaddedVectorTest/6 (0 ms total) 33: 33: [----------] 11 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator 33: [ RUN ] PaddedVectorTest/7.DefaultConstructorWorks 33: [ OK ] PaddedVectorTest/7.DefaultConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/7.ResizeWorks 33: [ OK ] PaddedVectorTest/7.ResizeWorks (0 ms) 33: [ RUN ] PaddedVectorTest/7.ReserveWorks 33: [ OK ] PaddedVectorTest/7.ReserveWorks (0 ms) 33: [ RUN ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve 33: [ OK ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve (0 ms) 33: [ RUN ] PaddedVectorTest/7.MoveConstructorWorks 33: [ OK ] PaddedVectorTest/7.MoveConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks 33: [ OK ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/7.MoveAssignmentWorks 33: [ OK ] PaddedVectorTest/7.MoveAssignmentWorks (0 ms) 33: [ RUN ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical 33: [ OK ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical (0 ms) 33: [ RUN ] PaddedVectorTest/7.CanCopyAssign 33: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms) 33: [ RUN ] PaddedVectorTest/7.CanMoveAssign 33: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms) 33: [ RUN ] PaddedVectorTest/7.CanSwap 33: [ OK ] PaddedVectorTest/7.CanSwap (0 ms) 33: [----------] 11 tests from PaddedVectorTest/7 (0 ms total) 33: 33: [----------] 11 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 33: [ RUN ] PaddedVectorTest/8.DefaultConstructorWorks 33: [ OK ] PaddedVectorTest/8.DefaultConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/8.ResizeWorks 33: [ OK ] PaddedVectorTest/8.ResizeWorks (0 ms) 33: [ RUN ] PaddedVectorTest/8.ReserveWorks 33: [ OK ] PaddedVectorTest/8.ReserveWorks (0 ms) 33: [ RUN ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve 33: [ OK ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve (0 ms) 33: [ RUN ] PaddedVectorTest/8.MoveConstructorWorks 33: [ OK ] PaddedVectorTest/8.MoveConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks 33: [ OK ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/8.MoveAssignmentWorks 33: [ OK ] PaddedVectorTest/8.MoveAssignmentWorks (0 ms) 33: [ RUN ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical 33: [ OK ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical (0 ms) 33: [ RUN ] PaddedVectorTest/8.CanCopyAssign 33: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms) 33: [ RUN ] PaddedVectorTest/8.CanMoveAssign 33: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms) 33: [ RUN ] PaddedVectorTest/8.CanSwap 33: [ OK ] PaddedVectorTest/8.CanSwap (0 ms) 33: [----------] 11 tests from PaddedVectorTest/8 (0 ms total) 33: 33: [----------] 11 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 33: [ RUN ] PaddedVectorTest/9.DefaultConstructorWorks 33: [ OK ] PaddedVectorTest/9.DefaultConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/9.ResizeWorks 33: [ OK ] PaddedVectorTest/9.ResizeWorks (0 ms) 33: [ RUN ] PaddedVectorTest/9.ReserveWorks 33: [ OK ] PaddedVectorTest/9.ReserveWorks (0 ms) 33: [ RUN ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve 33: [ OK ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve (0 ms) 33: [ RUN ] PaddedVectorTest/9.MoveConstructorWorks 33: [ OK ] PaddedVectorTest/9.MoveConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks 33: [ OK ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/9.MoveAssignmentWorks 33: [ OK ] PaddedVectorTest/9.MoveAssignmentWorks (0 ms) 33: [ RUN ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical 33: [ OK ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical (0 ms) 33: [ RUN ] PaddedVectorTest/9.CanCopyAssign 33: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms) 33: [ RUN ] PaddedVectorTest/9.CanMoveAssign 33: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms) 33: [ RUN ] PaddedVectorTest/9.CanSwap 33: [ OK ] PaddedVectorTest/9.CanSwap (0 ms) 33: [----------] 11 tests from PaddedVectorTest/9 (0 ms total) 33: 33: [----------] 41 tests from RVecTest 33: [ RUN ] RVecTest.CanBeStoredInVector 33: [ OK ] RVecTest.CanBeStoredInVector (0 ms) 33: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec 33: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms) 33: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec 33: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms) 33: [ RUN ] RVecTest.WorksAsMutable_rvec 33: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms) 33: [ RUN ] RVecTest.WorksAs_rvec_Array 33: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms) 33: [ RUN ] RVecTest.ComparesEqual 33: [ OK ] RVecTest.ComparesEqual (0 ms) 33: [ RUN ] RVecTest.ComparesUnequal 33: [ OK ] RVecTest.ComparesUnequal (0 ms) 33: [ RUN ] RVecTest.CanAddRVecToRvec 33: [ OK ] RVecTest.CanAddRVecToRvec (0 ms) 33: [ RUN ] RVecTest.CanAddAssignRVecToRvec 33: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms) 33: [ RUN ] RVecTest.CanSubtractRVecFromRvec 33: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms) 33: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec 33: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms) 33: [ RUN ] RVecTest.CanDotProductRVecByRvec 33: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms) 33: [ RUN ] RVecTest.CanCrossProductRVecByRvec 33: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms) 33: [ RUN ] RVecTest.CanDivideRVecInplace 33: [ OK ] RVecTest.CanDivideRVecInplace (0 ms) 33: [ RUN ] RVecTest.CanScaleRVec 33: [ OK ] RVecTest.CanScaleRVec (0 ms) 33: [ RUN ] RVecTest.CanDivideRVec 33: [ OK ] RVecTest.CanDivideRVec (0 ms) 33: [ RUN ] RVecTest.CanDoUnitvFromRVec 33: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms) 33: [ RUN ] RVecTest.CanSqLengthOfRVec 33: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms) 33: [ RUN ] RVecTest.CanLengthOfRVec 33: [ OK ] RVecTest.CanLengthOfRVec (0 ms) 33: [ RUN ] RVecTest.CanCastToRVec 33: [ OK ] RVecTest.CanCastToRVec (0 ms) 33: [ RUN ] RVecTest.CanCastToDVec 33: [ OK ] RVecTest.CanCastToDVec (0 ms) 33: [ RUN ] RVecTest.CanLeftScalarMultiply 33: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms) 33: [ RUN ] RVecTest.CanRightScalarMultiply 33: [ OK ] RVecTest.CanRightScalarMultiply (0 ms) 33: [ RUN ] RVecTest.CanGetUnitvFromRVec 33: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms) 33: [ RUN ] RVecTest.CanGetSqLengthOfRVec 33: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms) 33: [ RUN ] RVecTest.CanGetLengthOfRVec 33: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms) 33: [ RUN ] RVecTest.CanDoCrossProductOfRVec 33: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms) 33: [ RUN ] RVecTest.CanDoDotProductOfRVec 33: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms) 33: [ RUN ] RVecTest.CanScaleByVector 33: [ OK ] RVecTest.CanScaleByVector (0 ms) 33: [ RUN ] RVecTest.CanNegate 33: [ OK ] RVecTest.CanNegate (0 ms) 33: [ RUN ] RVecTest.asIVec 33: [ OK ] RVecTest.asIVec (0 ms) 33: [ RUN ] RVecTest.elementWiseMin 33: [ OK ] RVecTest.elementWiseMin (0 ms) 33: [ RUN ] RVecTest.elementWiseMax 33: [ OK ] RVecTest.elementWiseMax (0 ms) 33: [ RUN ] RVecTest.WorksAs_dvec_Reference 33: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms) 33: [ RUN ] RVecTest.WorksAs_ivec_Reference 33: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms) 33: [ RUN ] RVecTest.WorksAs_rvec_Reference 33: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms) 33: [ RUN ] RVecTest.CopyConstructorWorks 33: [ OK ] RVecTest.CopyConstructorWorks (0 ms) 33: [ RUN ] RVecTest.CopyAssignmentWorks 33: [ OK ] RVecTest.CopyAssignmentWorks (0 ms) 33: [ RUN ] RVecTest.MoveConstructorWorks 33: [ OK ] RVecTest.MoveConstructorWorks (0 ms) 33: [ RUN ] RVecTest.MoveAssignmentWorks 33: [ OK ] RVecTest.MoveAssignmentWorks (0 ms) 33: [ RUN ] RVecTest.UsableInConstexpr 33: [ OK ] RVecTest.UsableInConstexpr (0 ms) 33: [----------] 41 tests from RVecTest (0 ms total) 33: 33: [----------] Global test environment tear-down 33: [==========] 328 tests from 41 test suites ran. (68 ms total) 33: [ PASSED ] 328 tests. 33/90 Test #33: MathUnitTests ............................. Passed 0.12 sec test 34 Start 34: MdrunUtilityUnitTests 34: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/mdrunutility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/MdrunUtilityUnitTests.xml" 34: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdrunutility/tests 34: Test timeout computed to be: 30 34: [==========] Running 21 tests from 2 test suites. 34: [----------] Global test environment set-up. 34: [----------] 4 tests from MDModulesNotifierTest 34: [ RUN ] MDModulesNotifierTest.AddConsumer 34: [ OK ] MDModulesNotifierTest.AddConsumer (0 ms) 34: [ RUN ] MDModulesNotifierTest.AddConsumerWithPointerParameter 34: [ OK ] MDModulesNotifierTest.AddConsumerWithPointerParameter (0 ms) 34: [ RUN ] MDModulesNotifierTest.AddTwoDifferentConsumers 34: [ OK ] MDModulesNotifierTest.AddTwoDifferentConsumers (0 ms) 34: [ RUN ] MDModulesNotifierTest.AddConsumerOfTwoResources 34: [ OK ] MDModulesNotifierTest.AddConsumerOfTwoResources (0 ms) 34: [----------] 4 tests from MDModulesNotifierTest (0 ms total) 34: 34: [----------] 17 tests from ThreadAffinityTest 34: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled 34: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (0 ms) 34: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported 34: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms) 34: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads 34: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (0 ms) 34: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads 34: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (0 ms) 34: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads 34: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (0 ms) 34: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware 34: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (0 ms) 34: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads 34: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (0 ms) 34: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset 34: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (0 ms) 34: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride 34: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (0 ms) 34: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto 34: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (0 ms) 34: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced 34: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (0 ms) 34: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced 34: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (0 ms) 34: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread 34: NOTE: Affinity setting failed. 34: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (0 ms) 34: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto 34: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (2 ms) 34: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced 34: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (0 ms) 34: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads 34: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (0 ms) 34: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing 34: NOTE: Affinity setting for 1/2 threads failed. 34: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (0 ms) 34: [----------] 17 tests from ThreadAffinityTest (4 ms total) 34: 34: [----------] Global test environment tear-down 34: [==========] 21 tests from 2 test suites ran. (4 ms total) 34: [ PASSED ] 21 tests. 34/90 Test #34: MdrunUtilityUnitTests ..................... Passed 0.02 sec test 35 Start 35: MdrunUtilityMpiUnitTests 35: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/mdrunutility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/MdrunUtilityMpiUnitTests.xml" 35: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdrunutility/tests 35: Test timeout computed to be: 30 35: [==========] Running 13 tests from 2 test suites. 35: [----------] Global test environment set-up. 35: [----------] 6 tests from ThreadAffinityMultiRankTest 35: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode 35: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (4 ms) 35: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride 35: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (3 ms) 35: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes 35: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (17 ms) 35: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled 35: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (1 ms) 35: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto 35: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (1 ms) 35: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce 35: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (1 ms) 35: [----------] 6 tests from ThreadAffinityMultiRankTest (29 ms total) 35: 35: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest 35: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMainOnly 35: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMainOnly (3 ms) 35: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMainOnly 35: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMainOnly (1 ms) 35: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMain 35: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMain (5 ms) 35: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMainOnly 35: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMainOnly (3 ms) 35: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMainOnly 35: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMainOnly (1 ms) 35: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMainOnly 35: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMainOnly (1 ms) 35: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMainOnly 35: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMainOnly (1 ms) 35: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (18 ms total) 35: 35: [----------] Global test environment tear-down 35: [==========] 13 tests from 2 test suites ran. (48 ms total) 35: [ PASSED ] 13 tests. 35/90 Test #35: MdrunUtilityMpiUnitTests .................. Passed 0.07 sec test 36 Start 36: MDSpanTests 36: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/mdspan-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/MDSpanTests.xml" 36: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdspan/tests 36: Test timeout computed to be: 30 36: [==========] Running 32 tests from 7 test suites. 36: [----------] Global test environment set-up. 36: [----------] 4 tests from BasicAccessorPolicy 36: [ RUN ] BasicAccessorPolicy.Decay 36: [ OK ] BasicAccessorPolicy.Decay (0 ms) 36: [ RUN ] BasicAccessorPolicy.Access 36: [ OK ] BasicAccessorPolicy.Access (0 ms) 36: [ RUN ] BasicAccessorPolicy.Offset 36: [ OK ] BasicAccessorPolicy.Offset (0 ms) 36: [ RUN ] BasicAccessorPolicy.CopyAccessor 36: [ OK ] BasicAccessorPolicy.CopyAccessor (0 ms) 36: [----------] 4 tests from BasicAccessorPolicy (0 ms total) 36: 36: [----------] 4 tests from ExtentsTest 36: [ RUN ] ExtentsTest.Construction 36: [ OK ] ExtentsTest.Construction (0 ms) 36: [ RUN ] ExtentsTest.PurelyStatic 36: [ OK ] ExtentsTest.PurelyStatic (0 ms) 36: [ RUN ] ExtentsTest.RankNought 36: [ OK ] ExtentsTest.RankNought (0 ms) 36: [ RUN ] ExtentsTest.Assignment 36: [ OK ] ExtentsTest.Assignment (0 ms) 36: [----------] 4 tests from ExtentsTest (0 ms total) 36: 36: [----------] 8 tests from MdSpanExtension 36: [ RUN ] MdSpanExtension.SlicingAllStatic 36: [ OK ] MdSpanExtension.SlicingAllStatic (0 ms) 36: [ RUN ] MdSpanExtension.SlicingDynamic 36: [ OK ] MdSpanExtension.SlicingDynamic (0 ms) 36: [ RUN ] MdSpanExtension.SlicingAllStatic3D 36: [ OK ] MdSpanExtension.SlicingAllStatic3D (0 ms) 36: [ RUN ] MdSpanExtension.SlicingEqualsView3D 36: [ OK ] MdSpanExtension.SlicingEqualsView3D (0 ms) 36: [ RUN ] MdSpanExtension.additionWorks 36: [ OK ] MdSpanExtension.additionWorks (0 ms) 36: [ RUN ] MdSpanExtension.subtractionWorks 36: [ OK ] MdSpanExtension.subtractionWorks (0 ms) 36: [ RUN ] MdSpanExtension.multiplicationWorks 36: [ OK ] MdSpanExtension.multiplicationWorks (0 ms) 36: [ RUN ] MdSpanExtension.divisionWorks 36: [ OK ] MdSpanExtension.divisionWorks (0 ms) 36: [----------] 8 tests from MdSpanExtension (0 ms total) 36: 36: [----------] 3 tests from LayoutTests 36: [ RUN ] LayoutTests.LayoutRightConstruction 36: [ OK ] LayoutTests.LayoutRightConstruction (0 ms) 36: [ RUN ] LayoutTests.LayoutRightProperties 36: [ OK ] LayoutTests.LayoutRightProperties (0 ms) 36: [ RUN ] LayoutTests.LayoutRightOperator 36: [ OK ] LayoutTests.LayoutRightOperator (0 ms) 36: [----------] 3 tests from LayoutTests (0 ms total) 36: 36: [----------] 1 test from MdSpanTest 36: [ RUN ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly 36: [ OK ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly (0 ms) 36: [----------] 1 test from MdSpanTest (0 ms total) 36: 36: [----------] 6 tests from MdSpanTest/0, where TypeParam = gmx::basic_mdspan, gmx::layout_right, gmx::accessor_basic > 36: [ RUN ] MdSpanTest/0.Rank 36: [ OK ] MdSpanTest/0.Rank (0 ms) 36: [ RUN ] MdSpanTest/0.DynamicRank 36: [ OK ] MdSpanTest/0.DynamicRank (0 ms) 36: [ RUN ] MdSpanTest/0.Extents 36: [ OK ] MdSpanTest/0.Extents (0 ms) 36: [ RUN ] MdSpanTest/0.Strides 36: [ OK ] MdSpanTest/0.Strides (0 ms) 36: [ RUN ] MdSpanTest/0.Properties 36: [ OK ] MdSpanTest/0.Properties (0 ms) 36: [ RUN ] MdSpanTest/0.Operator 36: [ OK ] MdSpanTest/0.Operator (0 ms) 36: [----------] 6 tests from MdSpanTest/0 (0 ms total) 36: 36: [----------] 6 tests from MdSpanTest/1, where TypeParam = gmx::basic_mdspan, gmx::layout_right, gmx::accessor_basic > 36: [ RUN ] MdSpanTest/1.Rank 36: [ OK ] MdSpanTest/1.Rank (0 ms) 36: [ RUN ] MdSpanTest/1.DynamicRank 36: [ OK ] MdSpanTest/1.DynamicRank (0 ms) 36: [ RUN ] MdSpanTest/1.Extents 36: [ OK ] MdSpanTest/1.Extents (0 ms) 36: [ RUN ] MdSpanTest/1.Strides 36: [ OK ] MdSpanTest/1.Strides (0 ms) 36: [ RUN ] MdSpanTest/1.Properties 36: [ OK ] MdSpanTest/1.Properties (0 ms) 36: [ RUN ] MdSpanTest/1.Operator 36: [ OK ] MdSpanTest/1.Operator (0 ms) 36: [----------] 6 tests from MdSpanTest/1 (0 ms total) 36: 36: [----------] Global test environment tear-down 36: [==========] 32 tests from 7 test suites ran. (0 ms total) 36: [ PASSED ] 32 tests. 36/90 Test #36: MDSpanTests ............................... Passed 0.02 sec test 37 Start 37: MdtypesUnitTest 37: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/mdtypes-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/MdtypesUnitTest.xml" 37: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/mdtypes/tests 37: Test timeout computed to be: 30 37: [==========] Running 97 tests from 7 test suites. 37: [----------] Global test environment set-up. 37: [----------] 4 tests from ForeingLambdaTermsDhdl 37: [ RUN ] ForeingLambdaTermsDhdl.RateCheckWorks 37: [ OK ] ForeingLambdaTermsDhdl.RateCheckWorks (0 ms) 37: [ RUN ] ForeingLambdaTermsDhdl.AllLinear 37: [ OK ] ForeingLambdaTermsDhdl.AllLinear (0 ms) 37: [ RUN ] ForeingLambdaTermsDhdl.AllLinearNegative 37: [ OK ] ForeingLambdaTermsDhdl.AllLinearNegative (0 ms) 37: [ RUN ] ForeingLambdaTermsDhdl.SeparateVdwCoul 37: [ OK ] ForeingLambdaTermsDhdl.SeparateVdwCoul (0 ms) 37: [----------] 4 tests from ForeingLambdaTermsDhdl (0 ms total) 37: 37: [----------] 4 tests from ObservablesReducerTest 37: [ RUN ] ObservablesReducerTest.CanMoveAssign 37: [ OK ] ObservablesReducerTest.CanMoveAssign (0 ms) 37: [ RUN ] ObservablesReducerTest.CanMoveConstruct 37: [ OK ] ObservablesReducerTest.CanMoveConstruct (0 ms) 37: [ RUN ] ObservablesReducerTest.CanBuildAndUseWithNoSubscribers 37: [ OK ] ObservablesReducerTest.CanBuildAndUseWithNoSubscribers (0 ms) 37: [ RUN ] ObservablesReducerTest.CanBuildAndUseWithOneSubscriber 37: [ OK ] ObservablesReducerTest.CanBuildAndUseWithOneSubscriber (0 ms) 37: [----------] 4 tests from ObservablesReducerTest (0 ms total) 37: 37: [----------] 2 tests from CheckpointDataTest 37: [ RUN ] CheckpointDataTest.SingleDataTest 37: [ OK ] CheckpointDataTest.SingleDataTest (26 ms) 37: [ RUN ] CheckpointDataTest.MultiDataTest 37: [ OK ] CheckpointDataTest.MultiDataTest (548 ms) 37: [----------] 2 tests from CheckpointDataTest (574 ms total) 37: 37: [----------] 7 tests from ForceBuffers 37: [ RUN ] ForceBuffers.ConstructsUnpinned 37: [ OK ] ForceBuffers.ConstructsUnpinned (0 ms) 37: [ RUN ] ForceBuffers.ConstructsPinned 37: [ OK ] ForceBuffers.ConstructsPinned (0 ms) 37: [ RUN ] ForceBuffers.ConstructsEmpty 37: [ OK ] ForceBuffers.ConstructsEmpty (0 ms) 37: [ RUN ] ForceBuffers.ResizeWorks 37: [ OK ] ForceBuffers.ResizeWorks (0 ms) 37: [ RUN ] ForceBuffers.PaddingWorks 37: [ OK ] ForceBuffers.PaddingWorks (0 ms) 37: [ RUN ] ForceBuffers.CopyWorks 37: [ OK ] ForceBuffers.CopyWorks (0 ms) 37: [ RUN ] ForceBuffers.CopyDoesNotPin 37: [ OK ] ForceBuffers.CopyDoesNotPin (0 ms) 37: [----------] 7 tests from ForceBuffers (0 ms total) 37: 37: [----------] 5 tests from MultipleTimeStepping 37: [ RUN ] MultipleTimeStepping.ChecksNumLevels 37: [ OK ] MultipleTimeStepping.ChecksNumLevels (0 ms) 37: [ RUN ] MultipleTimeStepping.SelectsForceGroups 37: [ OK ] MultipleTimeStepping.SelectsForceGroups (0 ms) 37: [ RUN ] MultipleTimeStepping.ChecksStepFactor 37: [ OK ] MultipleTimeStepping.ChecksStepFactor (0 ms) 37: [ RUN ] MultipleTimeStepping.ChecksPmeIsAtLastLevel 37: [ OK ] MultipleTimeStepping.ChecksPmeIsAtLastLevel (0 ms) 37: [ RUN ] MultipleTimeStepping.ChecksIntegrator 37: [ OK ] MultipleTimeStepping.ChecksIntegrator (0 ms) 37: [----------] 5 tests from MultipleTimeStepping (0 ms total) 37: 37: [----------] 60 tests from WithVariousSubscriberCounts/ObservablesReducerIntegrationTest 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks3 (0 ms) 37: [----------] 60 tests from WithVariousSubscriberCounts/ObservablesReducerIntegrationTest (1 ms total) 37: 37: [----------] 15 tests from ChecksStepInterval/MtsIntervalTest 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/0 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/0 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/1 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/1 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/2 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/2 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/3 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/3 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/4 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/4 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/5 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/5 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/6 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/6 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/7 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/7 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/8 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/8 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/9 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/9 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/10 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/10 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/11 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/11 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/12 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/12 (2 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/13 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/13 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/14 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/14 (0 ms) 37: [----------] 15 tests from ChecksStepInterval/MtsIntervalTest (2 ms total) 37: 37: [----------] Global test environment tear-down 37: [==========] 97 tests from 7 test suites ran. (579 ms total) 37: [ PASSED ] 97 tests. 37/90 Test #37: MdtypesUnitTest ........................... Passed 0.61 sec test 38 Start 38: OnlineHelpUnitTests 38: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/onlinehelp-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/OnlineHelpUnitTests.xml" 38: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/onlinehelp/tests 38: Test timeout computed to be: 30 38: [==========] Running 22 tests from 4 test suites. 38: [----------] Global test environment set-up. 38: [----------] 6 tests from TextTableFormatterTest 38: [ RUN ] TextTableFormatterTest.HandlesBasicCase 38: [ OK ] TextTableFormatterTest.HandlesBasicCase (0 ms) 38: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles 38: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (0 ms) 38: [ RUN ] TextTableFormatterTest.HandlesIndentation 38: [ OK ] TextTableFormatterTest.HandlesIndentation (0 ms) 38: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines 38: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (0 ms) 38: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding 38: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (0 ms) 38: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns 38: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (0 ms) 38: [----------] 6 tests from TextTableFormatterTest (0 ms total) 38: 38: [----------] 3 tests from HelpManagerTest 38: [ RUN ] HelpManagerTest.HandlesRootTopic 38: [ OK ] HelpManagerTest.HandlesRootTopic (0 ms) 38: [ RUN ] HelpManagerTest.HandlesSubTopics 38: [ OK ] HelpManagerTest.HandlesSubTopics (0 ms) 38: [ RUN ] HelpManagerTest.HandlesInvalidTopics 38: [ OK ] HelpManagerTest.HandlesInvalidTopics (0 ms) 38: [----------] 3 tests from HelpManagerTest (0 ms total) 38: 38: [----------] 2 tests from HelpTopicFormattingTest 38: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic 38: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (0 ms) 38: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics 38: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (0 ms) 38: [----------] 2 tests from HelpTopicFormattingTest (0 ms total) 38: 38: [----------] 11 tests from HelpWriterContextTest 38: [ RUN ] HelpWriterContextTest.FormatsParagraphs 38: [ OK ] HelpWriterContextTest.FormatsParagraphs (0 ms) 38: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs 38: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (0 ms) 38: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace 38: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (0 ms) 38: [ RUN ] HelpWriterContextTest.FormatsLiteralText 38: [ OK ] HelpWriterContextTest.FormatsLiteralText (0 ms) 38: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning 38: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (0 ms) 38: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation 38: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (0 ms) 38: [ RUN ] HelpWriterContextTest.FormatsBulletList 38: [ OK ] HelpWriterContextTest.FormatsBulletList (0 ms) 38: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList 38: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (0 ms) 38: [ RUN ] HelpWriterContextTest.FormatsSimpleTable 38: [ OK ] HelpWriterContextTest.FormatsSimpleTable (0 ms) 38: [ RUN ] HelpWriterContextTest.FormatsGridTable 38: [ OK ] HelpWriterContextTest.FormatsGridTable (0 ms) 38: [ RUN ] HelpWriterContextTest.FormatsTitles 38: [ OK ] HelpWriterContextTest.FormatsTitles (0 ms) 38: [----------] 11 tests from HelpWriterContextTest (0 ms total) 38: 38: [----------] Global test environment tear-down 38: [==========] 22 tests from 4 test suites ran. (1 ms total) 38: [ PASSED ] 22 tests. 38/90 Test #38: OnlineHelpUnitTests ....................... Passed 0.09 sec test 39 Start 39: OptionsUnitTests 39: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/options-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/OptionsUnitTests.xml" 39: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options/tests 39: Test timeout computed to be: 30 39: [==========] Running 112 tests from 18 test suites. 39: [----------] Global test environment set-up. 39: [----------] 5 tests from AbstractOptionStorageTest 39: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish 39: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (0 ms) 39: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval 39: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (0 ms) 39: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition 39: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (0 ms) 39: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition 39: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (0 ms) 39: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues 39: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (0 ms) 39: [----------] 5 tests from AbstractOptionStorageTest (0 ms total) 39: 39: [----------] 10 tests from FileNameOptionTest 39: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension 39: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (0 ms) 39: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue 39: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms) 39: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption 39: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms) 39: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension 39: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms) 39: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension 39: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms) 39: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension 39: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms) 39: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix 39: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (0 ms) 39: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix 39: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms) 39: [ RUN ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension 39: [ OK ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension (0 ms) 39: [ RUN ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue 39: [ OK ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue (0 ms) 39: [----------] 10 tests from FileNameOptionTest (0 ms total) 39: 39: [----------] 16 tests from FileNameOptionManagerTest 39: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension 39: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms) 39: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension 39: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms) 39: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile 39: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (0 ms) 39: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile 39: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (0 ms) 39: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile 39: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (0 ms) 39: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile 39: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms) 39: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified 39: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms) 39: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified 39: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms) 39: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified 39: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms) 39: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile 39: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms) 39: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile 39: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms) 39: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile 39: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms) 39: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile 39: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms) 39: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile 39: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms) 39: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking 39: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms) 39: [ RUN ] FileNameOptionManagerTest.AcceptsCompressedInputFile 39: [ OK ] FileNameOptionManagerTest.AcceptsCompressedInputFile (0 ms) 39: [----------] 16 tests from FileNameOptionManagerTest (0 ms total) 39: 39: [----------] 1 test from OptionsTest 39: [ RUN ] OptionsTest.FailsOnNonsafeStorage 39: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms) 39: [----------] 1 test from OptionsTest (0 ms total) 39: 39: [----------] 9 tests from OptionsAssignerTest 39: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter 39: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms) 39: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue 39: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms) 39: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter 39: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (0 ms) 39: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter 39: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms) 39: [ RUN ] OptionsAssignerTest.HandlesMissingValue 39: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms) 39: [ RUN ] OptionsAssignerTest.HandlesExtraValue 39: [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms) 39: [ RUN ] OptionsAssignerTest.HandlesGroups 39: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms) 39: [ RUN ] OptionsAssignerTest.HandlesSections 39: [ OK ] OptionsAssignerTest.HandlesSections (0 ms) 39: [ RUN ] OptionsAssignerTest.HandlesMultipleSources 39: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms) 39: [----------] 9 tests from OptionsAssignerTest (0 ms total) 39: 39: [----------] 4 tests from OptionsAssignerBooleanTest 39: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue 39: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms) 39: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue 39: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms) 39: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo 39: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms) 39: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue 39: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms) 39: [----------] 4 tests from OptionsAssignerBooleanTest (0 ms total) 39: 39: [----------] 13 tests from OptionsAssignerIntegerTest 39: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue 39: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue 39: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue 39: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow 39: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue 39: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet 39: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet 39: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues 39: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.StoresToVector 39: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors 39: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue 39: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue 39: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment 39: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms) 39: [----------] 13 tests from OptionsAssignerIntegerTest (0 ms total) 39: 39: [----------] 5 tests from OptionsAssignerDoubleTest 39: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue 39: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms) 39: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat 39: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms) 39: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue 39: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (0 ms) 39: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue 39: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms) 39: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue 39: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms) 39: [----------] 5 tests from OptionsAssignerDoubleTest (0 ms total) 39: 39: [----------] 9 tests from OptionsAssignerStringTest 39: [ RUN ] OptionsAssignerStringTest.StoresSingleValue 39: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms) 39: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue 39: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms) 39: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray 39: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms) 39: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue 39: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms) 39: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue 39: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms) 39: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue 39: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms) 39: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue 39: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms) 39: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable 39: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms) 39: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector 39: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms) 39: [----------] 9 tests from OptionsAssignerStringTest (0 ms total) 39: 39: [----------] 6 tests from OptionsAssignerEnumTest 39: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue 39: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms) 39: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues 39: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms) 39: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange 39: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms) 39: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue 39: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms) 39: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable 39: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms) 39: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector 39: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms) 39: [----------] 6 tests from OptionsAssignerEnumTest (0 ms total) 39: 39: [----------] 8 tests from RepeatingOptionSectionTest 39: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance 39: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms) 39: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption 39: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms) 39: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance 39: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms) 39: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue 39: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms) 39: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances 39: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms) 39: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault 39: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms) 39: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault 39: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms) 39: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections 39: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms) 39: [----------] 8 tests from RepeatingOptionSectionTest (0 ms total) 39: 39: [----------] 1 test from TimeUnitManagerTest 39: [ RUN ] TimeUnitManagerTest.BasicOperations 39: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms) 39: [----------] 1 test from TimeUnitManagerTest (0 ms total) 39: 39: [----------] 4 tests from TimeUnitBehaviorTest 39: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue 39: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms) 39: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues 39: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms) 39: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources 39: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms) 39: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks 39: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms) 39: [----------] 4 tests from TimeUnitBehaviorTest (0 ms total) 39: 39: [----------] 2 tests from TreeValueSupportAssignTest 39: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree 39: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (0 ms) 39: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays 39: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms) 39: [----------] 2 tests from TreeValueSupportAssignTest (0 ms total) 39: 39: [----------] 1 test from TreeValueSupportAssignErrorTest 39: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue 39: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (0 ms) 39: [----------] 1 test from TreeValueSupportAssignErrorTest (0 ms total) 39: 39: [----------] 5 tests from TreeValueSupportCheckTest 39: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty 39: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms) 39: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree 39: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms) 39: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1 39: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms) 39: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2 39: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms) 39: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue 39: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms) 39: [----------] 5 tests from TreeValueSupportCheckTest (0 ms total) 39: 39: [----------] 6 tests from TreeValueSupportAdjustTest 39: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues 39: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (0 ms) 39: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues 39: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (0 ms) 39: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues 39: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (0 ms) 39: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues 39: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (0 ms) 39: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues 39: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (0 ms) 39: [ RUN ] TreeValueSupportAdjustTest.OrdersValues 39: [ OK ] TreeValueSupportAdjustTest.OrdersValues (0 ms) 39: [----------] 6 tests from TreeValueSupportAdjustTest (0 ms total) 39: 39: [----------] 7 tests from TreeValueSupportTest 39: [ RUN ] TreeValueSupportTest.SupportsBooleanOption 39: [ OK ] TreeValueSupportTest.SupportsBooleanOption (0 ms) 39: [ RUN ] TreeValueSupportTest.SupportsIntegerOption 39: [ OK ] TreeValueSupportTest.SupportsIntegerOption (0 ms) 39: [ RUN ] TreeValueSupportTest.SupportsInt64Option 39: [ OK ] TreeValueSupportTest.SupportsInt64Option (0 ms) 39: [ RUN ] TreeValueSupportTest.SupportsStringOption 39: [ OK ] TreeValueSupportTest.SupportsStringOption (0 ms) 39: [ RUN ] TreeValueSupportTest.SupportsFloatOption 39: [ OK ] TreeValueSupportTest.SupportsFloatOption (0 ms) 39: [ RUN ] TreeValueSupportTest.SupportsDoubleOption 39: [ OK ] TreeValueSupportTest.SupportsDoubleOption (0 ms) 39: [ RUN ] TreeValueSupportTest.SupportsEnumOption 39: [ OK ] TreeValueSupportTest.SupportsEnumOption (0 ms) 39: [----------] 7 tests from TreeValueSupportTest (0 ms total) 39: 39: [----------] Global test environment tear-down 39: [==========] 112 tests from 18 test suites ran. (3 ms total) 39: [ PASSED ] 112 tests. 39/90 Test #39: OptionsUnitTests .......................... Passed 0.13 sec test 40 Start 40: PbcutilUnitTest 40: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/pbcutil-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/PbcutilUnitTest.xml" 40: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/pbcutil/tests 40: Test timeout computed to be: 30 40: [==========] Running 37 tests from 5 test suites. 40: [----------] Global test environment set-up. 40: [----------] 1 test from ShiftTest 40: [ RUN ] ShiftTest.CoordinateShiftWorks 40: [ OK ] ShiftTest.CoordinateShiftWorks (0 ms) 40: [----------] 1 test from ShiftTest (0 ms total) 40: 40: [----------] 2 tests from MShift 40: [ RUN ] MShift.shiftsAndUnshifts 40: [ OK ] MShift.shiftsAndUnshifts (0 ms) 40: [ RUN ] MShift.shiftsAndUnshiftsSelf 40: [ OK ] MShift.shiftsAndUnshiftsSelf (0 ms) 40: [----------] 2 tests from MShift (0 ms total) 40: 40: [----------] 5 tests from PbcTest 40: [ RUN ] PbcTest.CalcShiftsWorks 40: [ OK ] PbcTest.CalcShiftsWorks (0 ms) 40: [ RUN ] PbcTest.PutAtomsInCubicBoxAlreadyInBox 40: [ OK ] PbcTest.PutAtomsInCubicBoxAlreadyInBox (0 ms) 40: [ RUN ] PbcTest.PutAtomsInCubicBoxFromOutsideBox 40: [ OK ] PbcTest.PutAtomsInCubicBoxFromOutsideBox (0 ms) 40: [ RUN ] PbcTest.PutAtomsInTriclinicBoxFromOutsideBox 40: [ OK ] PbcTest.PutAtomsInTriclinicBoxFromOutsideBox (0 ms) 40: [ RUN ] PbcTest.PutAtomsInBoxHandlesInf 40: [ OK ] PbcTest.PutAtomsInBoxHandlesInf (0 ms) 40: [----------] 5 tests from PbcTest (0 ms total) 40: 40: [----------] 2 tests from PbcEnumsTest 40: [ RUN ] PbcEnumsTest.CenteringTypeNamesAreCorrect 40: [ OK ] PbcEnumsTest.CenteringTypeNamesAreCorrect (0 ms) 40: [ RUN ] PbcEnumsTest.UnitCellTypeNamesAreCorrect 40: [ OK ] PbcEnumsTest.UnitCellTypeNamesAreCorrect (0 ms) 40: [----------] 2 tests from PbcEnumsTest (0 ms total) 40: 40: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 (0 ms) 40: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest (6 ms total) 40: 40: [----------] Global test environment tear-down 40: [==========] 37 tests from 5 test suites ran. (7 ms total) 40: [ PASSED ] 37 tests. 40/90 Test #40: PbcutilUnitTest ........................... Passed 0.03 sec test 41 Start 41: RandomUnitTests 41: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/random-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/RandomUnitTests.xml" 41: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/random/tests 41: Test timeout computed to be: 30 41: [==========] Running 44 tests from 10 test suites. 41: [----------] Global test environment set-up. 41: [----------] 4 tests from ExponentialDistributionTest 41: [ RUN ] ExponentialDistributionTest.Output 41: [ OK ] ExponentialDistributionTest.Output (0 ms) 41: [ RUN ] ExponentialDistributionTest.Logical 41: [ OK ] ExponentialDistributionTest.Logical (0 ms) 41: [ RUN ] ExponentialDistributionTest.Reset 41: [ OK ] ExponentialDistributionTest.Reset (0 ms) 41: [ RUN ] ExponentialDistributionTest.AltParam 41: [ OK ] ExponentialDistributionTest.AltParam (0 ms) 41: [----------] 4 tests from ExponentialDistributionTest (0 ms total) 41: 41: [----------] 4 tests from GammaDistributionTest 41: [ RUN ] GammaDistributionTest.Output 41: [ OK ] GammaDistributionTest.Output (0 ms) 41: [ RUN ] GammaDistributionTest.Logical 41: [ OK ] GammaDistributionTest.Logical (0 ms) 41: [ RUN ] GammaDistributionTest.Reset 41: [ OK ] GammaDistributionTest.Reset (0 ms) 41: [ RUN ] GammaDistributionTest.AltParam 41: [ OK ] GammaDistributionTest.AltParam (0 ms) 41: [----------] 4 tests from GammaDistributionTest (0 ms total) 41: 41: [----------] 4 tests from NormalDistributionTest 41: [ RUN ] NormalDistributionTest.Output 41: [ OK ] NormalDistributionTest.Output (0 ms) 41: [ RUN ] NormalDistributionTest.Logical 41: [ OK ] NormalDistributionTest.Logical (0 ms) 41: [ RUN ] NormalDistributionTest.Reset 41: [ OK ] NormalDistributionTest.Reset (0 ms) 41: [ RUN ] NormalDistributionTest.AltParam 41: [ OK ] NormalDistributionTest.AltParam (0 ms) 41: [----------] 4 tests from NormalDistributionTest (0 ms total) 41: 41: [----------] 1 test from SeedTest 41: [ RUN ] SeedTest.makeRandomSeed 41: [ OK ] SeedTest.makeRandomSeed (0 ms) 41: [----------] 1 test from SeedTest (0 ms total) 41: 41: [----------] 6 tests from TabulatedNormalDistributionTest 41: [ RUN ] TabulatedNormalDistributionTest.Output14 41: [ OK ] TabulatedNormalDistributionTest.Output14 (0 ms) 41: [ RUN ] TabulatedNormalDistributionTest.Output16 41: [ OK ] TabulatedNormalDistributionTest.Output16 (0 ms) 41: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14 41: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (0 ms) 41: [ RUN ] TabulatedNormalDistributionTest.Logical 41: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms) 41: [ RUN ] TabulatedNormalDistributionTest.Reset 41: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms) 41: [ RUN ] TabulatedNormalDistributionTest.AltParam 41: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms) 41: [----------] 6 tests from TabulatedNormalDistributionTest (0 ms total) 41: 41: [----------] 1 test from TabulatedNormalDistributionTableTest 41: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties 41: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (0 ms) 41: [----------] 1 test from TabulatedNormalDistributionTableTest (0 ms total) 41: 41: [----------] 6 tests from ThreeFry2x64Test 41: [ RUN ] ThreeFry2x64Test.Logical 41: [ OK ] ThreeFry2x64Test.Logical (0 ms) 41: [ RUN ] ThreeFry2x64Test.InternalCounterSequence 41: [ OK ] ThreeFry2x64Test.InternalCounterSequence (0 ms) 41: [ RUN ] ThreeFry2x64Test.Reseed 41: [ OK ] ThreeFry2x64Test.Reseed (0 ms) 41: [ RUN ] ThreeFry2x64Test.Discard 41: [ OK ] ThreeFry2x64Test.Discard (0 ms) 41: [ RUN ] ThreeFry2x64Test.InvalidCounter 41: [ OK ] ThreeFry2x64Test.InvalidCounter (0 ms) 41: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter 41: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms) 41: [----------] 6 tests from ThreeFry2x64Test (0 ms total) 41: 41: [----------] 4 tests from UniformIntDistributionTest 41: [ RUN ] UniformIntDistributionTest.Output 41: [ OK ] UniformIntDistributionTest.Output (0 ms) 41: [ RUN ] UniformIntDistributionTest.Logical 41: [ OK ] UniformIntDistributionTest.Logical (0 ms) 41: [ RUN ] UniformIntDistributionTest.Reset 41: [ OK ] UniformIntDistributionTest.Reset (0 ms) 41: [ RUN ] UniformIntDistributionTest.AltParam 41: [ OK ] UniformIntDistributionTest.AltParam (0 ms) 41: [----------] 4 tests from UniformIntDistributionTest (0 ms total) 41: 41: [----------] 5 tests from UniformRealDistributionTest 41: [ RUN ] UniformRealDistributionTest.GenerateCanonical 41: [ OK ] UniformRealDistributionTest.GenerateCanonical (0 ms) 41: [ RUN ] UniformRealDistributionTest.Output 41: [ OK ] UniformRealDistributionTest.Output (0 ms) 41: [ RUN ] UniformRealDistributionTest.Logical 41: [ OK ] UniformRealDistributionTest.Logical (0 ms) 41: [ RUN ] UniformRealDistributionTest.Reset 41: [ OK ] UniformRealDistributionTest.Reset (0 ms) 41: [ RUN ] UniformRealDistributionTest.AltParam 41: [ OK ] UniformRealDistributionTest.AltParam (0 ms) 41: [----------] 5 tests from UniformRealDistributionTest (0 ms total) 41: 41: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test 41: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0 41: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (0 ms) 41: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1 41: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (0 ms) 41: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2 41: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (0 ms) 41: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 41: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (0 ms) 41: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 41: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (0 ms) 41: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 41: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (0 ms) 41: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 41: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (0 ms) 41: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 41: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (0 ms) 41: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 41: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (0 ms) 41: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (0 ms total) 41: 41: [----------] Global test environment tear-down 41: [==========] 44 tests from 10 test suites ran. (4 ms total) 41: [ PASSED ] 44 tests. 41/90 Test #41: RandomUnitTests ........................... Passed 0.03 sec test 42 Start 42: RestraintTests 42: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/restraintpotential-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/RestraintTests.xml" 42: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/restraint/tests 42: Test timeout computed to be: 30 42: [==========] Running 1 test from 1 test suite. 42: [----------] Global test environment set-up. 42: [----------] 1 test from RestraintManager 42: [ RUN ] RestraintManager.restraintList 42: [ OK ] RestraintManager.restraintList (0 ms) 42: [----------] 1 test from RestraintManager (0 ms total) 42: 42: [----------] Global test environment tear-down 42: [==========] 1 test from 1 test suite ran. (0 ms total) 42: [ PASSED ] 1 test. 42/90 Test #42: RestraintTests ............................ Passed 0.02 sec test 43 Start 43: TableUnitTests 43: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/table-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/TableUnitTests.xml" 43: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tables/tests 43: Test timeout computed to be: 30 43: [==========] Running 20 tests from 2 test suites. 43: [----------] Global test environment set-up. 43: [----------] 10 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable 43: [ RUN ] SplineTableTest/0.HandlesIncorrectInput 43: [ OK ] SplineTableTest/0.HandlesIncorrectInput (1 ms) 43: [ RUN ] SplineTableTest/0.Sinc 43: [ OK ] SplineTableTest/0.Sinc (0 ms) 43: [ RUN ] SplineTableTest/0.LJ12 43: [ OK ] SplineTableTest/0.LJ12 (17 ms) 43: [ RUN ] SplineTableTest/0.PmeCorrection 43: [ OK ] SplineTableTest/0.PmeCorrection (1 ms) 43: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput 43: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (0 ms) 43: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr 43: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (0 ms) 43: [ RUN ] SplineTableTest/0.TwoFunctions 43: [ OK ] SplineTableTest/0.TwoFunctions (33 ms) 43: [ RUN ] SplineTableTest/0.ThreeFunctions 43: [ OK ] SplineTableTest/0.ThreeFunctions (36 ms) 43: [ RUN ] SplineTableTest/0.Simd 43: [ OK ] SplineTableTest/0.Simd (7 ms) 43: [ RUN ] SplineTableTest/0.SimdTwoFunctions 43: [ OK ] SplineTableTest/0.SimdTwoFunctions (31 ms) 43: [----------] 10 tests from SplineTableTest/0 (131 ms total) 43: 43: [----------] 10 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable 43: [ RUN ] SplineTableTest/1.HandlesIncorrectInput 43: [ OK ] SplineTableTest/1.HandlesIncorrectInput (1 ms) 43: [ RUN ] SplineTableTest/1.Sinc 43: [ OK ] SplineTableTest/1.Sinc (1 ms) 43: [ RUN ] SplineTableTest/1.LJ12 43: [ OK ] SplineTableTest/1.LJ12 (39 ms) 43: [ RUN ] SplineTableTest/1.PmeCorrection 43: [ OK ] SplineTableTest/1.PmeCorrection (1 ms) 43: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput 43: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (0 ms) 43: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr 43: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (0 ms) 43: [ RUN ] SplineTableTest/1.TwoFunctions 43: [ OK ] SplineTableTest/1.TwoFunctions (73 ms) 43: [ RUN ] SplineTableTest/1.ThreeFunctions 43: [ OK ] SplineTableTest/1.ThreeFunctions (77 ms) 43: [ RUN ] SplineTableTest/1.Simd 43: [ OK ] SplineTableTest/1.Simd (15 ms) 43: [ RUN ] SplineTableTest/1.SimdTwoFunctions 43: [ OK ] SplineTableTest/1.SimdTwoFunctions (64 ms) 43: [----------] 10 tests from SplineTableTest/1 (275 ms total) 43: 43: [----------] Global test environment tear-down 43: [==========] 20 tests from 2 test suites ran. (407 ms total) 43: [ PASSED ] 20 tests. 43/90 Test #43: TableUnitTests ............................ Passed 0.43 sec test 44 Start 44: TaskAssignmentUnitTests 44: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/taskassignment-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/TaskAssignmentUnitTests.xml" 44: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/taskassignment/tests 44: Test timeout computed to be: 30 44: [==========] Running 3 tests from 2 test suites. 44: [----------] Global test environment set-up. 44: [----------] 2 tests from UserTaskAssignmentStringHandlingTest 44: [ RUN ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork 44: [ OK ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork (0 ms) 44: [ RUN ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid 44: [ OK ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid (0 ms) 44: [----------] 2 tests from UserTaskAssignmentStringHandlingTest (0 ms total) 44: 44: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest 44: [ RUN ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow 44: [ OK ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow (0 ms) 44: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest (0 ms total) 44: 44: [----------] Global test environment tear-down 44: [==========] 3 tests from 2 test suites ran. (0 ms total) 44: [ PASSED ] 3 tests. 44/90 Test #44: TaskAssignmentUnitTests ................... Passed 0.02 sec test 45 Start 45: GmxTimingTests 45: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/timing-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/GmxTimingTests.xml" 45: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/timing/tests 45: Test timeout computed to be: 30 45: [==========] Running 6 tests from 1 test suite. 45: [----------] Global test environment set-up. 45: [----------] 6 tests from TimingTest 45: [ RUN ] TimingTest.ElementCountingWorks 45: [ OK ] TimingTest.ElementCountingWorks (0 ms) 45: [ RUN ] TimingTest.ElementNoCountingWorks 45: [ OK ] TimingTest.ElementNoCountingWorks (0 ms) 45: [ RUN ] TimingTest.SubElementCountingWorks 45: [ OK ] TimingTest.SubElementCountingWorks (0 ms) 45: [ RUN ] TimingTest.SubElementNoCountingWorks 45: [ OK ] TimingTest.SubElementNoCountingWorks (0 ms) 45: [ RUN ] TimingTest.RunWallCycle 45: [ OK ] TimingTest.RunWallCycle (1 ms) 45: [ RUN ] TimingTest.RunWallCycleSub 45: [ OK ] TimingTest.RunWallCycleSub (0 ms) 45: [----------] 6 tests from TimingTest (1 ms total) 45: 45: [----------] Global test environment tear-down 45: [==========] 6 tests from 1 test suite ran. (1 ms total) 45: [ PASSED ] 6 tests. 45/90 Test #45: GmxTimingTests ............................ Passed 0.02 sec test 46 Start 46: TopologyTest 46: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/topology-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/TopologyTest.xml" 46: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/topology/tests 46: Test timeout computed to be: 30 46: [==========] Running 153 tests from 10 test suites. 46: [----------] Global test environment set-up. 46: [----------] 3 tests from PdbAtomEntryTest 46: [ RUN ] PdbAtomEntryTest.CanCreateBasicEntry 46: [ OK ] PdbAtomEntryTest.CanCreateBasicEntry (0 ms) 46: [ RUN ] PdbAtomEntryTest.CanCreateEntryWithOccupAndBfac 46: [ OK ] PdbAtomEntryTest.CanCreateEntryWithOccupAndBfac (0 ms) 46: [ RUN ] PdbAtomEntryTest.CanCreateFullEntry 46: [ OK ] PdbAtomEntryTest.CanCreateFullEntry (0 ms) 46: [----------] 3 tests from PdbAtomEntryTest (0 ms total) 46: 46: [----------] 3 tests from ExclusionBlockTest 46: [ RUN ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks 46: [ OK ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks (0 ms) 46: [ RUN ] ExclusionBlockTest.ConvertExclusionBlockToBlocka 46: [ OK ] ExclusionBlockTest.ConvertExclusionBlockToBlocka (0 ms) 46: [ RUN ] ExclusionBlockTest.MergeExclusions 46: [ OK ] ExclusionBlockTest.MergeExclusions (0 ms) 46: [----------] 3 tests from ExclusionBlockTest (0 ms total) 46: 46: [----------] 6 tests from InteractionListTest 46: [ RUN ] InteractionListTest.EmptyWorks 46: [ OK ] InteractionListTest.EmptyWorks (0 ms) 46: [ RUN ] InteractionListTest.CanAddInteractionArray 46: [ OK ] InteractionListTest.CanAddInteractionArray (0 ms) 46: [ RUN ] InteractionListTest.CanAddInteractionArrayMultipleAtoms 46: [ OK ] InteractionListTest.CanAddInteractionArrayMultipleAtoms (0 ms) 46: [ RUN ] InteractionListTest.CanAddInteractionPointer 46: [ OK ] InteractionListTest.CanAddInteractionPointer (0 ms) 46: [ RUN ] InteractionListTest.CanAddListToOtherList 46: [ OK ] InteractionListTest.CanAddListToOtherList (0 ms) 46: [ RUN ] InteractionListTest.ClearingWorks 46: [ OK ] InteractionListTest.ClearingWorks (0 ms) 46: [----------] 6 tests from InteractionListTest (0 ms total) 46: 46: [----------] 3 tests from IndexTest 46: [ RUN ] IndexTest.AnalyseWorksDefaultGroups 46: 46: WARNING: Masses and atomic (Van der Waals) radii will be guessed 46: based on residue and atom names, since they could not be 46: definitively assigned from the information in your input 46: files. These guessed numbers might deviate from the mass 46: and radius of the atom type. Please check the output 46: files if necessary. Note, that this functionality may 46: be removed in a future GROMACS version. Please, consider 46: using another file format for your input. 46: 46: [ OK ] IndexTest.AnalyseWorksDefaultGroups (5 ms) 46: [ RUN ] IndexTest.WriteIndexWorks 46: 46: WARNING: Masses and atomic (Van der Waals) radii will be guessed 46: based on residue and atom names, since they could not be 46: definitively assigned from the information in your input 46: files. These guessed numbers might deviate from the mass 46: and radius of the atom type. Please check the output 46: files if necessary. Note, that this functionality may 46: be removed in a future GROMACS version. Please, consider 46: using another file format for your input. 46: 46: [ OK ] IndexTest.WriteIndexWorks (12 ms) 46: [ RUN ] IndexTest.WriteAndReadIndexWorks 46: 46: WARNING: Masses and atomic (Van der Waals) radii will be guessed 46: based on residue and atom names, since they could not be 46: definitively assigned from the information in your input 46: files. These guessed numbers might deviate from the mass 46: and radius of the atom type. Please check the output 46: files if necessary. Note, that this functionality may 46: be removed in a future GROMACS version. Please, consider 46: using another file format for your input. 46: 46: [ OK ] IndexTest.WriteAndReadIndexWorks (4 ms) 46: [----------] 3 tests from IndexTest (22 ms total) 46: 46: [----------] 4 tests from MtopTest 46: [ RUN ] MtopTest.RangeBasedLoop 46: [ OK ] MtopTest.RangeBasedLoop (0 ms) 46: [ RUN ] MtopTest.Operators 46: [ OK ] MtopTest.Operators (0 ms) 46: [ RUN ] MtopTest.CanFindResidueStartAndEndAtoms 46: [ OK ] MtopTest.CanFindResidueStartAndEndAtoms (0 ms) 46: [ RUN ] MtopTest.CanSortPerturbedInteractionsCorrectly 46: [ OK ] MtopTest.CanSortPerturbedInteractionsCorrectly (0 ms) 46: [----------] 4 tests from MtopTest (0 ms total) 46: 46: [----------] 2 tests from IListRangeTest 46: [ RUN ] IListRangeTest.RangeBasedLoopWorks 46: [ OK ] IListRangeTest.RangeBasedLoopWorks (0 ms) 46: [ RUN ] IListRangeTest.RangeBasedLoopWithIntermolecularInteraction 46: [ OK ] IListRangeTest.RangeBasedLoopWithIntermolecularInteraction (0 ms) 46: [----------] 2 tests from IListRangeTest (0 ms total) 46: 46: [----------] 13 tests from StringTableTest 46: [ RUN ] StringTableTest.AddSingleEntry 46: [ OK ] StringTableTest.AddSingleEntry (4 ms) 46: [ RUN ] StringTableTest.CanAccessWithAt 46: [ OK ] StringTableTest.CanAccessWithAt (0 ms) 46: [ RUN ] StringTableTest.CanAccessWithBracket 46: [ OK ] StringTableTest.CanAccessWithBracket (0 ms) 46: [ RUN ] StringTableTest.ThrowsOutOfRange 46: [ OK ] StringTableTest.ThrowsOutOfRange (0 ms) 46: [ RUN ] StringTableTest.StringCompareIsCorrect 46: [ OK ] StringTableTest.StringCompareIsCorrect (0 ms) 46: [ RUN ] StringTableTest.AddTwoDistinctEntries 46: [ OK ] StringTableTest.AddTwoDistinctEntries (0 ms) 46: [ RUN ] StringTableTest.TryToAddDuplicates 46: [ OK ] StringTableTest.TryToAddDuplicates (0 ms) 46: [ RUN ] StringTableTest.AddLargeNumberOfEntries 46: [ OK ] StringTableTest.AddLargeNumberOfEntries (0 ms) 46: [ RUN ] StringTableTest.NoDuplicatesInLargeTable 46: [ OK ] StringTableTest.NoDuplicatesInLargeTable (0 ms) 46: [ RUN ] StringTableTest.CanWriteToBuffer 46: [ OK ] StringTableTest.CanWriteToBuffer (0 ms) 46: [ RUN ] StringTableTest.Roundtrip 46: [ OK ] StringTableTest.Roundtrip (0 ms) 46: [ RUN ] StringTableTest.RoundtripWithCorrectStringIndices 46: [ OK ] StringTableTest.RoundtripWithCorrectStringIndices (0 ms) 46: [ RUN ] StringTableTest.CanCopyToLegacyTable 46: [ OK ] StringTableTest.CanCopyToLegacyTable (0 ms) 46: [----------] 13 tests from StringTableTest (7 ms total) 46: 46: [----------] 6 tests from LegacySymtabTest 46: [ RUN ] LegacySymtabTest.EmptyOnOpen 46: [ OK ] LegacySymtabTest.EmptyOnOpen (0 ms) 46: [ RUN ] LegacySymtabTest.AddSingleEntry 46: [ OK ] LegacySymtabTest.AddSingleEntry (0 ms) 46: [ RUN ] LegacySymtabTest.AddTwoDistinctEntries 46: [ OK ] LegacySymtabTest.AddTwoDistinctEntries (0 ms) 46: [ RUN ] LegacySymtabTest.TryToAddDuplicates 46: [ OK ] LegacySymtabTest.TryToAddDuplicates (0 ms) 46: [ RUN ] LegacySymtabTest.AddLargeNumberOfEntries 46: [ OK ] LegacySymtabTest.AddLargeNumberOfEntries (0 ms) 46: [ RUN ] LegacySymtabTest.NoDuplicatesInLargeTable 46: [ OK ] LegacySymtabTest.NoDuplicatesInLargeTable (0 ms) 46: [----------] 6 tests from LegacySymtabTest (0 ms total) 46: 46: [----------] 5 tests from TopSortTest 46: [ RUN ] TopSortTest.WorksOnEmptyIdef 46: [ OK ] TopSortTest.WorksOnEmptyIdef (0 ms) 46: [ RUN ] TopSortTest.WorksOnIdefWithNoPerturbedInteraction 46: [ OK ] TopSortTest.WorksOnIdefWithNoPerturbedInteraction (0 ms) 46: [ RUN ] TopSortTest.WorksOnIdefWithPerturbedInteractions 46: [ OK ] TopSortTest.WorksOnIdefWithPerturbedInteractions (0 ms) 46: [ RUN ] TopSortTest.SortsIdefWithPerturbedInteractions 46: [ OK ] TopSortTest.SortsIdefWithPerturbedInteractions (0 ms) 46: [ RUN ] TopSortTest.SortsMoreComplexIdefWithPerturbedInteractions 46: [ OK ] TopSortTest.SortsMoreComplexIdefWithPerturbedInteractions (0 ms) 46: [----------] 5 tests from TopSortTest (0 ms total) 46: 46: [----------] 108 tests from BuildsValidDataStructure/SimulationParticleTest 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/0 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/0 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/1 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/1 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/2 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/2 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/3 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/3 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/4 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/4 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/5 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/5 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/6 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/6 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/7 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/7 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/8 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/8 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/9 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/9 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/10 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/10 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/11 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/11 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/12 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/12 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/13 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/13 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/14 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/14 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/15 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/15 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/16 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/16 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/17 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/17 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/18 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/18 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/19 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/19 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/20 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/20 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/21 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/21 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/22 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/22 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/23 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/23 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/24 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/24 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/25 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/25 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/26 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/26 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/27 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/27 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/28 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/28 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/29 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/29 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/30 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/30 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/31 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/31 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/32 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/32 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/33 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/33 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/34 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/34 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/35 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/35 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/36 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/36 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/37 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/37 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/38 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/38 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/39 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/39 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/40 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/40 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/41 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/41 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/42 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/42 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/43 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/43 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/44 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/44 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/45 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/45 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/46 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/46 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/47 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/47 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/48 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/48 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/49 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/49 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/50 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/50 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/51 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/51 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/52 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/52 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/53 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/53 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/0 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/0 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/1 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/1 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/2 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/2 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/3 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/3 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/4 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/4 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/5 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/5 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/6 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/6 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/7 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/7 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/8 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/8 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/9 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/9 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/10 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/10 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/11 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/11 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/12 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/12 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/13 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/13 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/14 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/14 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/15 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/15 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/16 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/16 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/17 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/17 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/18 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/18 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/19 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/19 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/20 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/20 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/21 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/21 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/22 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/22 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/23 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/23 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/24 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/24 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/25 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/25 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/26 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/26 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/27 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/27 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/28 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/28 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/29 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/29 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/30 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/30 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/31 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/31 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/32 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/32 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/33 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/33 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/34 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/34 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/35 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/35 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/36 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/36 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/37 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/37 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/38 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/38 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/39 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/39 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/40 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/40 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/41 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/41 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/42 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/42 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/43 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/43 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/44 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/44 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/45 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/45 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/46 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/46 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/47 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/47 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/48 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/48 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/49 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/49 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/50 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/50 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/51 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/51 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/52 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/52 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/53 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/53 (0 ms) 46: [----------] 108 tests from BuildsValidDataStructure/SimulationParticleTest (13 ms total) 46: 46: [----------] Global test environment tear-down 46: [==========] 153 tests from 10 test suites ran. (43 ms total) 46: [ PASSED ] 153 tests. 46: 46: YOU HAVE 1 DISABLED TEST 46: 46/90 Test #46: TopologyTest .............................. Passed 0.08 sec test 47 Start 47: PullTest 47: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/pull-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/PullTest.xml" 47: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/pulling/tests 47: Test timeout computed to be: 30 47: [==========] Running 10 tests from 1 test suite. 47: [----------] Global test environment set-up. 47: [----------] 10 tests from PullTest 47: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox 47: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (0 ms) 47: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox 47: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms) 47: [ RUN ] PullTest.MaxPullDistanceXyzTricBox 47: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms) 47: [ RUN ] PullTest.MaxPullDistanceXyzLongBox 47: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms) 47: [ RUN ] PullTest.MaxPullDistanceXySkewedBox 47: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms) 47: [ RUN ] PullTest.TransformationCoordSimple 47: [ OK ] PullTest.TransformationCoordSimple (0 ms) 47: [ RUN ] PullTest.TransformationCoordAdvanced 47: [ OK ] PullTest.TransformationCoordAdvanced (0 ms) 47: [ RUN ] PullTest.TransformationCoordTime 47: [ OK ] PullTest.TransformationCoordTime (0 ms) 47: [ RUN ] PullTest.TransformationCoordTimeNotAllowed 47: [ OK ] PullTest.TransformationCoordTimeNotAllowed (0 ms) 47: [ RUN ] PullTest.TransformationCoordDummyExpression 47: [ OK ] PullTest.TransformationCoordDummyExpression (2 ms) 47: [----------] 10 tests from PullTest (2 ms total) 47: 47: [----------] Global test environment tear-down 47: [==========] 10 tests from 1 test suite ran. (2 ms total) 47: [ PASSED ] 10 tests. 47/90 Test #47: PullTest .................................. Passed 0.03 sec test 48 Start 48: SimdUnitTests 48: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/simd-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/SimdUnitTests.xml" 48: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/simd/tests 48: Test timeout computed to be: 30 48: [==========] Running 247 tests from 19 test suites. 48: [----------] Global test environment set-up. 48: [----------] 6 tests from SimdBootstrapTest 48: [ RUN ] SimdBootstrapTest.loadStore 48: [ OK ] SimdBootstrapTest.loadStore (0 ms) 48: [ RUN ] SimdBootstrapTest.loadU 48: [ OK ] SimdBootstrapTest.loadU (0 ms) 48: [ RUN ] SimdBootstrapTest.storeU 48: [ OK ] SimdBootstrapTest.storeU (0 ms) 48: [ RUN ] SimdBootstrapTest.loadStoreI 48: [ OK ] SimdBootstrapTest.loadStoreI (0 ms) 48: [ RUN ] SimdBootstrapTest.loadUI 48: [ OK ] SimdBootstrapTest.loadUI (0 ms) 48: [ RUN ] SimdBootstrapTest.storeUI 48: [ OK ] SimdBootstrapTest.storeUI (0 ms) 48: [----------] 6 tests from SimdBootstrapTest (0 ms total) 48: 48: [----------] 41 tests from SimdScalarTest 48: [ RUN ] SimdScalarTest.load 48: [ OK ] SimdScalarTest.load (0 ms) 48: [ RUN ] SimdScalarTest.loadU 48: [ OK ] SimdScalarTest.loadU (0 ms) 48: [ RUN ] SimdScalarTest.store 48: [ OK ] SimdScalarTest.store (0 ms) 48: [ RUN ] SimdScalarTest.storeU 48: [ OK ] SimdScalarTest.storeU (0 ms) 48: [ RUN ] SimdScalarTest.setZero 48: [ OK ] SimdScalarTest.setZero (0 ms) 48: [ RUN ] SimdScalarTest.andNot 48: [ OK ] SimdScalarTest.andNot (0 ms) 48: [ RUN ] SimdScalarTest.fma 48: [ OK ] SimdScalarTest.fma (0 ms) 48: [ RUN ] SimdScalarTest.fms 48: [ OK ] SimdScalarTest.fms (0 ms) 48: [ RUN ] SimdScalarTest.fnma 48: [ OK ] SimdScalarTest.fnma (0 ms) 48: [ RUN ] SimdScalarTest.fnms 48: [ OK ] SimdScalarTest.fnms (0 ms) 48: [ RUN ] SimdScalarTest.maskAdd 48: [ OK ] SimdScalarTest.maskAdd (0 ms) 48: [ RUN ] SimdScalarTest.maskzMul 48: [ OK ] SimdScalarTest.maskzMul (0 ms) 48: [ RUN ] SimdScalarTest.maskzFma 48: [ OK ] SimdScalarTest.maskzFma (0 ms) 48: [ RUN ] SimdScalarTest.abs 48: [ OK ] SimdScalarTest.abs (0 ms) 48: [ RUN ] SimdScalarTest.max 48: [ OK ] SimdScalarTest.max (0 ms) 48: [ RUN ] SimdScalarTest.min 48: [ OK ] SimdScalarTest.min (0 ms) 48: [ RUN ] SimdScalarTest.round 48: [ OK ] SimdScalarTest.round (0 ms) 48: [ RUN ] SimdScalarTest.trunc 48: [ OK ] SimdScalarTest.trunc (0 ms) 48: [ RUN ] SimdScalarTest.reduce 48: [ OK ] SimdScalarTest.reduce (0 ms) 48: [ RUN ] SimdScalarTest.testBits 48: [ OK ] SimdScalarTest.testBits (0 ms) 48: [ RUN ] SimdScalarTest.anyTrue 48: [ OK ] SimdScalarTest.anyTrue (0 ms) 48: [ RUN ] SimdScalarTest.selectByMask 48: [ OK ] SimdScalarTest.selectByMask (0 ms) 48: [ RUN ] SimdScalarTest.selectByNotMask 48: [ OK ] SimdScalarTest.selectByNotMask (0 ms) 48: [ RUN ] SimdScalarTest.blend 48: [ OK ] SimdScalarTest.blend (0 ms) 48: [ RUN ] SimdScalarTest.cvtR2I 48: [ OK ] SimdScalarTest.cvtR2I (0 ms) 48: [ RUN ] SimdScalarTest.cvttR2I 48: [ OK ] SimdScalarTest.cvttR2I (0 ms) 48: [ RUN ] SimdScalarTest.cvtI2R 48: [ OK ] SimdScalarTest.cvtI2R (0 ms) 48: [ RUN ] SimdScalarTest.cvtF2D 48: [ OK ] SimdScalarTest.cvtF2D (0 ms) 48: [ RUN ] SimdScalarTest.cvtD2D 48: [ OK ] SimdScalarTest.cvtD2D (0 ms) 48: [ RUN ] SimdScalarTest.loadI 48: [ OK ] SimdScalarTest.loadI (0 ms) 48: [ RUN ] SimdScalarTest.loadUI 48: [ OK ] SimdScalarTest.loadUI (0 ms) 48: [ RUN ] SimdScalarTest.storeI 48: [ OK ] SimdScalarTest.storeI (0 ms) 48: [ RUN ] SimdScalarTest.storeUI 48: [ OK ] SimdScalarTest.storeUI (0 ms) 48: [ RUN ] SimdScalarTest.andNotI 48: [ OK ] SimdScalarTest.andNotI (0 ms) 48: [ RUN ] SimdScalarTest.testBitsI 48: [ OK ] SimdScalarTest.testBitsI (0 ms) 48: [ RUN ] SimdScalarTest.selectByMaskI 48: [ OK ] SimdScalarTest.selectByMaskI (0 ms) 48: [ RUN ] SimdScalarTest.selectByNotMaskI 48: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms) 48: [ RUN ] SimdScalarTest.blendI 48: [ OK ] SimdScalarTest.blendI (0 ms) 48: [ RUN ] SimdScalarTest.cvtB2IB 48: [ OK ] SimdScalarTest.cvtB2IB (0 ms) 48: [ RUN ] SimdScalarTest.cvtIB2B 48: [ OK ] SimdScalarTest.cvtIB2B (0 ms) 48: [ RUN ] SimdScalarTest.expandScalarsToTriplets 48: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms) 48: [----------] 41 tests from SimdScalarTest (0 ms total) 48: 48: [----------] 8 tests from SimdScalarUtilTest 48: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose 48: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms) 48: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose 48: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms) 48: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU 48: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms) 48: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU 48: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms) 48: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU 48: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms) 48: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose 48: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms) 48: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose 48: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms) 48: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum 48: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms) 48: [----------] 8 tests from SimdScalarUtilTest (0 ms total) 48: 48: [----------] 37 tests from SimdScalarMathTest 48: [ RUN ] SimdScalarMathTest.copysign 48: [ OK ] SimdScalarMathTest.copysign (0 ms) 48: [ RUN ] SimdScalarMathTest.invsqrtPair 48: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms) 48: [ RUN ] SimdScalarMathTest.inv 48: [ OK ] SimdScalarMathTest.inv (0 ms) 48: [ RUN ] SimdScalarMathTest.maskzInvsqrt 48: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms) 48: [ RUN ] SimdScalarMathTest.log 48: [ OK ] SimdScalarMathTest.log (0 ms) 48: [ RUN ] SimdScalarMathTest.exp2 48: [ OK ] SimdScalarMathTest.exp2 (0 ms) 48: [ RUN ] SimdScalarMathTest.exp 48: [ OK ] SimdScalarMathTest.exp (0 ms) 48: [ RUN ] SimdScalarMathTest.erf 48: [ OK ] SimdScalarMathTest.erf (0 ms) 48: [ RUN ] SimdScalarMathTest.erfc 48: [ OK ] SimdScalarMathTest.erfc (0 ms) 48: [ RUN ] SimdScalarMathTest.sincos 48: [ OK ] SimdScalarMathTest.sincos (0 ms) 48: [ RUN ] SimdScalarMathTest.sin 48: [ OK ] SimdScalarMathTest.sin (0 ms) 48: [ RUN ] SimdScalarMathTest.cos 48: [ OK ] SimdScalarMathTest.cos (0 ms) 48: [ RUN ] SimdScalarMathTest.tan 48: [ OK ] SimdScalarMathTest.tan (0 ms) 48: [ RUN ] SimdScalarMathTest.asin 48: [ OK ] SimdScalarMathTest.asin (0 ms) 48: [ RUN ] SimdScalarMathTest.acos 48: [ OK ] SimdScalarMathTest.acos (0 ms) 48: [ RUN ] SimdScalarMathTest.atan 48: [ OK ] SimdScalarMathTest.atan (0 ms) 48: [ RUN ] SimdScalarMathTest.atan2 48: [ OK ] SimdScalarMathTest.atan2 (0 ms) 48: [ RUN ] SimdScalarMathTest.pmeForceCorrection 48: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms) 48: [ RUN ] SimdScalarMathTest.pmePotentialCorrection 48: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms) 48: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy 48: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.invSingleAccuracy 48: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy 48: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.logSingleAccuracy 48: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy 48: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.expSingleAccuracy 48: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.erfSingleAccuracy 48: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy 48: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy 48: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.sinSingleAccuracy 48: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.cosSingleAccuracy 48: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.tanSingleAccuracy 48: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.asinSingleAccuracy 48: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.acosSingleAccuracy 48: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.atanSingleAccuracy 48: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy 48: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy 48: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy 48: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 48: [----------] 37 tests from SimdScalarMathTest (0 ms total) 48: 48: [----------] 1 test from SimdTest 48: [ RUN ] SimdTest.GmxAligned 48: [ OK ] SimdTest.GmxAligned (0 ms) 48: [----------] 1 test from SimdTest (0 ms total) 48: 48: [----------] 42 tests from SimdFloatingpointTest 48: [ RUN ] SimdFloatingpointTest.setZero 48: [ OK ] SimdFloatingpointTest.setZero (0 ms) 48: [ RUN ] SimdFloatingpointTest.set 48: [ OK ] SimdFloatingpointTest.set (0 ms) 48: [ RUN ] SimdFloatingpointTest.add 48: [ OK ] SimdFloatingpointTest.add (0 ms) 48: [ RUN ] SimdFloatingpointTest.maskAdd 48: [ OK ] SimdFloatingpointTest.maskAdd (0 ms) 48: [ RUN ] SimdFloatingpointTest.sub 48: [ OK ] SimdFloatingpointTest.sub (0 ms) 48: [ RUN ] SimdFloatingpointTest.mul 48: [ OK ] SimdFloatingpointTest.mul (0 ms) 48: [ RUN ] SimdFloatingpointTest.maskzMul 48: [ OK ] SimdFloatingpointTest.maskzMul (0 ms) 48: [ RUN ] SimdFloatingpointTest.fma 48: [ OK ] SimdFloatingpointTest.fma (0 ms) 48: [ RUN ] SimdFloatingpointTest.maskzFma 48: [ OK ] SimdFloatingpointTest.maskzFma (0 ms) 48: [ RUN ] SimdFloatingpointTest.fms 48: [ OK ] SimdFloatingpointTest.fms (0 ms) 48: [ RUN ] SimdFloatingpointTest.fnma 48: [ OK ] SimdFloatingpointTest.fnma (0 ms) 48: [ RUN ] SimdFloatingpointTest.fnms 48: [ OK ] SimdFloatingpointTest.fnms (0 ms) 48: [ RUN ] SimdFloatingpointTest.abs 48: [ OK ] SimdFloatingpointTest.abs (0 ms) 48: [ RUN ] SimdFloatingpointTest.neg 48: [ OK ] SimdFloatingpointTest.neg (0 ms) 48: [ RUN ] SimdFloatingpointTest.and 48: [ OK ] SimdFloatingpointTest.and (0 ms) 48: [ RUN ] SimdFloatingpointTest.or 48: [ OK ] SimdFloatingpointTest.or (0 ms) 48: [ RUN ] SimdFloatingpointTest.xor 48: [ OK ] SimdFloatingpointTest.xor (0 ms) 48: [ RUN ] SimdFloatingpointTest.andNot 48: [ OK ] SimdFloatingpointTest.andNot (0 ms) 48: [ RUN ] SimdFloatingpointTest.max 48: [ OK ] SimdFloatingpointTest.max (0 ms) 48: [ RUN ] SimdFloatingpointTest.min 48: [ OK ] SimdFloatingpointTest.min (0 ms) 48: [ RUN ] SimdFloatingpointTest.round 48: [ OK ] SimdFloatingpointTest.round (0 ms) 48: [ RUN ] SimdFloatingpointTest.roundMode 48: [ OK ] SimdFloatingpointTest.roundMode (0 ms) 48: [ RUN ] SimdFloatingpointTest.trunc 48: [ OK ] SimdFloatingpointTest.trunc (0 ms) 48: [ RUN ] SimdFloatingpointTest.frexp 48: [ OK ] SimdFloatingpointTest.frexp (0 ms) 48: [ RUN ] SimdFloatingpointTest.ldexp 48: [ OK ] SimdFloatingpointTest.ldexp (0 ms) 48: [ RUN ] SimdFloatingpointTest.rsqrt 48: [ OK ] SimdFloatingpointTest.rsqrt (0 ms) 48: [ RUN ] SimdFloatingpointTest.maskzRsqrt 48: [ OK ] SimdFloatingpointTest.maskzRsqrt (0 ms) 48: [ RUN ] SimdFloatingpointTest.rcp 48: [ OK ] SimdFloatingpointTest.rcp (0 ms) 48: [ RUN ] SimdFloatingpointTest.maskzRcp 48: [ OK ] SimdFloatingpointTest.maskzRcp (0 ms) 48: [ RUN ] SimdFloatingpointTest.cmpEqAndSelectByMask 48: [ OK ] SimdFloatingpointTest.cmpEqAndSelectByMask (0 ms) 48: [ RUN ] SimdFloatingpointTest.selectByNotMask 48: [ OK ] SimdFloatingpointTest.selectByNotMask (0 ms) 48: [ RUN ] SimdFloatingpointTest.cmpNe 48: [ OK ] SimdFloatingpointTest.cmpNe (0 ms) 48: [ RUN ] SimdFloatingpointTest.cmpLe 48: [ OK ] SimdFloatingpointTest.cmpLe (0 ms) 48: [ RUN ] SimdFloatingpointTest.cmpLt 48: [ OK ] SimdFloatingpointTest.cmpLt (0 ms) 48: [ RUN ] SimdFloatingpointTest.testBits 48: [ OK ] SimdFloatingpointTest.testBits (0 ms) 48: [ RUN ] SimdFloatingpointTest.andB 48: [ OK ] SimdFloatingpointTest.andB (0 ms) 48: [ RUN ] SimdFloatingpointTest.orB 48: [ OK ] SimdFloatingpointTest.orB (0 ms) 48: [ RUN ] SimdFloatingpointTest.anyTrueB 48: [ OK ] SimdFloatingpointTest.anyTrueB (0 ms) 48: [ RUN ] SimdFloatingpointTest.blend 48: [ OK ] SimdFloatingpointTest.blend (0 ms) 48: [ RUN ] SimdFloatingpointTest.reduce 48: [ OK ] SimdFloatingpointTest.reduce (0 ms) 48: [ RUN ] SimdFloatingpointTest.cvtFloat2Double 48: [ OK ] SimdFloatingpointTest.cvtFloat2Double (0 ms) 48: [ RUN ] SimdFloatingpointTest.cvtDouble2Float 48: [ OK ] SimdFloatingpointTest.cvtDouble2Float (0 ms) 48: [----------] 42 tests from SimdFloatingpointTest (0 ms total) 48: 48: [----------] 13 tests from SimdFloatingpointUtilTest 48: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose4 48: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose4 (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose2 48: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose2 (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 48: [ OK ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.transposeScatterStoreU3 48: [ OK ] SimdFloatingpointUtilTest.transposeScatterStoreU3 (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3 48: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3 (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping 48: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3 48: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3 (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping 48: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.expandScalarsToTriplets 48: [ OK ] SimdFloatingpointUtilTest.expandScalarsToTriplets (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 48: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 48: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 48: [ OK ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.reduceIncr4Sum 48: [ OK ] SimdFloatingpointUtilTest.reduceIncr4Sum (0 ms) 48: [----------] 13 tests from SimdFloatingpointUtilTest (0 ms total) 48: 48: [----------] 23 tests from SimdIntegerTest 48: [ RUN ] SimdIntegerTest.setZero 48: [ OK ] SimdIntegerTest.setZero (0 ms) 48: [ RUN ] SimdIntegerTest.set 48: [ OK ] SimdIntegerTest.set (0 ms) 48: [ RUN ] SimdIntegerTest.add 48: [ OK ] SimdIntegerTest.add (0 ms) 48: [ RUN ] SimdIntegerTest.sub 48: [ OK ] SimdIntegerTest.sub (0 ms) 48: [ RUN ] SimdIntegerTest.mul 48: [ OK ] SimdIntegerTest.mul (0 ms) 48: [ RUN ] SimdIntegerTest.and 48: [ OK ] SimdIntegerTest.and (0 ms) 48: [ RUN ] SimdIntegerTest.andNot 48: [ OK ] SimdIntegerTest.andNot (0 ms) 48: [ RUN ] SimdIntegerTest.or 48: [ OK ] SimdIntegerTest.or (0 ms) 48: [ RUN ] SimdIntegerTest.xor 48: [ OK ] SimdIntegerTest.xor (0 ms) 48: [ RUN ] SimdIntegerTest.extract 48: [ OK ] SimdIntegerTest.extract (0 ms) 48: [ RUN ] SimdIntegerTest.cvtR2I 48: [ OK ] SimdIntegerTest.cvtR2I (0 ms) 48: [ RUN ] SimdIntegerTest.cvttR2I 48: [ OK ] SimdIntegerTest.cvttR2I (0 ms) 48: [ RUN ] SimdIntegerTest.cvtI2R 48: [ OK ] SimdIntegerTest.cvtI2R (0 ms) 48: [ RUN ] SimdIntegerTest.cmpEqAndSelectMask 48: [ OK ] SimdIntegerTest.cmpEqAndSelectMask (0 ms) 48: [ RUN ] SimdIntegerTest.cmpEqAndSelectNotMask 48: [ OK ] SimdIntegerTest.cmpEqAndSelectNotMask (0 ms) 48: [ RUN ] SimdIntegerTest.cmpLt 48: [ OK ] SimdIntegerTest.cmpLt (0 ms) 48: [ RUN ] SimdIntegerTest.testBits 48: [ OK ] SimdIntegerTest.testBits (0 ms) 48: [ RUN ] SimdIntegerTest.andB 48: [ OK ] SimdIntegerTest.andB (0 ms) 48: [ RUN ] SimdIntegerTest.orB 48: [ OK ] SimdIntegerTest.orB (0 ms) 48: [ RUN ] SimdIntegerTest.anyTrue 48: [ OK ] SimdIntegerTest.anyTrue (0 ms) 48: [ RUN ] SimdIntegerTest.blend 48: [ OK ] SimdIntegerTest.blend (0 ms) 48: [ RUN ] SimdIntegerTest.cvtB2IB 48: [ OK ] SimdIntegerTest.cvtB2IB (0 ms) 48: [ RUN ] SimdIntegerTest.cvtIB2B 48: [ OK ] SimdIntegerTest.cvtIB2B (0 ms) 48: [----------] 23 tests from SimdIntegerTest (0 ms total) 48: 48: [----------] 56 tests from SimdMathTest 48: [ RUN ] SimdMathTest.generateTestPointsDouble 48: [ OK ] SimdMathTest.generateTestPointsDouble (0 ms) 48: [ RUN ] SimdMathTest.copysign 48: [ OK ] SimdMathTest.copysign (0 ms) 48: [ RUN ] SimdMathTest.invsqrt 48: [ OK ] SimdMathTest.invsqrt (0 ms) 48: [ RUN ] SimdMathTest.maskzInvsqrt 48: [ OK ] SimdMathTest.maskzInvsqrt (0 ms) 48: [ RUN ] SimdMathTest.invsqrtPair 48: [ OK ] SimdMathTest.invsqrtPair (0 ms) 48: [ RUN ] SimdMathTest.sqrt 48: [ OK ] SimdMathTest.sqrt (1 ms) 48: [ RUN ] SimdMathTest.sqrtUnsafe 48: [ OK ] SimdMathTest.sqrtUnsafe (0 ms) 48: [ RUN ] SimdMathTest.inv 48: [ OK ] SimdMathTest.inv (1 ms) 48: [ RUN ] SimdMathTest.maskzInv 48: [ OK ] SimdMathTest.maskzInv (0 ms) 48: [ RUN ] SimdMathTest.cbrt 48: [ OK ] SimdMathTest.cbrt (1 ms) 48: [ RUN ] SimdMathTest.invcbrt 48: [ OK ] SimdMathTest.invcbrt (1 ms) 48: [ RUN ] SimdMathTest.log2 48: [ OK ] SimdMathTest.log2 (0 ms) 48: [ RUN ] SimdMathTest.log 48: [ OK ] SimdMathTest.log (0 ms) 48: [ RUN ] SimdMathTest.exp2 48: [ OK ] SimdMathTest.exp2 (3 ms) 48: [ RUN ] SimdMathTest.exp2Unsafe 48: [ OK ] SimdMathTest.exp2Unsafe (0 ms) 48: [ RUN ] SimdMathTest.exp 48: [ OK ] SimdMathTest.exp (4 ms) 48: [ RUN ] SimdMathTest.expUnsafe 48: [ OK ] SimdMathTest.expUnsafe (0 ms) 48: [ RUN ] SimdMathTest.pow 48: [ OK ] SimdMathTest.pow (0 ms) 48: [ RUN ] SimdMathTest.powUnsafe 48: [ OK ] SimdMathTest.powUnsafe (0 ms) 48: [ RUN ] SimdMathTest.erf 48: [ OK ] SimdMathTest.erf (1 ms) 48: [ RUN ] SimdMathTest.erfc 48: [ OK ] SimdMathTest.erfc (1 ms) 48: [ RUN ] SimdMathTest.sin 48: [ OK ] SimdMathTest.sin (1 ms) 48: [ RUN ] SimdMathTest.cos 48: [ OK ] SimdMathTest.cos (2 ms) 48: [ RUN ] SimdMathTest.tan 48: [ OK ] SimdMathTest.tan (2 ms) 48: [ RUN ] SimdMathTest.asin 48: [ OK ] SimdMathTest.asin (0 ms) 48: [ RUN ] SimdMathTest.acos 48: [ OK ] SimdMathTest.acos (1 ms) 48: [ RUN ] SimdMathTest.atan 48: [ OK ] SimdMathTest.atan (1 ms) 48: [ RUN ] SimdMathTest.atan2 48: [ OK ] SimdMathTest.atan2 (0 ms) 48: [ RUN ] SimdMathTest.pmeForceCorrection 48: [ OK ] SimdMathTest.pmeForceCorrection (0 ms) 48: [ RUN ] SimdMathTest.pmePotentialCorrection 48: [ OK ] SimdMathTest.pmePotentialCorrection (0 ms) 48: [ RUN ] SimdMathTest.invsqrtSingleAccuracy 48: [ OK ] SimdMathTest.invsqrtSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.invsqrtPairSingleAccuracy 48: [ OK ] SimdMathTest.invsqrtPairSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.sqrtSingleAccuracy 48: [ OK ] SimdMathTest.sqrtSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.sqrtSingleAccuracyUnsafe 48: [ OK ] SimdMathTest.sqrtSingleAccuracyUnsafe (0 ms) 48: [ RUN ] SimdMathTest.invSingleAccuracy 48: [ OK ] SimdMathTest.invSingleAccuracy (1 ms) 48: [ RUN ] SimdMathTest.cbrtSingleAccuracy 48: [ OK ] SimdMathTest.cbrtSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.invcbrtSingleAccuracy 48: [ OK ] SimdMathTest.invcbrtSingleAccuracy (1 ms) 48: [ RUN ] SimdMathTest.log2SingleAccuracy 48: [ OK ] SimdMathTest.log2SingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.logSingleAccuracy 48: [ OK ] SimdMathTest.logSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.exp2SingleAccuracy 48: [ OK ] SimdMathTest.exp2SingleAccuracy (3 ms) 48: [ RUN ] SimdMathTest.exp2SingleAccuracyUnsafe 48: [ OK ] SimdMathTest.exp2SingleAccuracyUnsafe (0 ms) 48: [ RUN ] SimdMathTest.expSingleAccuracy 48: [ OK ] SimdMathTest.expSingleAccuracy (4 ms) 48: [ RUN ] SimdMathTest.expSingleAccuracyUnsafe 48: [ OK ] SimdMathTest.expSingleAccuracyUnsafe (0 ms) 48: [ RUN ] SimdMathTest.powSingleAccuracy 48: [ OK ] SimdMathTest.powSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.powSingleAccuracyUnsafe 48: [ OK ] SimdMathTest.powSingleAccuracyUnsafe (0 ms) 48: [ RUN ] SimdMathTest.erfSingleAccuracy 48: [ OK ] SimdMathTest.erfSingleAccuracy (1 ms) 48: [ RUN ] SimdMathTest.erfcSingleAccuracy 48: [ OK ] SimdMathTest.erfcSingleAccuracy (1 ms) 48: [ RUN ] SimdMathTest.sinSingleAccuracy 48: [ OK ] SimdMathTest.sinSingleAccuracy (1 ms) 48: [ RUN ] SimdMathTest.cosSingleAccuracy 48: [ OK ] SimdMathTest.cosSingleAccuracy (1 ms) 48: [ RUN ] SimdMathTest.tanSingleAccuracy 48: [ OK ] SimdMathTest.tanSingleAccuracy (2 ms) 48: [ RUN ] SimdMathTest.asinSingleAccuracy 48: [ OK ] SimdMathTest.asinSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.acosSingleAccuracy 48: [ OK ] SimdMathTest.acosSingleAccuracy (1 ms) 48: [ RUN ] SimdMathTest.atanSingleAccuracy 48: [ OK ] SimdMathTest.atanSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.atan2SingleAccuracy 48: [ OK ] SimdMathTest.atan2SingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.pmeForceCorrectionSingleAccuracy 48: [ OK ] SimdMathTest.pmeForceCorrectionSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.pmePotentialCorrectionSingleAccuracy 48: [ OK ] SimdMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 48: [----------] 56 tests from SimdMathTest (62 ms total) 48: 48: [----------] 1 test from EmptyArrayRefTest 48: [ RUN ] EmptyArrayRefTest.IsEmpty 48: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 48: [----------] 1 test from EmptyArrayRefTest (0 ms total) 48: 48: [----------] 3 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 48: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 48: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 48: [ RUN ] ArrayRefTest/0.ConstructFromArrayRefWorks 48: [ OK ] ArrayRefTest/0.ConstructFromArrayRefWorks (0 ms) 48: [ RUN ] ArrayRefTest/0.ConstructFromArrayWorks 48: [ OK ] ArrayRefTest/0.ConstructFromArrayWorks (0 ms) 48: [----------] 3 tests from ArrayRefTest/0 (0 ms total) 48: 48: [----------] 3 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 48: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 48: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 48: [ RUN ] ArrayRefTest/1.ConstructFromArrayRefWorks 48: [ OK ] ArrayRefTest/1.ConstructFromArrayRefWorks (0 ms) 48: [ RUN ] ArrayRefTest/1.ConstructFromArrayWorks 48: [ OK ] ArrayRefTest/1.ConstructFromArrayWorks (0 ms) 48: [----------] 3 tests from ArrayRefTest/1 (0 ms total) 48: 48: [----------] 3 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 48: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 48: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 48: [ RUN ] ArrayRefTest/2.ConstructFromArrayRefWorks 48: [ OK ] ArrayRefTest/2.ConstructFromArrayRefWorks (0 ms) 48: [ RUN ] ArrayRefTest/2.ConstructFromArrayWorks 48: [ OK ] ArrayRefTest/2.ConstructFromArrayWorks (0 ms) 48: [----------] 3 tests from ArrayRefTest/2 (0 ms total) 48: 48: [----------] 3 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 48: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 48: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 48: [ RUN ] ArrayRefTest/3.ConstructFromArrayRefWorks 48: [ OK ] ArrayRefTest/3.ConstructFromArrayRefWorks (0 ms) 48: [ RUN ] ArrayRefTest/3.ConstructFromArrayWorks 48: [ OK ] ArrayRefTest/3.ConstructFromArrayWorks (0 ms) 48: [----------] 3 tests from ArrayRefTest/3 (0 ms total) 48: 48: [----------] 1 test from ArrayRefReadWriteTest/0, where TypeParam = gmx::ArrayRef 48: [ RUN ] ArrayRefReadWriteTest/0.Assignment 48: [ OK ] ArrayRefReadWriteTest/0.Assignment (0 ms) 48: [----------] 1 test from ArrayRefReadWriteTest/0 (0 ms total) 48: 48: [----------] 1 test from ArrayRefReadWriteTest/1, where TypeParam = gmx::ArrayRef 48: [ RUN ] ArrayRefReadWriteTest/1.Assignment 48: [ OK ] ArrayRefReadWriteTest/1.Assignment (0 ms) 48: [----------] 1 test from ArrayRefReadWriteTest/1 (0 ms total) 48: 48: [----------] 1 test from ArrayRefArithmeticTest/0, where TypeParam = gmx::ArrayRef 48: [ RUN ] ArrayRefArithmeticTest/0.Basic 48: [ OK ] ArrayRefArithmeticTest/0.Basic (0 ms) 48: [----------] 1 test from ArrayRefArithmeticTest/0 (0 ms total) 48: 48: [----------] 1 test from ArrayRefArithmeticTest/1, where TypeParam = gmx::ArrayRef 48: [ RUN ] ArrayRefArithmeticTest/1.Basic 48: [ OK ] ArrayRefArithmeticTest/1.Basic (0 ms) 48: [----------] 1 test from ArrayRefArithmeticTest/1 (0 ms total) 48: 48: [----------] 3 tests from SimdVectorOperationsTest 48: [ RUN ] SimdVectorOperationsTest.iprod 48: [ OK ] SimdVectorOperationsTest.iprod (0 ms) 48: [ RUN ] SimdVectorOperationsTest.norm2 48: [ OK ] SimdVectorOperationsTest.norm2 (0 ms) 48: [ RUN ] SimdVectorOperationsTest.cprod 48: [ OK ] SimdVectorOperationsTest.cprod (0 ms) 48: [----------] 3 tests from SimdVectorOperationsTest (0 ms total) 48: 48: [----------] Global test environment tear-down 48: [==========] 247 tests from 19 test suites ran. (64 ms total) 48: [ PASSED ] 247 tests. 48/90 Test #48: SimdUnitTests ............................. Passed 0.09 sec test 49 Start 49: CompatibilityHelpersTests 49: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/compat-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/CompatibilityHelpersTests.xml" 49: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/compat/tests 49: Test timeout computed to be: 30 49: [==========] Running 9 tests from 6 test suites. 49: [----------] Global test environment set-up. 49: [----------] 4 tests from TemplateMPTest 49: [ RUN ] TemplateMPTest.MpWithIndexInt 49: [ OK ] TemplateMPTest.MpWithIndexInt (0 ms) 49: [ RUN ] TemplateMPTest.MpWithIndexIntBad 49: [ OK ] TemplateMPTest.MpWithIndexIntBad (0 ms) 49: [ RUN ] TemplateMPTest.MpWithIndexBool 49: [ OK ] TemplateMPTest.MpWithIndexBool (0 ms) 49: [ RUN ] TemplateMPTest.MpWithIndexEnum 49: [ OK ] TemplateMPTest.MpWithIndexEnum (0 ms) 49: [----------] 4 tests from TemplateMPTest (0 ms total) 49: 49: [----------] 1 test from NotNullConstruction 49: [ RUN ] NotNullConstruction.Works 49: [ OK ] NotNullConstruction.Works (0 ms) 49: [----------] 1 test from NotNullConstruction (0 ms total) 49: 49: [----------] 1 test from NotNullCasting 49: [ RUN ] NotNullCasting.Works 49: [ OK ] NotNullCasting.Works (0 ms) 49: [----------] 1 test from NotNullCasting (0 ms total) 49: 49: [----------] 1 test from NotNullAssignment 49: [ RUN ] NotNullAssignment.Works 49: [ OK ] NotNullAssignment.Works (0 ms) 49: [----------] 1 test from NotNullAssignment (0 ms total) 49: 49: [----------] 1 test from MakeNotNull 49: [ RUN ] MakeNotNull.Works 49: [ OK ] MakeNotNull.Works (0 ms) 49: [----------] 1 test from MakeNotNull (0 ms total) 49: 49: [----------] 1 test from NotNull 49: [ RUN ] NotNull.WorksInContainers 49: [ OK ] NotNull.WorksInContainers (0 ms) 49: [----------] 1 test from NotNull (0 ms total) 49: 49: [----------] Global test environment tear-down 49: [==========] 9 tests from 6 test suites ran. (0 ms total) 49: [ PASSED ] 9 tests. 49/90 Test #49: CompatibilityHelpersTests ................. Passed 0.02 sec test 50 Start 50: GmxAnaTest 50: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/gmxana-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/GmxAnaTest.xml" 50: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxana/tests 50: Test timeout computed to be: 600 50: [==========] Running 31 tests from 4 test suites. 50: [----------] Global test environment set-up. 50: [----------] 7 tests from Entropy 50: [ RUN ] Entropy.Schlitter_300_NoLinear 50: [ OK ] Entropy.Schlitter_300_NoLinear (0 ms) 50: [ RUN ] Entropy.Schlitter_300_Linear 50: [ OK ] Entropy.Schlitter_300_Linear (0 ms) 50: [ RUN ] Entropy.QuasiHarmonic_300_NoLinear 50: [ OK ] Entropy.QuasiHarmonic_300_NoLinear (0 ms) 50: [ RUN ] Entropy.QuasiHarmonic_200_NoLinear 50: [ OK ] Entropy.QuasiHarmonic_200_NoLinear (0 ms) 50: [ RUN ] Entropy.QuasiHarmonic_200_Linear 50: [ OK ] Entropy.QuasiHarmonic_200_Linear (0 ms) 50: [ RUN ] Entropy.EntropyCompare_200_Linear 50: [ OK ] Entropy.EntropyCompare_200_Linear (0 ms) 50: [ RUN ] Entropy.EntropyCompare_300_Linear 50: [ OK ] Entropy.EntropyCompare_300_Linear (0 ms) 50: [----------] 7 tests from Entropy (0 ms total) 50: 50: [----------] 2 tests from GmxChiTest 50: [ RUN ] GmxChiTest.gmxchiWorksWithAll 50: Analyzing from residue 1 to residue 11 50: 10 residues with dihedrals found 50: 46 dihedrals found 50: Reading frames from gro file 'First 10 residues from 1AKI t= 0.00000 step= 0', 156 atoms. 50: Reading frame 0 time 0.000 Reading frame 1 time 0.020 Reading frame 2 time 0.040 Last frame 2 time 0.040 50: j after resetting (nr. active dihedrals) = 46 50: Printing phiLYS1.xvg Printing phiVAL2.xvg Printing phiPHE3.xvg Printing phiGLY4.xvg Printing phiARG5.xvg Printing phiCYS6.xvg Printing phiGLU7.xvg Printing phiLEU8.xvg Printing phiALA9.xvg Printing phiALA10.xvg Printing psiLYS1.xvg Printing psiVAL2.xvg Printing psiPHE3.xvg Printing psiGLY4.xvg Printing psiARG5.xvg Printing psiCYS6.xvg Printing psiGLU7.xvg Printing psiLEU8.xvg Printing psiALA9.xvg Printing psiALA10.xvg Printing omegaVAL2.xvg Printing omegaPHE3.xvg Printing omegaGLY4.xvg Printing omegaARG5.xvg Printing omegaCYS6.xvg Printing omegaGLU7.xvg Printing omegaLEU8.xvg Printing omegaALA9.xvg Printing omegaALA10.xvg Printing chi1LYS1.xvg Printing chi1VAL2.xvg Printing chi1PHE3.xvg Printing chi1ARG5.xvg Printing chi1CYS6.xvg Printing chi1GLU7.xvg Printing chi1LEU8.xvg Printing chi2LYS1.xvg Printing chi2PHE3.xvg Printing chi2ARG5.xvg Printing chi2GLU7.xvg Printing chi2LEU8.xvg Printing chi3LYS1.xvg Printing chi3ARG5.xvg Printing chi3GLU7.xvg Printing chi4LYS1.xvg Printing chi4ARG5.xvg 50: Now calculating transitions... 50: Total number of transitions: 0 50: Now printing out transitions and OPs... 50: Now printing out rotamer occupancies... 50: Now calculating Chi product trajectories... 50: Printing chiproductLYS1.xvg and histo-chiprodLYS1.xvg Printing chiproductVAL2.xvg and histo-chiprodVAL2.xvg Printing chiproductPHE3.xvg and histo-chiprodPHE3.xvg Printing chiproductARG5.xvg and histo-chiprodARG5.xvg Printing chiproductCYS6.xvg and histo-chiprodCYS6.xvg Printing chiproductGLU7.xvg and histo-chiprodGLU7.xvg Printing chiproductLEU8.xvg and histo-chiprodLEU8.xvg 50: [ OK ] GmxChiTest.gmxchiWorksWithAll (1138 ms) 50: [ RUN ] GmxChiTest.gmxchiWorksWithr0AndrN 50: Analyzing from residue 2 to residue 6 50: 5 residues with dihedrals found 50: 23 dihedrals found 50: Reading frames from gro file 'First 10 residues from 1AKI t= 0.00000 step= 0', 156 atoms. 50: Reading frame 0 time 0.000 Reading frame 1 time 0.020 Reading frame 2 time 0.040 Last frame 2 time 0.040 50: j after resetting (nr. active dihedrals) = 23 50: Printing phiVAL2.xvg Printing phiPHE3.xvg Printing phiGLY4.xvg Printing phiARG5.xvg Printing phiCYS6.xvg Printing psiVAL2.xvg Printing psiPHE3.xvg Printing psiGLY4.xvg Printing psiARG5.xvg Printing psiCYS6.xvg Printing omegaVAL2.xvg Printing omegaPHE3.xvg Printing omegaGLY4.xvg Printing omegaARG5.xvg Printing omegaCYS6.xvg Printing chi1VAL2.xvg Printing chi1PHE3.xvg Printing chi1ARG5.xvg Printing chi1CYS6.xvg Printing chi2PHE3.xvg Printing chi2ARG5.xvg Printing chi3ARG5.xvg Printing chi4ARG5.xvg 50: Now calculating transitions... 50: Total number of transitions: 0 50: Now printing out transitions and OPs... 50: Now printing out rotamer occupancies... 50: Now calculating Chi product trajectories... 50: Printing chiproductVAL2.xvg and histo-chiprodVAL2.xvg Printing chiproductPHE3.xvg and histo-chiprodPHE3.xvg Printing chiproductARG5.xvg and histo-chiprodARG5.xvg Printing chiproductCYS6.xvg and histo-chiprodCYS6.xvg 50: [ OK ] GmxChiTest.gmxchiWorksWithr0AndrN (822 ms) 50: [----------] 2 tests from GmxChiTest (2095 ms total) 50: 50: [----------] 10 tests from MindistTest 50: [ RUN ] MindistTest.mindistWorksWithSingleAtoms 50: Group 0 ( atom1) has 1 elements 50: Group 1 ( atom2) has 1 elements 50: Group 2 ( atom3) has 1 elements 50: Group 3 ( atoms12) has 2 elements 50: Group 4 ( atoms23) has 2 elements 50: Group 5 ( atoms123) has 3 elements 50: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 50: Reading frame 0 time 0.000 Last frame 0 time 0.000 50: Selected 0: 'atom1' 50: Selected 1: 'atom2' 50: [ OK ] MindistTest.mindistWorksWithSingleAtoms (11 ms) 50: [ RUN ] MindistTest.mindistWorksWithMultipleAtoms 50: Group 0 ( atom1) has 1 elements 50: Group 1 ( atom2) has 1 elements 50: Group 2 ( atom3) has 1 elements 50: Group 3 ( atoms12) has 2 elements 50: Group 4 ( atoms23) has 2 elements 50: Group 5 ( atoms123) has 3 elements 50: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 50: Reading frame 0 time 0.000 Last frame 0 time 0.000 50: Selected 2: 'atom3' 50: Selected 3: 'atoms12' 50: [ OK ] MindistTest.mindistWorksWithMultipleAtoms (0 ms) 50: [ RUN ] MindistTest.mindistDoesNotPickUpContacts 50: Group 0 ( atom1) has 1 elements 50: Group 1 ( atom2) has 1 elements 50: Group 2 ( atom3) has 1 elements 50: Group 3 ( atoms12) has 2 elements 50: Group 4 ( atoms23) has 2 elements 50: Group 5 ( atoms123) has 3 elements 50: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 50: Reading frame 0 time 0.000 Last frame 0 time 0.000 50: Selected 0: 'atom1' 50: Selected 1: 'atom2' 50: [ OK ] MindistTest.mindistDoesNotPickUpContacts (1 ms) 50: [ RUN ] MindistTest.mindistPicksUpContacts 50: Group 0 ( atom1) has 1 elements 50: Group 1 ( atom2) has 1 elements 50: Group 2 ( atom3) has 1 elements 50: Group 3 ( atoms12) has 2 elements 50: Group 4 ( atoms23) has 2 elements 50: Group 5 ( atoms123) has 3 elements 50: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 50: Reading frame 0 time 0.000 Last frame 0 time 0.000 50: Selected 0: 'atom1' 50: Selected 1: 'atom2' 50: [ OK ] MindistTest.mindistPicksUpContacts (88 ms) 50: [ RUN ] MindistTest.ngWorks 50: Group 0 ( atom1) has 1 elements 50: Group 1 ( atom2) has 1 elements 50: Group 2 ( atom3) has 1 elements 50: Group 3 ( atoms12) has 2 elements 50: Group 4 ( atoms23) has 2 elements 50: Group 5 ( atoms123) has 3 elements 50: Select a group: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 50: Reading frame 0 time 0.000 Last frame 0 time 0.000 50: Selected 0: 'atom1' 50: Selected 1: 'atom2' 50: Selected 2: 'atom3' 50: [ OK ] MindistTest.ngWorks (1 ms) 50: [ RUN ] MindistTest.groupWorks 50: Group 0 ( atom1) has 1 elements 50: Group 1 ( atom2) has 1 elements 50: Group 2 ( atom3) has 1 elements 50: Group 3 ( atoms12) has 2 elements 50: Group 4 ( atoms23) has 2 elements 50: Group 5 ( atoms123) has 3 elements 50: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 50: Reading frame 0 time 0.000 Last frame 0 time 0.000 50: Selected 3: 'atoms12' 50: Selected 2: 'atom3' 50: [ OK ] MindistTest.groupWorks (456 ms) 50: [ RUN ] MindistTest.maxDistWorks 50: Group 0 ( atom1) has 1 elements 50: Group 1 ( atom2) has 1 elements 50: Group 2 ( atom3) has 1 elements 50: Group 3 ( atoms12) has 2 elements 50: Group 4 ( atoms23) has 2 elements 50: Group 5 ( atoms123) has 3 elements 50: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 50: Reading frame 0 time 0.000 Last frame 0 time 0.000 50: Selected 2: 'atom3' 50: Selected 3: 'atoms12' 50: [ OK ] MindistTest.maxDistWorks (1 ms) 50: [ RUN ] MindistTest.noPbcWorks 50: Group 0 ( atom1) has 1 elements 50: Group 1 ( atom2) has 1 elements 50: Group 2 ( atom3) has 1 elements 50: Group 3 ( atoms12) has 2 elements 50: Group 4 ( atoms23) has 2 elements 50: Group 5 ( atoms123) has 3 elements 50: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 50: Reading frame 0 time 0.000 Last frame 0 time 0.000 50: Selected 0: 'atom1' 50: Selected 1: 'atom2' 50: [ OK ] MindistTest.noPbcWorks (165 ms) 50: [ RUN ] MindistTest.resPerTimeWorks 50: Group 0 ( atom1) has 1 elements 50: Group 1 ( atom2) has 1 elements 50: Group 2 ( atom3) has 1 elements 50: Group 3 ( atoms12) has 2 elements 50: Group 4 ( atoms23) has 2 elements 50: Group 5 ( atoms123) has 3 elements 50: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 50: Reading frame 0 time 0.000 Last frame 0 time 0.000 50: Selected 3: 'atoms12' 50: Selected 2: 'atom3' 50: [ OK ] MindistTest.resPerTimeWorks (0 ms) 50: [ RUN ] MindistTest.matrixWorks 50: Group 0 ( atom1) has 1 elements 50: Group 1 ( atom2) has 1 elements 50: Group 2 ( atom3) has 1 elements 50: Group 3 ( atoms12) has 2 elements 50: Group 4 ( atoms23) has 2 elements 50: Group 5 ( atoms123) has 3 elements 50: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 50: Reading frame 0 time 0.000 Last frame 0 time 0.000 50: Selected 5: 'atoms123' 50: Special case: making distance matrix between all atoms in group atoms123 50: [ OK ] MindistTest.matrixWorks (0 ms) 50: [----------] 10 tests from MindistTest (729 ms total) 50: 50: [----------] 12 tests from NoFatalErrorWhenWritingFrom/GmxTraj 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: trr version: GMX_trn_file (single precision) 50: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 (4 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 (1 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 50: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 (0 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 50: Reading frame 1 time 1.000 Last frame 1 time 1.000 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 (0 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 (0 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 (4 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/0 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frame 0 time 0.000 50: WARNING: If there are molecules in the input trajectory file 50: that are broken across periodic boundaries, they 50: cannot be made whole (or treated as whole) without 50: you providing a run input file. 50: 50: Reading frame 1 time 1.000 Last frame 1 time 1.000 50: 50: WARNING: Masses and atomic (Van der Waals) radii will be guessed 50: based on residue and atom names, since they could not be 50: definitively assigned from the information in your input 50: files. These guessed numbers might deviate from the mass 50: and radius of the atom type. Please check the output 50: files if necessary. Note, that this functionality may 50: be removed in a future GROMACS version. Please, consider 50: using another file format for your input. 50: 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/0 (2 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/1 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frame 0 time 0.000 50: WARNING: If there are molecules in the input trajectory file 50: that are broken across periodic boundaries, they 50: cannot be made whole (or treated as whole) without 50: you providing a run input file. 50: 50: Reading frame 1 time 1.000 Last frame 1 time 1.000 50: 50: WARNING: Masses and atomic (Van der Waals) radii will be guessed 50: based on residue and atom names, since they could not be 50: definitively assigned from the information in your input 50: files. These guessed numbers might deviate from the mass 50: and radius of the atom type. Please check the output 50: files if necessary. Note, that this functionality may 50: be removed in a future GROMACS version. Please, consider 50: using another file format for your input. 50: 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/1 (1 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/2 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 50: Reading frame 0 time 0.000 50: WARNING: If there are molecules in the input trajectory file 50: that are broken across periodic boundaries, they 50: cannot be made whole (or treated as whole) without 50: you providing a run input file. 50: 50: Reading frame 1 time 1.000 Last frame 1 time 1.000 50: 50: WARNING: Masses and atomic (Van der Waals) radii will be guessed 50: based on residue and atom names, since they could not be 50: definitively assigned from the information in your input 50: files. These guessed numbers might deviate from the mass 50: and radius of the atom type. Please check the output 50: files if necessary. Note, that this functionality may 50: be removed in a future GROMACS version. Please, consider 50: using another file format for your input. 50: 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/2 (3 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/3 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 50: WARNING: If there are molecules in the input trajectory file 50: that are broken across periodic boundaries, they 50: cannot be made whole (or treated as whole) without 50: you providing a run input file. 50: 50: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 50: Reading frame 1 time 1.000 Last frame 1 time 1.000 50: 50: WARNING: Masses and atomic (Van der Waals) radii will be guessed 50: based on residue and atom names, since they could not be 50: definitively assigned from the information in your input 50: files. These guessed numbers might deviate from the mass 50: and radius of the atom type. Please check the output 50: files if necessary. Note, that this functionality may 50: be removed in a future GROMACS version. Please, consider 50: using another file format for your input. 50: 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/3 (2 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/4 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frame 0 time 0.000 50: WARNING: If there are molecules in the input trajectory file 50: that are broken across periodic boundaries, they 50: cannot be made whole (or treated as whole) without 50: you providing a run input file. 50: 50: Reading frame 1 time 1.000 Last frame 1 time 1.000 50: 50: WARNING: Masses and atomic (Van der Waals) radii will be guessed 50: based on residue and atom names, since they could not be 50: definitively assigned from the information in your input 50: files. These guessed numbers might deviate from the mass 50: and radius of the atom type. Please check the output 50: files if necessary. Note, that this functionality may 50: be removed in a future GROMACS version. Please, consider 50: using another file format for your input. 50: 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/4 (1 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/5 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frame 0 time 0.000 50: WARNING: If there are molecules in the input trajectory file 50: that are broken across periodic boundaries, they 50: cannot be made whole (or treated as whole) without 50: you providing a run input file. 50: 50: Reading frame 1 time 1.000 Last frame 1 time 1.000 50: 50: WARNING: Masses and atomic (Van der Waals) radii will be guessed 50: based on residue and atom names, since they could not be 50: definitively assigned from the information in your input 50: files. These guessed numbers might deviate from the mass 50: and radius of the atom type. Please check the output 50: files if necessary. Note, that this functionality may 50: be removed in a future GROMACS version. Please, consider 50: using another file format for your input. 50: 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/5 (4 ms) 50: [----------] 12 tests from NoFatalErrorWhenWritingFrom/GmxTraj (28 ms total) 50: 50: [----------] Global test environment tear-down 50: [==========] 31 tests from 4 test suites ran. (2854 ms total) 50: [ PASSED ] 31 tests. 50/90 Test #50: GmxAnaTest ................................ Passed 2.88 sec test 51 Start 51: GmxPreprocessTests 51: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/gmxpreprocess-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/GmxPreprocessTests.xml" 51: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests 51: Test timeout computed to be: 1920 51: [==========] Running 212 tests from 15 test suites. 51: [----------] Global test environment set-up. 51: [----------] 1 test from ConvertInteractionsTest 51: [ RUN ] ConvertInteractionsTest.DoingNothingWorks 51: [ OK ] ConvertInteractionsTest.DoingNothingWorks (0 ms) 51: [----------] 1 test from ConvertInteractionsTest (0 ms total) 51: 51: [----------] 4 tests from GenconfTest 51: [ RUN ] GenconfTest.nbox_Works 51: [ OK ] GenconfTest.nbox_Works (1 ms) 51: [ RUN ] GenconfTest.nbox_norenumber_Works 51: [ OK ] GenconfTest.nbox_norenumber_Works (0 ms) 51: [ RUN ] GenconfTest.nbox_dist_Works 51: [ OK ] GenconfTest.nbox_dist_Works (0 ms) 51: [ RUN ] GenconfTest.nbox_rot_Works 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: [ OK ] GenconfTest.nbox_rot_Works (1 ms) 51: [----------] 4 tests from GenconfTest (3 ms total) 51: 51: [----------] 2 tests from GenionTest 51: [ RUN ] GenionTest.HighConcentrationIonPlacement 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 51: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet 51: buffer. The cluster pair list does have a buffering effect, but choosing 51: a larger rlist might be necessary for good energy conservation. 51: 51: 51: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 51: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 51: < 0 51: 51: 51: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: Generating 1-4 interactions: fudge = 0.5 51: Number of degrees of freedom in T-Coupling group rest is 1308.00 51: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 51: 51: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 51: You are using a plain Coulomb cut-off, which might produce artifacts. 51: You might want to consider using PME electrostatics. 51: 51: 51: 51: There were 4 NOTEs 51: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 51: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 51: Group 0 ( System) has 653 elements 51: Group 1 ( Water) has 648 elements 51: Group 2 ( SOL) has 648 elements 51: Group 3 ( non-Water) has 5 elements 51: Group 4 ( Other) has 5 elements 51: Group 5 ( METH) has 5 elements 51: Select a group: Number of (3-atomic) solvent molecules: 216 51: Using random seed 1997. 51: Replacing solvent molecule 56 (atom 168) with NA 51: Replacing solvent molecule 120 (atom 360) with NA 51: Replacing solvent molecule 182 (atom 546) with NA 51: Replacing solvent molecule 71 (atom 213) with NA 51: Replacing solvent molecule 189 (atom 567) with CL 51: Replacing solvent molecule 54 (atom 162) with CL 51: Replacing solvent molecule 155 (atom 465) with CL 51: Replacing solvent molecule 99 (atom 297) with CL 51: 51: Setting the LD random seed to -1493210369 51: 51: Generated 331705 of the 331705 non-bonded parameter combinations 51: 51: Generated 331705 of the 331705 1-4 parameter combinations 51: 51: Excluding 2 bonded neighbours molecule type 'SOL' 51: 51: Excluding 3 bonded neighbours molecule type 'methane' 51: 51: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc216_with_methane.gro' 51: Analysing residue names: 51: There are: 216 Water residues 51: There are: 1 Other residues 51: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 51: 51: This run will generate roughly 0 Mb of data 51: Will try to add 4 NA ions and 4 CL ions. 51: Select a continuous group of solvent molecules 51: Selected 1: 'Water' 51: [ OK ] GenionTest.HighConcentrationIonPlacement (508 ms) 51: [ RUN ] GenionTest.NoIonPlacement 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 51: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet 51: buffer. The cluster pair list does have a buffering effect, but choosing 51: a larger rlist might be necessary for good energy conservation. 51: 51: 51: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 51: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 51: < 0 51: 51: 51: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: Generating 1-4 interactions: fudge = 0.5 51: Number of degrees of freedom in T-Coupling group rest is 1308.00 51: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 51: 51: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 51: You are using a plain Coulomb cut-off, which might produce artifacts. 51: You might want to consider using PME electrostatics. 51: 51: 51: 51: There were 4 NOTEs 51: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 51: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 51: No ions to add, will just copy input configuration. 51: Setting the LD random seed to 2126157807 51: 51: Generated 331705 of the 331705 non-bonded parameter combinations 51: 51: Generated 331705 of the 331705 1-4 parameter combinations 51: 51: Excluding 2 bonded neighbours molecule type 'SOL' 51: 51: Excluding 3 bonded neighbours molecule type 'methane' 51: 51: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc216_with_methane.gro' 51: Analysing residue names: 51: There are: 216 Water residues 51: There are: 1 Other residues 51: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 51: 51: This run will generate roughly 0 Mb of data 51: [ OK ] GenionTest.NoIonPlacement (608 ms) 51: [----------] 2 tests from GenionTest (1117 ms total) 51: 51: [----------] 1 test from GenRestrTest 51: [ RUN ] GenRestrTest.SimpleRestraintsGenerated 51: 51: Reading structure file 51: Group 0 ( System) has 156 elements 51: Group 1 ( Protein) has 156 elements 51: Group 2 ( Protein-H) has 75 elements 51: Group 3 ( C-alpha) has 10 elements 51: Group 4 ( Backbone) has 30 elements 51: Group 5 ( MainChain) has 40 elements 51: Group 6 ( MainChain+Cb) has 49 elements 51: Group 7 ( MainChain+H) has 52 elements 51: Group 8 ( SideChain) has 104 elements 51: Group 9 ( SideChain-H) has 35 elements 51: Select a group: Select group to position restrain 51: Selected 3: 'C-alpha' 51: [ OK ] GenRestrTest.SimpleRestraintsGenerated (1 ms) 51: [----------] 1 test from GenRestrTest (1 ms total) 51: 51: [----------] 9 tests from PreprocessingAtomTypesTest 51: [ RUN ] PreprocessingAtomTypesTest.EmptyOnCreate 51: [ OK ] PreprocessingAtomTypesTest.EmptyOnCreate (0 ms) 51: [ RUN ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid 51: [ OK ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid (0 ms) 51: [ RUN ] PreprocessingAtomTypesTest.AddTypeWorks 51: [ OK ] PreprocessingAtomTypesTest.AddTypeWorks (0 ms) 51: [ RUN ] PreprocessingAtomTypesTest.AddMultipleTypesWorks 51: [ OK ] PreprocessingAtomTypesTest.AddMultipleTypesWorks (0 ms) 51: [ RUN ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry 51: [ OK ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry (0 ms) 51: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFound 51: [ OK ] PreprocessingAtomTypesTest.CorrectNameFound (0 ms) 51: [ RUN ] PreprocessingAtomTypesTest.WrongNameNotFound 51: [ OK ] PreprocessingAtomTypesTest.WrongNameNotFound (0 ms) 51: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber 51: [ OK ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber (0 ms) 51: [ RUN ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber 51: [ OK ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber (0 ms) 51: [----------] 9 tests from PreprocessingAtomTypesTest (0 ms total) 51: 51: [----------] 10 tests from PreprocessingBondAtomTypeTest 51: [ RUN ] PreprocessingBondAtomTypeTest.EmptyOnCreate 51: [ OK ] PreprocessingBondAtomTypeTest.EmptyOnCreate (0 ms) 51: [ RUN ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid 51: [ OK ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid (0 ms) 51: [ RUN ] PreprocessingBondAtomTypeTest.AddTypeWorks 51: [ OK ] PreprocessingBondAtomTypeTest.AddTypeWorks (0 ms) 51: [ RUN ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks 51: [ OK ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks (0 ms) 51: [ RUN ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry 51: [ OK ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry (0 ms) 51: [ RUN ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType 51: [ OK ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType (0 ms) 51: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFound 51: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFound (0 ms) 51: [ RUN ] PreprocessingBondAtomTypeTest.WrongNameNotFound 51: [ OK ] PreprocessingBondAtomTypeTest.WrongNameNotFound (0 ms) 51: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber 51: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber (0 ms) 51: [ RUN ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber 51: [ OK ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber (0 ms) 51: [----------] 10 tests from PreprocessingBondAtomTypeTest (0 ms total) 51: 51: [----------] 3 tests from GromppDirectiveTest 51: [ RUN ] GromppDirectiveTest.edgeCaseAtomTypeNames 51: Ignoring obsolete mdp entry 'title' 51: Generating 1-4 interactions: fudge = 0.5 51: 51: NOTE 1 [file directives.top, line 59]: 51: In moleculetype 'A' 2 atoms are not bound by a potential or constraint to 51: any other atom in the same moleculetype. Although technically this might 51: not cause issues in a simulation, this often means that the user forgot 51: to add a bond/potential/constraint or put multiple molecules in the same 51: moleculetype definition by mistake. Run with -v to get information for 51: each atom. 51: 51: Number of degrees of freedom in T-Coupling group rest is 9.00 51: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 51: 51: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_edgeCaseAtomTypeNames_directives.mdp]: 51: NVE simulation: will use the initial temperature of 300.000 K for 51: determining the Verlet buffer size 51: 51: 51: There were 2 NOTEs 51: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_edgeCaseAtomTypeNames_directives.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 51: Setting the LD random seed to -1284841483 51: 51: Generated 10 of the 10 non-bonded parameter combinations 51: 51: Generated 10 of the 10 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to -1107370565 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: Analysing residue names: 51: There are: 1 Other residues 51: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 51: 51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 51: 51: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 51: 51: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 51: 51: Note that mdrun will redetermine rlist based on the actual pair-list setup 51: 51: This run will generate roughly 0 Mb of data 51: [ OK ] GromppDirectiveTest.edgeCaseAtomTypeNames (117 ms) 51: [ RUN ] GromppDirectiveTest.NoteOnDihedralNotSumToZero 51: Ignoring obsolete mdp entry 'title' 51: Generating 1-4 interactions: fudge = 0.5 51: 51: NOTE 1 [file directives.top, line 59]: 51: 1 dihedrals with function type 3 (Ryckaert-Bellemans or Fourier) have 51: coefficients that do not sum to zero. This does not affect the simulation 51: and can be ignored, unless you are comparing potential energy values with 51: other force field ports and/or MD software. 51: First such dihedral in molecule A, involving atoms 0 2 1 3 51: 51: 51: NOTE 2 [file directives.top, line 59]: 51: In moleculetype 'A' 2 atoms are not bound by a potential or constraint to 51: any other atom in the same moleculetype. Although technically this might 51: not cause issues in a simulation, this often means that the user forgot 51: to add a bond/potential/constraint or put multiple molecules in the same 51: moleculetype definition by mistake. Run with -v to get information for 51: each atom. 51: 51: Number of degrees of freedom in T-Coupling group rest is 9.00 51: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 51: 51: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_NoteOnDihedralNotSumToZero_directives.mdp]: 51: NVE simulation: will use the initial temperature of 300.000 K for 51: determining the Verlet buffer size 51: 51: 51: There were 3 NOTEs 51: Setting the LD random seed to -564211975 51: 51: Generated 10 of the 10 non-bonded parameter combinations 51: 51: Generated 10 of the 10 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to -1086697010 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: Analysing residue names: 51: There are: 1 Other residues 51: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 51: 51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 51: 51: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 51: 51: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 51: 51: Note that mdrun will redetermine rlist based on the actual pair-list setup 51: 51: This run will generate roughly 0 Mb of data 51: [ OK ] GromppDirectiveTest.NoteOnDihedralNotSumToZero (143 ms) 51: [ RUN ] GromppDirectiveTest.WarnOnDihedralSumDifferentForFreeEnergy 51: Setting the LD random seed to -2020608561 51: 51: Generated 10 of the 10 non-bonded parameter combinations 51: 51: Generated 10 of the 10 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to -1628442757 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: Analysing residue names: 51: There are: 1 Other residues 51: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 51: 51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 51: 51: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 51: 51: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 51: 51: Note that mdrun will redetermine rlist based on the actual pair-list setup 51: 51: This run will generate roughly 0 Mb of data 51: [ OK ] GromppDirectiveTest.WarnOnDihedralSumDifferentForFreeEnergy (467 ms) 51: [----------] 3 tests from GromppDirectiveTest (728 ms total) 51: 51: [----------] 6 tests from InsertMoleculesTest 51: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration 51: Reading solute configuration 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. (1964) 51: DOI: 10.1021/j100785a001 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Using random seed 1997 51: Try 1 success (now 8 atoms)! 51: 51: Added 1 molecules (out of 1 requested) 51: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoExistingConfiguration_out.gro 51: 51: Output configuration contains 8 atoms in 4 residues 51: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration (2 ms) 51: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. (1964) 51: DOI: 10.1021/j100785a001 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Using random seed 1997 51: Try 1 success (now 2 atoms)! 51: Try 2 success (now 4 atoms)! 51: Try 3 success (now 6 atoms)! 51: Try 4 success (now 8 atoms)! 51: Try 5 success (now 10 atoms)! 51: 51: Added 5 molecules (out of 5 requested) 51: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBox_out.gro 51: 51: Output configuration contains 10 atoms in 10 residues 51: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox (0 ms) 51: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBoxConcentration 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. (1964) 51: DOI: 10.1021/j100785a001 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Using random seed 1997 51: Try 1 success (now 2 atoms)! 51: Try 2 success (now 4 atoms)! 51: Try 3 success (now 6 atoms)! 51: Try 4 success (now 8 atoms)! 51: Try 5 success (now 10 atoms)! 51: 51: Added 5 molecules (out of 5 requested) 51: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBoxConcentration_out.gro 51: 51: Output configuration contains 10 atoms in 10 residues 51: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBoxConcentration (0 ms) 51: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox 51: Reading solute configuration 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. (1964) 51: DOI: 10.1021/j100785a001 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Using random seed 1997 51: Try 1 success (now 8 atoms)! 51: Try 2 success (now 10 atoms)! 51: 51: Added 2 molecules (out of 2 requested) 51: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEnlargedBox_out.gro 51: 51: Output configuration contains 10 atoms in 4 residues 51: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox (1 ms) 51: [ RUN ] InsertMoleculesTest.InsertsMoleculesWithReplacement 51: Reading solute configuration 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. (1964) 51: DOI: 10.1021/j100785a001 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Using random seed 1997 51: Try 1 success (now 650 atoms)! 51: Try 2 success (now 652 atoms)! 51: Try 3 success (now 654 atoms)! 51: Try 4 success (now 656 atoms)! 51: 51: Added 4 molecules (out of 4 requested) 51: Replaced 8 residues (24 atoms) 51: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesWithReplacement_out.gro 51: 51: Output configuration contains 632 atoms in 212 residues 51: [ OK ] InsertMoleculesTest.InsertsMoleculesWithReplacement (4 ms) 51: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. (1964) 51: DOI: 10.1021/j100785a001 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Using random seed 1997 51: Read 4 positions from file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_5.dat 51: 51: Try 1 success (now 2 atoms)! 51: Try 2 success (now 4 atoms)! 51: Try 3 Try 4 Try 5 Try 6 Try 7 Try 8 Try 9 Try 10 Try 11 Try 12 skipped position (0.990, 2.010, 3.000) 51: Try 13 success (now 6 atoms)! 51: 51: Added 3 molecules (out of 4 requested) 51: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_out.gro 51: 51: Output configuration contains 6 atoms in 3 residues 51: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions (1 ms) 51: [----------] 6 tests from InsertMoleculesTest (10 ms total) 51: 51: [----------] 3 tests from MassRepartitioning 51: [ RUN ] MassRepartitioning.ValidCaseWorks 51: The smallest mass in the system is 2, setting the minimum mass to 6 51: [ OK ] MassRepartitioning.ValidCaseWorks (0 ms) 51: [ RUN ] MassRepartitioning.UnboundGivesWarning 51: 51: WARNING 1 [file unknown]: 51: The are 1 atoms that have a mass below the mass repartitioning limit but 51: are not bound. These masses cannot be repartitioned. 51: 51: The smallest mass in the system is 2, setting the minimum mass to 6 51: [ OK ] MassRepartitioning.UnboundGivesWarning (0 ms) 51: [ RUN ] MassRepartitioning.LightPartnerGivesError 51: 51: ERROR 1 [file unknown]: 51: Light atoms are bound to at least one atom that has a too low mass for 51: repartitioning 51: 51: The smallest mass in the system is 2, setting the minimum mass to 6 51: [ OK ] MassRepartitioning.LightPartnerGivesError (0 ms) 51: [----------] 3 tests from MassRepartitioning (0 ms total) 51: 51: [----------] 35 tests from GetIrTest 51: [ RUN ] GetIrTest.HandlesDifferentKindsOfMdpLines 51: Ignoring obsolete mdp entry 'title' 51: Replacing old mdp entry 'xtc_grps' by 'compressed-x-grps' 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.HandlesDifferentKindsOfMdpLines (2 ms) 51: [ RUN ] GetIrTest.RejectsNonCommentLineWithNoEquals 51: [ OK ] GetIrTest.RejectsNonCommentLineWithNoEquals (8 ms) 51: [ RUN ] GetIrTest.AcceptsKeyWithoutValue 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsKeyWithoutValue_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.AcceptsKeyWithoutValue (2 ms) 51: [ RUN ] GetIrTest.RejectsValueWithoutKey 51: [ OK ] GetIrTest.RejectsValueWithoutKey (9 ms) 51: [ RUN ] GetIrTest.RejectsEmptyKeyAndEmptyValue 51: [ OK ] GetIrTest.RejectsEmptyKeyAndEmptyValue (8 ms) 51: [ RUN ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsDefineParametersWithValuesIncludingAssignment_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment (2 ms) 51: [ RUN ] GetIrTest.AcceptsEmptyLines 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsEmptyLines_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.AcceptsEmptyLines (2 ms) 51: [ RUN ] GetIrTest.MtsCheckNstcalcenergy 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstcalcenergy_input.mdp]: 51: With MTS, nstcalcenergy = 5 should be a multiple of mts-factor = 2 51: 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstcalcenergy_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.MtsCheckNstcalcenergy (1 ms) 51: [ RUN ] GetIrTest.MtsCheckNstenergy 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 51: With MTS, nstenergy = 5 should be a multiple of mts-factor = 2 51: 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 51: Setting nstcalcenergy (100) equal to nstenergy (5) 51: 51: 51: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.MtsCheckNstenergy (1 ms) 51: [ RUN ] GetIrTest.MtsCheckNstpcouple 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp, line 7]: 51: Pressure coupling incorrect number of values (I need exactly 1) 51: 51: 51: ERROR 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp, line 7]: 51: Pressure coupling incorrect number of values (I need exactly 1) 51: 51: 51: ERROR 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 51: With multiple time stepping, nstpcouple should be a multiple of 51: mts-factor 51: 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: 51: ERROR 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 51: The Berendsen barostat does not generate any strictly correct ensemble, 51: and should not be used for new production simulations (in our opinion). 51: We recommend using the C-rescale barostat instead. 51: 51: 51: ERROR 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 51: compressibility must be > 0 when using pressure coupling Berendsen 51: 51: 51: [ OK ] GetIrTest.MtsCheckNstpcouple (1 ms) 51: [ RUN ] GetIrTest.MtsCheckNstdhdl 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 51: With MTS, nstdhdl = 5 should be a multiple of mts-factor = 2 51: 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 51: Setting nstcalcenergy (100) equal to nstdhdl (5) 51: 51: 51: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: 51: ERROR 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 51: Lambda state must be set, either with init-lambda-state or with 51: init-lambda 51: 51: [ OK ] GetIrTest.MtsCheckNstdhdl (1 ms) 51: [ RUN ] GetIrTest.MtsCheckSDNotSupported 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckSDNotSupported_input.mdp]: 51: Multiple time stepping is only supported with integrator md 51: 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckSDNotSupported_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.MtsCheckSDNotSupported (1 ms) 51: [ RUN ] GetIrTest.AcceptsElectricField 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricField_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.AcceptsElectricField (2 ms) 51: [ RUN ] GetIrTest.AcceptsElectricFieldPulsed 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldPulsed_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.AcceptsElectricFieldPulsed (2 ms) 51: [ RUN ] GetIrTest.AcceptsElectricFieldOscillating 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldOscillating_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.AcceptsElectricFieldOscillating (2 ms) 51: [ RUN ] GetIrTest.RejectsDuplicateOldAndNewKeys 51: [ OK ] GetIrTest.RejectsDuplicateOldAndNewKeys (5 ms) 51: [ RUN ] GetIrTest.AcceptsImplicitSolventNo 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsImplicitSolventNo_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.AcceptsImplicitSolventNo (2 ms) 51: [ RUN ] GetIrTest.RejectsImplicitSolventYes 51: [ OK ] GetIrTest.RejectsImplicitSolventYes (7 ms) 51: [ RUN ] GetIrTest.AcceptsMimic 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsMimic_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.AcceptsMimic (2 ms) 51: [ RUN ] GetIrTest.AcceptsTransformationCoord 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsTransformationCoord_input.mdp, line 11]: 51: pull-coord2 has a non-zero force constant and is also referenced in 51: pull-coord1-expression. Make sure that this is intended. In most use 51: cases, the pull coordinates referenced by a transformation coordinate 51: should have their force constant set to zero. 51: 51: 51: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsTransformationCoord_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.AcceptsTransformationCoord (2 ms) 51: [ RUN ] GetIrTest.InvalidTransformationCoordWithConstraint 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordWithConstraint_input.mdp, line 7]: 51: pull-coord1 cannot have type 'constraint' and geometry 'transformation' 51: 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordWithConstraint_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.InvalidTransformationCoordWithConstraint (1 ms) 51: [ RUN ] GetIrTest.InvalidPullCoordWithConstraintInTransformationExpression 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidPullCoordWithConstraintInTransformationExpression_input.mdp, line 10]: 51: pull-coord2 can not use pull-coord1 in the transformation since this is a 51: constraint 51: 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidPullCoordWithConstraintInTransformationExpression_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.InvalidPullCoordWithConstraintInTransformationExpression (2 ms) 51: [ RUN ] GetIrTest.InvalidTransformationCoordDxValue 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordDxValue_input.mdp, line 7]: 51: pull-coord1-dx cannot be set to zero for pull coordinate of geometry 51: 'transformation' 51: 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordDxValue_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.InvalidTransformationCoordDxValue (1 ms) 51: [ RUN ] GetIrTest.MissingTransformationCoordExpression 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MissingTransformationCoordExpression_input.mdp, line 5]: 51: pull-coord1-expression not set for pull coordinate of geometry 51: 'transformation' 51: 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MissingTransformationCoordExpression_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.MissingTransformationCoordExpression (1 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep 51: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep (1 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep_negativeDelta 51: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep_negativeDelta (1 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep 51: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep (1 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep_negativeDelta 51: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep_negativeDelta (1 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_SC_And_OneStepTooMuch_input.mdp]: 51: With init-lambda = 0 and delta_lambda = 1e-05 and no explicit input, 51: coul-lambdas and vdw-lambdas will be greater than 1 after step 100000 of 51: in total 100001 steps. This is not compatible with using soft-core 51: potentials. 51: 51: 51: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch (1 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta_input.mdp]: 51: With init-lambda = 1 and delta_lambda = -1e-05, the lambda components 51: won't change anymore after step 100000 until the end of the simulation 51: after 100001 steps. 51: 51: 51: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta (1 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta_input.mdp]: 51: With init-lambda = 1 and delta_lambda = -1e-05, the lambda components 51: won't change anymore after step 100000 until the end of the simulation 51: after 100001 steps. 51: 51: 51: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta (1 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_input.mdp]: 51: With init-lambda-state = 0 and delta_lambda = 1e-05, the lambda 51: components won't change anymore after step 100000 until the end of the 51: simulation after 100001 steps. 51: 51: 51: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch (1 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta_input.mdp]: 51: With init-lambda-state = 2 and delta_lambda = -1e-05, the lambda 51: components won't change anymore after step 100000 until the end of the 51: simulation after 100001 steps. 51: 51: 51: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta (1 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep 51: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep (1 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep_negativeDelta 51: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep_negativeDelta (1 ms) 51: [----------] 35 tests from GetIrTest (98 ms total) 51: 51: [----------] 6 tests from SolvateTest 51: [ RUN ] SolvateTest.cs_box_Works 51: Reading solvent configuration 51: 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. (1964) 51: DOI: 10.1021/j100785a001 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Generating solvent configuration 51: Will generate new solvent configuration of 1x1x1 boxes 51: Solvent box contains 270 atoms in 90 residues 51: Removed 129 solvent atoms due to solvent-solvent overlap 51: Sorting configuration 51: Found 1 molecule type: 51: SOL ( 3 atoms): 47 residues 51: Generated solvent containing 141 atoms in 47 residues 51: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_box_Works_out.gro 51: 51: Output configuration contains 141 atoms in 47 residues 51: Volume : 1.331 (nm^3) 51: Density : 1056.36 (g/l) 51: Number of solvent molecules: 47 51: 51: [ OK ] SolvateTest.cs_box_Works (3 ms) 51: [ RUN ] SolvateTest.cs_cp_Works 51: Reading solute configuration 51: Reading solvent configuration 51: 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. (1964) 51: DOI: 10.1021/j100785a001 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Generating solvent configuration 51: Will generate new solvent configuration of 2x2x2 boxes 51: Solvent box contains 3660 atoms in 1220 residues 51: Removed 987 solvent atoms due to solvent-solvent overlap 51: Removed 15 solvent atoms due to solute-solvent overlap 51: Sorting configuration 51: Found 1 molecule type: 51: SOL ( 3 atoms): 886 residues 51: Generated solvent containing 2658 atoms in 886 residues 51: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_Works_out.gro 51: 51: Output configuration contains 2664 atoms in 888 residues 51: Volume : 27.2709 (nm^3) 51: Density : 974.777 (g/l) 51: Number of solvent molecules: 886 51: 51: [ OK ] SolvateTest.cs_cp_Works (19 ms) 51: [ RUN ] SolvateTest.cs_cp_p_Works 51: Reading solute configuration 51: Reading solvent configuration 51: 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. (1964) 51: DOI: 10.1021/j100785a001 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Generating solvent configuration 51: Will generate new solvent configuration of 2x2x2 boxes 51: Solvent box contains 3660 atoms in 1220 residues 51: Removed 987 solvent atoms due to solvent-solvent overlap 51: Removed 15 solvent atoms due to solute-solvent overlap 51: Sorting configuration 51: Found 1 molecule type: 51: SOL ( 3 atoms): 886 residues 51: Generated solvent containing 2658 atoms in 886 residues 51: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_out.gro 51: 51: Output configuration contains 2664 atoms in 888 residues 51: Volume : 27.2709 (nm^3) 51: Density : 974.777 (g/l) 51: Number of solvent molecules: 886 51: 51: Processing topology 51: Adding line for 886 solvent molecules with resname (SOL) to topology file (/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_spc-and-methanol.top) 51: [ OK ] SolvateTest.cs_cp_p_Works (206 ms) 51: [ RUN ] SolvateTest.shell_Works 51: Reading solute configuration 51: Reading solvent configuration 51: 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. (1964) 51: DOI: 10.1021/j100785a001 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Generating solvent configuration 51: Will generate new solvent configuration of 2x2x2 boxes 51: Solvent box contains 3660 atoms in 1220 residues 51: Removed 987 solvent atoms due to solvent-solvent overlap 51: Removed 1902 solvent atoms more than 1.000000 nm from solute. 51: Removed 15 solvent atoms due to solute-solvent overlap 51: Sorting configuration 51: Found 1 molecule type: 51: SOL ( 3 atoms): 252 residues 51: Generated solvent containing 756 atoms in 252 residues 51: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_shell_Works_out.gro 51: 51: Output configuration contains 762 atoms in 254 residues 51: Volume : 27.2709 (nm^3) 51: Density : 279.3 (g/l) 51: Number of solvent molecules: 252 51: 51: [ OK ] SolvateTest.shell_Works (106 ms) 51: [ RUN ] SolvateTest.update_Topology_Works 51: Reading solute configuration 51: Reading solvent configuration 51: 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. (1964) 51: DOI: 10.1021/j100785a001 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Generating solvent configuration 51: Will generate new solvent configuration of 3x3x3 boxes 51: Solvent box contains 14952 atoms in 4984 residues 51: Removed 2787 solvent atoms due to solvent-solvent overlap 51: Removed 30 solvent atoms due to solute-solvent overlap 51: Sorting configuration 51: Found 2 different molecule types: 51: HOH ( 3 atoms): 1876 residues 51: SOL ( 3 atoms): 2169 residues 51: Generated solvent containing 0 atoms in 0 residues 51: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_out.gro 51: 51: Output configuration contains 12141 atoms in 4047 residues 51: Volume : 125 (nm^3) 51: Density : 968.963 (g/l) 51: Number of solvent molecules: 4045 51: 51: Processing topology 51: Adding line for 1876 solvent molecules with resname (HOH) to topology file (/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 51: Adding line for 2169 solvent molecules with resname (SOL) to topology file (/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 51: [ OK ] SolvateTest.update_Topology_Works (279 ms) 51: [ RUN ] SolvateTest.cs_pdb_big_box_Works 51: Reading solvent configuration 51: 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. (1964) 51: DOI: 10.1021/j100785a001 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Generating solvent configuration 51: Will generate new solvent configuration of 2x2x2 boxes 51: Solvent box contains 1218 atoms in 406 residues 51: Removed 555 solvent atoms due to solvent-solvent overlap 51: Sorting configuration 51: Found 1 molecule type: 51: SOL ( 3 atoms): 221 residues 51: Generated solvent containing 663 atoms in 221 residues 51: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_pdb_big_box_Works_out.gro 51: 51: Output configuration contains 663 atoms in 221 residues 51: Volume : 8 (nm^3) 51: Density : 826.409 (g/l) 51: Number of solvent molecules: 221 51: 51: [ OK ] SolvateTest.cs_pdb_big_box_Works (12 ms) 51: [----------] 6 tests from SolvateTest (627 ms total) 51: 51: [----------] 1 test from TopDirTests 51: [ RUN ] TopDirTests.NamesArrayHasCorrectSize 51: [ OK ] TopDirTests.NamesArrayHasCorrectSize (0 ms) 51: [----------] 1 test from TopDirTests (0 ms total) 51: 51: [----------] 95 tests from InteractionFunctionKind/ConvertInteractionsTest 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Bond 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Bond (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Morse 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Morse (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Cubic_Bonds 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Cubic_Bonds (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Connect_Bonds 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Connect_Bonds (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Harmonic_Pot_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Harmonic_Pot_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/FENE_Bonds 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/FENE_Bonds (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds_NC 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds_NC (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restraint_Pot_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restraint_Pot_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Angle 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Angle (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Angles 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Angles (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Lin__Angle 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Lin__Angle (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond_Cross 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond_Cross (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/BA_Cross 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/BA_Cross (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/U_B 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/U_B (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quartic_Angles 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quartic_Angles (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Angles 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Angles (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Proper_Dih_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Proper_Dih_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ryckaert_Bell_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ryckaert_Bell_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Dih_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Dih_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/CBT_Dih_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/CBT_Dih_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Fourier_Dih_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Fourier_Dih_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Improper_Dih_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Improper_Dih_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Per__Imp__Dih_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Per__Imp__Dih_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Dih_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Dih_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/CMAP_Dih_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/CMAP_Dih_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_2_Pol_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_2_Pol_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_3_Pol_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_3_Pol_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_4_Pol_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_4_Pol_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_Polariz_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_Polariz_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Nonpolar_Sol_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Nonpolar_Sol_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_14 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_14 (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb_14 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb_14 (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_14_q 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_14_q (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_Pairs_NB 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_Pairs_NB (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ__SR_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ__SR_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Buck_ham__SR_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Buck_ham__SR_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/B_ham 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/B_ham (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Disper__corr_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Disper__corr_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb__SR_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb__SR_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/RF_excl_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/RF_excl_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul__recip_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul__recip_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_recip_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_recip_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/DPD 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/DPD (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Polarization 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Polarization (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Water_Pol_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Water_Pol_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Thole_Pol_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Thole_Pol_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Anharm__Pol_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Anharm__Pol_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Position_Rest_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Position_Rest_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Flat_b__P_R_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Flat_b__P_R_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dis__Rest_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dis__Rest_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/D_R_Viol___nm_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/D_R_Viol___nm_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Orient__Rest_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Orient__Rest_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ori__R__RMSD 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ori__R__RMSD (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest__Z 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest__Z (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest__Vi_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest__Vi_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constraint 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constraint (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constr__No_Co_ 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constr__No_Co_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Settle 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Settle (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_1 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_1 (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_2 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_2 (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_2fd 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_2fd (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_3 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_3 (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_3fd 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_3fd (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3fad 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3fad (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3out 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3out (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_4fd 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_4fd (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_4fdn 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_4fdn (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_N 51: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_N (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/COM_Pull_En_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/COM_Pull_En_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dens__fitting 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dens__fitting (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quantum_En_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quantum_En_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/NN_Potential 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/NN_Potential (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Potential 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Potential (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Kinetic_En_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Kinetic_En_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Total_Energy 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Total_Energy (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Conserved_En_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Conserved_En_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Temperature 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Temperature (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__Temp_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__Temp_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pres__DC 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pres__DC (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pressure 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pressure (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dH_dl_constr_ 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dH_dl_constr_ (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVremain_dl 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVremain_dl (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dEkin_dl 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dEkin_dl (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVcoul_dl 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVcoul_dl (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVvdw_dl 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVvdw_dl (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVbonded_dl 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVbonded_dl (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVrestraint_dl 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVrestraint_dl (0 ms) 51: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVtemp_dl 51: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 51: Skipping interaction type that does not represent a interaction with parameters converted in grompp 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVtemp_dl (0 ms) 51: [----------] 95 tests from InteractionFunctionKind/ConvertInteractionsTest (2 ms total) 51: 51: [----------] 16 tests from CorrectVelocity/MaxwellTest 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/0 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/0 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/1 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/1 (5 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/2 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/2 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/3 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/3 (1 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/4 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/4 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/5 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/5 (1 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/6 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/6 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/7 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/7 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/8 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/8 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/9 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/9 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/10 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/10 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/11 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/11 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/12 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/12 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/13 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/13 (1 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/14 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/14 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/15 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/15 (1 ms) 51: [----------] 16 tests from CorrectVelocity/MaxwellTest (19 ms total) 51: 51: [----------] 20 tests from CMAPDefinesAndErrors/GromppDirectiveTest 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/0 51: Setting the LD random seed to -304300321 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/0 (290 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/1 51: Setting the LD random seed to -69238937 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/1 (236 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/2 51: Ignoring obsolete mdp entry 'title' 51: Generating 1-4 interactions: fudge = 0.5 51: 51: NOTE 1 [file directives-cmap.top, line 105]: 51: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 51: any other atom in the same moleculetype. Although technically this might 51: not cause issues in a simulation, this often means that the user forgot 51: to add a bond/potential/constraint or put multiple molecules in the same 51: moleculetype definition by mistake. Run with -v to get information for 51: each atom. 51: 51: Number of degrees of freedom in T-Coupling group rest is 12.00 51: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 51: 51: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_2_directives-cmap.mdp]: 51: NVE simulation: will use the initial temperature of 300.000 K for 51: determining the Verlet buffer size 51: 51: 51: There were 2 NOTEs 51: Setting the LD random seed to -67766289 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to -1141085730 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: Analysing residue names: 51: There are: 1 Other residues 51: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 51: 51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 51: 51: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 51: 51: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 51: 51: Note that mdrun will redetermine rlist based on the actual pair-list setup 51: 51: This run will generate roughly 0 Mb of data 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/2 (309 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/3 51: Setting the LD random seed to 1473474035 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/3 (338 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/4 51: Setting the LD random seed to -136577794 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to -6273 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/4 (416 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/5 51: Setting the LD random seed to -87326869 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/5 (109 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/6 51: Setting the LD random seed to -570704007 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to -1078006105 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/6 (494 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/7 51: Setting the LD random seed to -161595411 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to -3417130 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/7 (95 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/8 51: Setting the LD random seed to -889716743 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to -2164775 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/8 (671 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/9 51: Setting the LD random seed to 1705794260 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to -1251278951 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/9 (430 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/10 51: Setting the LD random seed to -1111539713 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to -621294338 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/10 (561 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/11 51: Setting the LD random seed to -537790529 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to -1677721892 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/11 (230 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/12 51: Setting the LD random seed to -1141646342 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to -847407238 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/12 (284 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/13 51: Ignoring obsolete mdp entry 'title' 51: Generating 1-4 interactions: fudge = 0.5 51: 51: NOTE 1 [file directives-cmap.top, line 105]: 51: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 51: any other atom in the same moleculetype. Although technically this might 51: not cause issues in a simulation, this often means that the user forgot 51: to add a bond/potential/constraint or put multiple molecules in the same 51: moleculetype definition by mistake. Run with -v to get information for 51: each atom. 51: 51: Number of degrees of freedom in T-Coupling group rest is 12.00 51: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 51: 51: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_13_directives-cmap.mdp]: 51: NVE simulation: will use the initial temperature of 300.000 K for 51: determining the Verlet buffer size 51: 51: 51: There were 2 NOTEs 51: Setting the LD random seed to -541330435 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to 1874788318 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: Analysing residue names: 51: There are: 1 Other residues 51: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 51: 51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 51: 51: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 51: 51: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 51: 51: Note that mdrun will redetermine rlist based on the actual pair-list setup 51: 51: This run will generate roughly 0 Mb of data 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/13 (363 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/14 51: Ignoring obsolete mdp entry 'title' 51: Generating 1-4 interactions: fudge = 0.5 51: 51: NOTE 1 [file directives-cmap.top, line 105]: 51: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 51: any other atom in the same moleculetype. Although technically this might 51: not cause issues in a simulation, this often means that the user forgot 51: to add a bond/potential/constraint or put multiple molecules in the same 51: moleculetype definition by mistake. Run with -v to get information for 51: each atom. 51: 51: Number of degrees of freedom in T-Coupling group rest is 12.00 51: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 51: 51: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_14_directives-cmap.mdp]: 51: NVE simulation: will use the initial temperature of 300.000 K for 51: determining the Verlet buffer size 51: 51: 51: There were 2 NOTEs 51: Setting the LD random seed to -268435618 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to -4474883 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: Analysing residue names: 51: There are: 1 Other residues 51: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 51: 51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 51: 51: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 51: 51: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 51: 51: Note that mdrun will redetermine rlist based on the actual pair-list setup 51: 51: This run will generate roughly 0 Mb of data 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/14 (402 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/15 51: Setting the LD random seed to -1715732741 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/15 (350 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/16 51: Setting the LD random seed to -573015075 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to -4194371 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: Analysing residue names: 51: There are: 1 Other residues 51: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 51: 51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 51: 51: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 51: 51: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 51: 51: Note that mdrun will redetermine rlist based on the actual pair-list setup 51: 51: This run will generate roughly 0 Mb of data 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/16 (169 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/17 51: Setting the LD random seed to -939569443 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/17 (214 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/18 51: Ignoring obsolete mdp entry 'title' 51: Generating 1-4 interactions: fudge = 0.5 51: 51: NOTE 1 [file directives-cmap.top, line 105]: 51: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 51: any other atom in the same moleculetype. Although technically this might 51: not cause issues in a simulation, this often means that the user forgot 51: to add a bond/potential/constraint or put multiple molecules in the same 51: moleculetype definition by mistake. Run with -v to get information for 51: each atom. 51: 51: Number of degrees of freedom in T-Coupling group rest is 12.00 51: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 51: 51: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_18_directives-cmap.mdp]: 51: NVE simulation: will use the initial temperature of 300.000 K for 51: determining the Verlet buffer size 51: 51: 51: There were 2 NOTEs 51: Setting the LD random seed to 1878769650 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to 124776446 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: Analysing residue names: 51: There are: 1 Other residues 51: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 51: 51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 51: 51: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 51: 51: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 51: 51: Note that mdrun will redetermine rlist based on the actual pair-list setup 51: 51: This run will generate roughly 0 Mb of data 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/18 (263 ms) 51: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/19 51: Setting the LD random seed to -121897551 51: 51: Generated 3 of the 3 non-bonded parameter combinations 51: 51: Generated 3 of the 3 1-4 parameter combinations 51: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/19 (149 ms) 51: [----------] 20 tests from CMAPDefinesAndErrors/GromppDirectiveTest (6383 ms total) 51: 51: [----------] Global test environment tear-down 51: [==========] 212 tests from 15 test suites ran. (8992 ms total) 51: [ PASSED ] 172 tests. 51: [ SKIPPED ] 40 tests, listed below: 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_2_Pol_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_3_Pol_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_4_Pol_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_Polariz_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Nonpolar_Sol_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb_14 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ__SR_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Buck_ham__SR_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/B_ham 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Disper__corr_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb__SR_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/RF_excl_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul__recip_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_recip_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/DPD 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/D_R_Viol___nm_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ori__R__RMSD 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest__Vi_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/COM_Pull_En_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dens__fitting 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quantum_En_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/NN_Potential 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Potential 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Kinetic_En_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Total_Energy 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Conserved_En_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Temperature 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__Temp_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pres__DC 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pressure 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dH_dl_constr_ 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVremain_dl 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dEkin_dl 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVcoul_dl 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVvdw_dl 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVbonded_dl 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVrestraint_dl 51: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVtemp_dl 51/90 Test #51: GmxPreprocessTests ........................ Passed 9.02 sec test 52 Start 52: Pdb2gmx1Test 52: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/pdb2gmx1-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/Pdb2gmx1Test.xml" 52: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests 52: Test timeout computed to be: 1920 52: [==========] Running 30 tests from 1 test suite. 52: [----------] Global test environment set-up. 52: [----------] 30 tests from Oplsaa/Pdb2gmxTest 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Before cleaning: 653 pairs 52: Before cleaning: 663 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 128 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (128 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 252 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 254, now 254 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 663 dihedrals, 51 impropers, 457 angles 52: 650 pairs, 254 bonds and 0 virtual sites 52: 52: Total mass 1846.112 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 52: 52: The Oplsaa force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (204 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 30 donors and 22 acceptors were found. 52: There are 36 hydrogen bonds 52: Will use HISE for residue 29 52: Will use HISE for residue 32 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS27 HIS29 52: SG90 NE2111 52: HIS29 NE2111 0.987 52: HIS32 NE2135 1.590 1.155 52: Before cleaning: 748 pairs 52: Before cleaning: 778 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 52: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 149 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (149 atoms, 16 residues) 52: 52: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue PHE33 as a ending terminus. 52: Start terminus THR-18: NH3+ 52: End terminus PHE-33: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 281 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 290, now 290 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 778 dihedrals, 72 impropers, 516 angles 52: 736 pairs, 290 bonds and 0 virtual sites 52: 52: Total mass 2088.357 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 52: 52: The Oplsaa force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (332 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 22 acceptors were found. 52: There are 26 hydrogen bonds 52: Will use HISE for residue 45 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS45 52: NE295 52: MET46 SD102 1.078 52: Before cleaning: 676 pairs 52: Before cleaning: 696 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 52: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 132 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (132 atoms, 16 residues) 52: 52: Identified residue ALA34 as a starting terminus. 52: 52: Identified residue ALA49 as a ending terminus. 52: Start terminus ALA-34: NH3+ 52: End terminus ALA-49: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 255 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 261, now 261 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 696 dihedrals, 56 impropers, 472 angles 52: 667 pairs, 261 bonds and 0 virtual sites 52: 52: Total mass 1861.128 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 52: 52: The Oplsaa force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (88 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 21 acceptors were found. 52: There are 30 hydrogen bonds 52: Will use HISE for residue 60 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS60 52: NE285 52: CYS62 SG98 0.803 52: Before cleaning: 603 pairs 52: Before cleaning: 618 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 52: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 117 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (117 atoms, 16 residues) 52: 52: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue LYS50 as a starting terminus. 52: 52: Identified residue PRO65 as a ending terminus. 52: Start terminus LYS-50: NH3+ 52: End terminus PRO-65: PRO-COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 228 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 232, now 232 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 618 dihedrals, 48 impropers, 419 angles 52: 597 pairs, 232 bonds and 0 virtual sites 52: 52: Total mass 1662.883 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 52: 52: The Oplsaa force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (403 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 89 donors and 98 acceptors were found. 52: There are 129 hydrogen bonds 52: Will use HISE for residue 31 52: Will use HISE for residue 51 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS25 HIS31 HIS51 52: SG14 NE264 NE2226 52: HIS31 NE264 1.921 52: HIS51 NE2226 1.498 2.650 52: CYS80 SG477 0.207 1.984 1.570 52: Linking CYS-25 SG-14 and CYS-80 SG-477... 52: Before cleaning: 2499 pairs 52: Before cleaning: 2524 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 52: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 58 488 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 'A' (488 atoms, 58 residues) 52: 52: Identified residue ASN24 as a starting terminus. 52: 52: Identified residue ARG81 as a ending terminus. 52: Start terminus ASN-24: NH3+ 52: End terminus ARG-81: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 58 residues with 936 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 951, now 951 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 2524 dihedrals, 208 impropers, 1704 angles 52: 2469 pairs, 951 bonds and 0 virtual sites 52: 52: Total mass 6908.578 a.m.u. 52: 52: Total charge -6.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 52: 52: The Oplsaa force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (239 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Marked 124 virtual sites 52: Added 16 dummy masses 52: Added 26 new constraints 52: Before cleaning: 653 pairs 52: Before cleaning: 663 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 128 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (128 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 252 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 254, now 254 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 663 dihedrals, 51 impropers, 457 angles 52: 650 pairs, 254 bonds and 130 virtual sites 52: 52: Total mass 1846.112 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 52: 52: The Oplsaa force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (79 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 30 donors and 22 acceptors were found. 52: There are 36 hydrogen bonds 52: Will use HISE for residue 29 52: Will use HISE for residue 32 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS27 HIS29 52: SG90 NE2111 52: HIS29 NE2111 0.987 52: HIS32 NE2135 1.590 1.155 52: Marked 132 virtual sites 52: Added 10 dummy masses 52: Added 19 new constraints 52: Before cleaning: 748 pairs 52: Before cleaning: 778 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 52: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 149 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (149 atoms, 16 residues) 52: 52: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue PHE33 as a ending terminus. 52: Start terminus THR-18: NH3+ 52: End terminus PHE-33: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 281 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 290, now 290 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 778 dihedrals, 72 impropers, 516 angles 52: 736 pairs, 290 bonds and 133 virtual sites 52: 52: Total mass 2088.357 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 52: 52: The Oplsaa force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (184 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 22 acceptors were found. 52: There are 26 hydrogen bonds 52: Will use HISE for residue 45 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS45 52: NE295 52: MET46 SD102 1.078 52: Marked 123 virtual sites 52: Added 22 dummy masses 52: Added 35 new constraints 52: Before cleaning: 676 pairs 52: Before cleaning: 696 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 52: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 132 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (132 atoms, 16 residues) 52: 52: Identified residue ALA34 as a starting terminus. 52: 52: Identified residue ALA49 as a ending terminus. 52: Start terminus ALA-34: NH3+ 52: End terminus ALA-49: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 255 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 261, now 261 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 696 dihedrals, 56 impropers, 472 angles 52: 667 pairs, 261 bonds and 132 virtual sites 52: 52: Total mass 1861.128 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 52: 52: The Oplsaa force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (156 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 21 acceptors were found. 52: There are 30 hydrogen bonds 52: Will use HISE for residue 60 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS60 52: NE285 52: CYS62 SG98 0.803 52: Marked 111 virtual sites 52: Added 18 dummy masses 52: Added 31 new constraints 52: Before cleaning: 603 pairs 52: Before cleaning: 618 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 52: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 117 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (117 atoms, 16 residues) 52: 52: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue LYS50 as a starting terminus. 52: 52: Identified residue PRO65 as a ending terminus. 52: Start terminus LYS-50: NH3+ 52: End terminus PRO-65: PRO-COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 228 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 232, now 232 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 618 dihedrals, 48 impropers, 419 angles 52: 597 pairs, 232 bonds and 116 virtual sites 52: 52: Total mass 1662.883 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 52: 52: The Oplsaa force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (476 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 89 donors and 98 acceptors were found. 52: There are 129 hydrogen bonds 52: Will use HISE for residue 31 52: Will use HISE for residue 51 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS25 HIS31 HIS51 52: SG14 NE264 NE2226 52: HIS31 NE264 1.921 52: HIS51 NE2226 1.498 2.650 52: CYS80 SG477 0.207 1.984 1.570 52: Linking CYS-25 SG-14 and CYS-80 SG-477... 52: Marked 447 virtual sites 52: Added 58 dummy masses 52: Added 101 new constraints 52: Before cleaning: 2499 pairs 52: Before cleaning: 2524 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 52: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 58 488 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 'A' (488 atoms, 58 residues) 52: 52: Identified residue ASN24 as a starting terminus. 52: 52: Identified residue ARG81 as a ending terminus. 52: Start terminus ASN-24: NH3+ 52: End terminus ARG-81: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 58 residues with 936 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 951, now 951 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 2524 dihedrals, 208 impropers, 1704 angles 52: 2469 pairs, 951 bonds and 462 virtual sites 52: 52: Total mass 6908.578 a.m.u. 52: 52: Total charge -6.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 52: 52: The Oplsaa force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (219 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Before cleaning: 653 pairs 52: Before cleaning: 663 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 128 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (128 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 252 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 254, now 254 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 663 dihedrals, 51 impropers, 457 angles 52: 650 pairs, 254 bonds and 0 virtual sites 52: 52: Total mass 1846.112 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 52: 52: The Oplsaa force field and the tip4p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (308 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 30 donors and 22 acceptors were found. 52: There are 36 hydrogen bonds 52: Will use HISE for residue 29 52: Will use HISE for residue 32 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS27 HIS29 52: SG90 NE2111 52: HIS29 NE2111 0.987 52: HIS32 NE2135 1.590 1.155 52: Before cleaning: 748 pairs 52: Before cleaning: 778 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 52: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 149 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (149 atoms, 16 residues) 52: 52: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue PHE33 as a ending terminus. 52: Start terminus THR-18: NH3+ 52: End terminus PHE-33: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 281 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 290, now 290 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 778 dihedrals, 72 impropers, 516 angles 52: 736 pairs, 290 bonds and 0 virtual sites 52: 52: Total mass 2088.357 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 52: 52: The Oplsaa force field and the tip4p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (528 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 22 acceptors were found. 52: There are 26 hydrogen bonds 52: Will use HISE for residue 45 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS45 52: NE295 52: MET46 SD102 1.078 52: Before cleaning: 676 pairs 52: Before cleaning: 696 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 52: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 132 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (132 atoms, 16 residues) 52: 52: Identified residue ALA34 as a starting terminus. 52: 52: Identified residue ALA49 as a ending terminus. 52: Start terminus ALA-34: NH3+ 52: End terminus ALA-49: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 255 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 261, now 261 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 696 dihedrals, 56 impropers, 472 angles 52: 667 pairs, 261 bonds and 0 virtual sites 52: 52: Total mass 1861.128 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 52: 52: The Oplsaa force field and the tip4p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (345 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 21 acceptors were found. 52: There are 30 hydrogen bonds 52: Will use HISE for residue 60 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS60 52: NE285 52: CYS62 SG98 0.803 52: Before cleaning: 603 pairs 52: Before cleaning: 618 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 52: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 117 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (117 atoms, 16 residues) 52: 52: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue LYS50 as a starting terminus. 52: 52: Identified residue PRO65 as a ending terminus. 52: Start terminus LYS-50: NH3+ 52: End terminus PRO-65: PRO-COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 228 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 232, now 232 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 618 dihedrals, 48 impropers, 419 angles 52: 597 pairs, 232 bonds and 0 virtual sites 52: 52: Total mass 1662.883 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 52: 52: The Oplsaa force field and the tip4p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (266 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 89 donors and 98 acceptors were found. 52: There are 129 hydrogen bonds 52: Will use HISE for residue 31 52: Will use HISE for residue 51 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS25 HIS31 HIS51 52: SG14 NE264 NE2226 52: HIS31 NE264 1.921 52: HIS51 NE2226 1.498 2.650 52: CYS80 SG477 0.207 1.984 1.570 52: Linking CYS-25 SG-14 and CYS-80 SG-477... 52: Before cleaning: 2499 pairs 52: Before cleaning: 2524 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 52: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 58 488 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 'A' (488 atoms, 58 residues) 52: 52: Identified residue ASN24 as a starting terminus. 52: 52: Identified residue ARG81 as a ending terminus. 52: Start terminus ASN-24: NH3+ 52: End terminus ARG-81: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 58 residues with 936 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 951, now 951 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 2524 dihedrals, 208 impropers, 1704 angles 52: 2469 pairs, 951 bonds and 0 virtual sites 52: 52: Total mass 6908.578 a.m.u. 52: 52: Total charge -6.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 52: 52: The Oplsaa force field and the tip4p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (152 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Marked 124 virtual sites 52: Added 16 dummy masses 52: Added 26 new constraints 52: Before cleaning: 653 pairs 52: Before cleaning: 663 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 128 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (128 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 252 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 254, now 254 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 663 dihedrals, 51 impropers, 457 angles 52: 650 pairs, 254 bonds and 130 virtual sites 52: 52: Total mass 1846.112 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 52: 52: The Oplsaa force field and the tip4p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (135 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 30 donors and 22 acceptors were found. 52: There are 36 hydrogen bonds 52: Will use HISE for residue 29 52: Will use HISE for residue 32 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS27 HIS29 52: SG90 NE2111 52: HIS29 NE2111 0.987 52: HIS32 NE2135 1.590 1.155 52: Marked 132 virtual sites 52: Added 10 dummy masses 52: Added 19 new constraints 52: Before cleaning: 748 pairs 52: Before cleaning: 778 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 52: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 149 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (149 atoms, 16 residues) 52: 52: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue PHE33 as a ending terminus. 52: Start terminus THR-18: NH3+ 52: End terminus PHE-33: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 281 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 290, now 290 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 778 dihedrals, 72 impropers, 516 angles 52: 736 pairs, 290 bonds and 133 virtual sites 52: 52: Total mass 2088.357 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 52: 52: The Oplsaa force field and the tip4p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (509 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 22 acceptors were found. 52: There are 26 hydrogen bonds 52: Will use HISE for residue 45 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS45 52: NE295 52: MET46 SD102 1.078 52: Marked 123 virtual sites 52: Added 22 dummy masses 52: Added 35 new constraints 52: Before cleaning: 676 pairs 52: Before cleaning: 696 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 52: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 132 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (132 atoms, 16 residues) 52: 52: Identified residue ALA34 as a starting terminus. 52: 52: Identified residue ALA49 as a ending terminus. 52: Start terminus ALA-34: NH3+ 52: End terminus ALA-49: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 255 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 261, now 261 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 696 dihedrals, 56 impropers, 472 angles 52: 667 pairs, 261 bonds and 132 virtual sites 52: 52: Total mass 1861.128 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 52: 52: The Oplsaa force field and the tip4p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (407 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 21 acceptors were found. 52: There are 30 hydrogen bonds 52: Will use HISE for residue 60 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS60 52: NE285 52: CYS62 SG98 0.803 52: Marked 111 virtual sites 52: Added 18 dummy masses 52: Added 31 new constraints 52: Before cleaning: 603 pairs 52: Before cleaning: 618 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 52: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 117 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (117 atoms, 16 residues) 52: 52: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue LYS50 as a starting terminus. 52: 52: Identified residue PRO65 as a ending terminus. 52: Start terminus LYS-50: NH3+ 52: End terminus PRO-65: PRO-COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 228 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 232, now 232 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 618 dihedrals, 48 impropers, 419 angles 52: 597 pairs, 232 bonds and 116 virtual sites 52: 52: Total mass 1662.883 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 52: 52: The Oplsaa force field and the tip4p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (233 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 89 donors and 98 acceptors were found. 52: There are 129 hydrogen bonds 52: Will use HISE for residue 31 52: Will use HISE for residue 51 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS25 HIS31 HIS51 52: SG14 NE264 NE2226 52: HIS31 NE264 1.921 52: HIS51 NE2226 1.498 2.650 52: CYS80 SG477 0.207 1.984 1.570 52: Linking CYS-25 SG-14 and CYS-80 SG-477... 52: Marked 447 virtual sites 52: Added 58 dummy masses 52: Added 101 new constraints 52: Before cleaning: 2499 pairs 52: Before cleaning: 2524 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 52: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 58 488 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 'A' (488 atoms, 58 residues) 52: 52: Identified residue ASN24 as a starting terminus. 52: 52: Identified residue ARG81 as a ending terminus. 52: Start terminus ASN-24: NH3+ 52: End terminus ARG-81: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 58 residues with 936 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 951, now 951 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 2524 dihedrals, 208 impropers, 1704 angles 52: 2469 pairs, 951 bonds and 462 virtual sites 52: 52: Total mass 6908.578 a.m.u. 52: 52: Total charge -6.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 52: 52: The Oplsaa force field and the tip4p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (673 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Before cleaning: 653 pairs 52: Before cleaning: 663 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 128 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (128 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 252 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 254, now 254 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 663 dihedrals, 51 impropers, 457 angles 52: 650 pairs, 254 bonds and 0 virtual sites 52: 52: Total mass 1846.112 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 52: 52: The Oplsaa force field and the tip5p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (441 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 30 donors and 22 acceptors were found. 52: There are 36 hydrogen bonds 52: Will use HISE for residue 29 52: Will use HISE for residue 32 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS27 HIS29 52: SG90 NE2111 52: HIS29 NE2111 0.987 52: HIS32 NE2135 1.590 1.155 52: Before cleaning: 748 pairs 52: Before cleaning: 778 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 52: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 149 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (149 atoms, 16 residues) 52: 52: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue PHE33 as a ending terminus. 52: Start terminus THR-18: NH3+ 52: End terminus PHE-33: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 281 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 290, now 290 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 778 dihedrals, 72 impropers, 516 angles 52: 736 pairs, 290 bonds and 0 virtual sites 52: 52: Total mass 2088.357 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 52: 52: The Oplsaa force field and the tip5p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (172 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 22 acceptors were found. 52: There are 26 hydrogen bonds 52: Will use HISE for residue 45 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS45 52: NE295 52: MET46 SD102 1.078 52: Before cleaning: 676 pairs 52: Before cleaning: 696 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 52: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 132 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (132 atoms, 16 residues) 52: 52: Identified residue ALA34 as a starting terminus. 52: 52: Identified residue ALA49 as a ending terminus. 52: Start terminus ALA-34: NH3+ 52: End terminus ALA-49: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 255 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 261, now 261 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 696 dihedrals, 56 impropers, 472 angles 52: 667 pairs, 261 bonds and 0 virtual sites 52: 52: Total mass 1861.128 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 52: 52: The Oplsaa force field and the tip5p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (239 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 21 acceptors were found. 52: There are 30 hydrogen bonds 52: Will use HISE for residue 60 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS60 52: NE285 52: CYS62 SG98 0.803 52: Before cleaning: 603 pairs 52: Before cleaning: 618 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 52: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 117 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (117 atoms, 16 residues) 52: 52: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue LYS50 as a starting terminus. 52: 52: Identified residue PRO65 as a ending terminus. 52: Start terminus LYS-50: NH3+ 52: End terminus PRO-65: PRO-COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 228 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 232, now 232 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 618 dihedrals, 48 impropers, 419 angles 52: 597 pairs, 232 bonds and 0 virtual sites 52: 52: Total mass 1662.883 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 52: 52: The Oplsaa force field and the tip5p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (554 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 89 donors and 98 acceptors were found. 52: There are 129 hydrogen bonds 52: Will use HISE for residue 31 52: Will use HISE for residue 51 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS25 HIS31 HIS51 52: SG14 NE264 NE2226 52: HIS31 NE264 1.921 52: HIS51 NE2226 1.498 2.650 52: CYS80 SG477 0.207 1.984 1.570 52: Linking CYS-25 SG-14 and CYS-80 SG-477... 52: Before cleaning: 2499 pairs 52: Before cleaning: 2524 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 52: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 58 488 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 'A' (488 atoms, 58 residues) 52: 52: Identified residue ASN24 as a starting terminus. 52: 52: Identified residue ARG81 as a ending terminus. 52: Start terminus ASN-24: NH3+ 52: End terminus ARG-81: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 58 residues with 936 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 951, now 951 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 2524 dihedrals, 208 impropers, 1704 angles 52: 2469 pairs, 951 bonds and 0 virtual sites 52: 52: Total mass 6908.578 a.m.u. 52: 52: Total charge -6.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 52: 52: The Oplsaa force field and the tip5p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (134 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Marked 124 virtual sites 52: Added 16 dummy masses 52: Added 26 new constraints 52: Before cleaning: 653 pairs 52: Before cleaning: 663 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 128 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (128 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 252 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 254, now 254 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 663 dihedrals, 51 impropers, 457 angles 52: 650 pairs, 254 bonds and 130 virtual sites 52: 52: Total mass 1846.112 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 52: 52: The Oplsaa force field and the tip5p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (232 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 30 donors and 22 acceptors were found. 52: There are 36 hydrogen bonds 52: Will use HISE for residue 29 52: Will use HISE for residue 32 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS27 HIS29 52: SG90 NE2111 52: HIS29 NE2111 0.987 52: HIS32 NE2135 1.590 1.155 52: Marked 132 virtual sites 52: Added 10 dummy masses 52: Added 19 new constraints 52: Before cleaning: 748 pairs 52: Before cleaning: 778 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 52: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 149 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (149 atoms, 16 residues) 52: 52: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue PHE33 as a ending terminus. 52: Start terminus THR-18: NH3+ 52: End terminus PHE-33: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 281 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 290, now 290 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 778 dihedrals, 72 impropers, 516 angles 52: 736 pairs, 290 bonds and 133 virtual sites 52: 52: Total mass 2088.357 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 52: 52: The Oplsaa force field and the tip5p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (323 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 22 acceptors were found. 52: There are 26 hydrogen bonds 52: Will use HISE for residue 45 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS45 52: NE295 52: MET46 SD102 1.078 52: Marked 123 virtual sites 52: Added 22 dummy masses 52: Added 35 new constraints 52: Before cleaning: 676 pairs 52: Before cleaning: 696 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 52: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 132 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (132 atoms, 16 residues) 52: 52: Identified residue ALA34 as a starting terminus. 52: 52: Identified residue ALA49 as a ending terminus. 52: Start terminus ALA-34: NH3+ 52: End terminus ALA-49: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 255 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 261, now 261 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 696 dihedrals, 56 impropers, 472 angles 52: 667 pairs, 261 bonds and 132 virtual sites 52: 52: Total mass 1861.128 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 52: 52: The Oplsaa force field and the tip5p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (146 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 21 acceptors were found. 52: There are 30 hydrogen bonds 52: Will use HISE for residue 60 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS60 52: NE285 52: CYS62 SG98 0.803 52: Marked 111 virtual sites 52: Added 18 dummy masses 52: Added 31 new constraints 52: Before cleaning: 603 pairs 52: Before cleaning: 618 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 52: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 117 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (117 atoms, 16 residues) 52: 52: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue LYS50 as a starting terminus. 52: 52: Identified residue PRO65 as a ending terminus. 52: Start terminus LYS-50: NH3+ 52: End terminus PRO-65: PRO-COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 228 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 232, now 232 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 618 dihedrals, 48 impropers, 419 angles 52: 597 pairs, 232 bonds and 116 virtual sites 52: 52: Total mass 1662.883 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 52: 52: The Oplsaa force field and the tip5p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (58 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 89 donors and 98 acceptors were found. 52: There are 129 hydrogen bonds 52: Will use HISE for residue 31 52: Will use HISE for residue 51 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS25 HIS31 HIS51 52: SG14 NE264 NE2226 52: HIS31 NE264 1.921 52: HIS51 NE2226 1.498 2.650 52: CYS80 SG477 0.207 1.984 1.570 52: Linking CYS-25 SG-14 and CYS-80 SG-477... 52: Marked 447 virtual sites 52: Added 58 dummy masses 52: Added 101 new constraints 52: Before cleaning: 2499 pairs 52: Before cleaning: 2524 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 52: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 58 488 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 'A' (488 atoms, 58 residues) 52: 52: Identified residue ASN24 as a starting terminus. 52: 52: Identified residue ARG81 as a ending terminus. 52: Start terminus ASN-24: NH3+ 52: End terminus ARG-81: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 58 residues with 936 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 951, now 951 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 2524 dihedrals, 208 impropers, 1704 angles 52: 2469 pairs, 951 bonds and 462 virtual sites 52: 52: Total mass 6908.578 a.m.u. 52: 52: Total charge -6.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 52: 52: The Oplsaa force field and the tip5p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (269 ms) 52: [----------] 30 tests from Oplsaa/Pdb2gmxTest (8525 ms total) 52: 52: [----------] Global test environment tear-down 52: [==========] 30 tests from 1 test suite ran. (8525 ms total) 52: [ PASSED ] 30 tests. 52/90 Test #52: Pdb2gmx1Test .............................. Passed 8.55 sec test 53 Start 53: Pdb2gmx2Test 53: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/pdb2gmx2-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/Pdb2gmx2Test.xml" 53: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests 53: Test timeout computed to be: 1920 53: [==========] Running 40 tests from 2 test suites. 53: [----------] Global test environment set-up. 53: [----------] 20 tests from G43a1/Pdb2gmxTest 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 25 donors and 23 acceptors were found. 53: There are 41 hydrogen bonds 53: Will use HISE for residue 8 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS3 HIS8 53: SG9 NE251 53: HIS8 NE251 1.055 53: MET12 SD83 0.763 0.990 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 267 pairs 53: Before cleaning: 305 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 53: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 128 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (128 atoms, 16 residues) 53: 53: Identified residue ALA2 as a starting terminus. 53: 53: Identified residue SER17 as a ending terminus. 53: Start terminus ALA-2: NH3+ 53: End terminus SER-17: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 165 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 172, now 167 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 90 dihedrals, 77 impropers, 241 angles 53: 267 pairs, 167 bonds and 0 virtual sites 53: 53: Total mass 1846.116 a.m.u. 53: 53: Total charge 0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 53: 53: The Gromos43a1 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (194 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 30 donors and 22 acceptors were found. 53: There are 36 hydrogen bonds 53: Will use HISE for residue 29 53: Will use HISE for residue 32 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS27 HIS29 53: SG90 NE2111 53: HIS29 NE2111 0.987 53: HIS32 NE2135 1.590 1.155 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 273 pairs 53: Before cleaning: 429 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 53: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 149 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (149 atoms, 16 residues) 53: 53: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue THR18 as a starting terminus. 53: 53: Identified residue PHE33 as a ending terminus. 53: Start terminus THR-18: NH3+ 53: End terminus PHE-33: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 202 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 216, now 211 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 93 dihedrals, 134 impropers, 316 angles 53: 273 pairs, 211 bonds and 0 virtual sites 53: 53: Total mass 2088.361 a.m.u. 53: 53: Total charge 1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 53: 53: The Gromos43a1 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (281 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 22 acceptors were found. 53: There are 26 hydrogen bonds 53: Will use HISE for residue 45 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS45 53: NE295 53: MET46 SD102 1.078 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 242 pairs 53: Before cleaning: 349 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 53: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 132 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (132 atoms, 16 residues) 53: 53: Identified residue ALA34 as a starting terminus. 53: 53: Identified residue ALA49 as a ending terminus. 53: Start terminus ALA-34: NH3+ 53: End terminus ALA-49: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 168 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 179, now 174 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 81 dihedrals, 102 impropers, 260 angles 53: 242 pairs, 174 bonds and 0 virtual sites 53: 53: Total mass 1861.132 a.m.u. 53: 53: Total charge -1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 53: 53: The Gromos43a1 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (266 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 21 acceptors were found. 53: There are 30 hydrogen bonds 53: Will use HISE for residue 60 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS60 53: NE285 53: CYS62 SG98 0.803 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 232 pairs 53: Before cleaning: 299 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 53: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 117 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (117 atoms, 16 residues) 53: 53: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue LYS50 as a starting terminus. 53: 53: Identified residue PRO65 as a ending terminus. 53: Start terminus LYS-50: NH3+ 53: End terminus PRO-65: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 150 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 159, now 154 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 78 dihedrals, 80 impropers, 227 angles 53: 232 pairs, 154 bonds and 0 virtual sites 53: 53: Total mass 1662.887 a.m.u. 53: 53: Total charge 0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 53: 53: The Gromos43a1 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (477 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 89 donors and 98 acceptors were found. 53: There are 129 hydrogen bonds 53: Will use HISE for residue 31 53: Will use HISE for residue 51 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS25 HIS31 HIS51 53: SG14 NE264 NE2226 53: HIS31 NE264 1.921 53: HIS51 NE2226 1.498 2.650 53: CYS80 SG477 0.207 1.984 1.570 53: Linking CYS-25 SG-14 and CYS-80 SG-477... 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 972 pairs 53: Before cleaning: 1256 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 53: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 53: 53: chain #res #atoms 53: 53: 1 'A' 58 488 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 'A' (488 atoms, 58 residues) 53: 53: Identified residue ASN24 as a starting terminus. 53: 53: Identified residue ARG81 as a ending terminus. 53: Start terminus ASN-24: NH3+ 53: End terminus ARG-81: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 58 residues with 635 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 655, now 650 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 321 dihedrals, 350 impropers, 955 angles 53: 972 pairs, 650 bonds and 0 virtual sites 53: 53: Total mass 6908.582 a.m.u. 53: 53: Total charge -6.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 53: 53: The Gromos43a1 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (1033 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 25 donors and 23 acceptors were found. 53: There are 41 hydrogen bonds 53: Will use HISE for residue 8 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS3 HIS8 53: SG9 NE251 53: HIS8 NE251 1.055 53: MET12 SD83 0.763 0.990 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 37 virtual sites 53: Added 4 dummy masses 53: Added 8 new constraints 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 267 pairs 53: Before cleaning: 305 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 53: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 128 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (128 atoms, 16 residues) 53: 53: Identified residue ALA2 as a starting terminus. 53: 53: Identified residue SER17 as a ending terminus. 53: Start terminus ALA-2: NH3+ 53: End terminus SER-17: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 165 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 172, now 167 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 90 dihedrals, 77 impropers, 241 angles 53: 267 pairs, 167 bonds and 37 virtual sites 53: 53: Total mass 1846.116 a.m.u. 53: 53: Total charge 0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 53: 53: The Gromos43a1 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (175 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 30 donors and 22 acceptors were found. 53: There are 36 hydrogen bonds 53: Will use HISE for residue 29 53: Will use HISE for residue 32 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS27 HIS29 53: SG90 NE2111 53: HIS29 NE2111 0.987 53: HIS32 NE2135 1.590 1.155 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 53 virtual sites 53: Added 4 dummy masses 53: Added 10 new constraints 53: 53: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 273 pairs 53: Before cleaning: 429 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 53: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 149 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (149 atoms, 16 residues) 53: 53: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue THR18 as a starting terminus. 53: 53: Identified residue PHE33 as a ending terminus. 53: Start terminus THR-18: NH3+ 53: End terminus PHE-33: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 202 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 216, now 211 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 93 dihedrals, 134 impropers, 316 angles 53: 273 pairs, 211 bonds and 51 virtual sites 53: 53: Total mass 2088.361 a.m.u. 53: 53: Total charge 1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 53: 53: The Gromos43a1 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (478 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 22 acceptors were found. 53: There are 26 hydrogen bonds 53: Will use HISE for residue 45 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS45 53: NE295 53: MET46 SD102 1.078 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 36 virtual sites 53: Added 4 dummy masses 53: Added 8 new constraints 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 242 pairs 53: Before cleaning: 349 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 53: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 132 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (132 atoms, 16 residues) 53: 53: Identified residue ALA34 as a starting terminus. 53: 53: Identified residue ALA49 as a ending terminus. 53: Start terminus ALA-34: NH3+ 53: End terminus ALA-49: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 168 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 179, now 174 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 81 dihedrals, 102 impropers, 260 angles 53: 242 pairs, 174 bonds and 36 virtual sites 53: 53: Total mass 1861.132 a.m.u. 53: 53: Total charge -1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 53: 53: The Gromos43a1 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (144 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 21 acceptors were found. 53: There are 30 hydrogen bonds 53: Will use HISE for residue 60 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS60 53: NE285 53: CYS62 SG98 0.803 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 33 virtual sites 53: Added 4 dummy masses 53: Added 10 new constraints 53: 53: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 232 pairs 53: Before cleaning: 299 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 53: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 117 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (117 atoms, 16 residues) 53: 53: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue LYS50 as a starting terminus. 53: 53: Identified residue PRO65 as a ending terminus. 53: Start terminus LYS-50: NH3+ 53: End terminus PRO-65: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 150 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 159, now 154 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 78 dihedrals, 80 impropers, 227 angles 53: 232 pairs, 154 bonds and 31 virtual sites 53: 53: Total mass 1662.887 a.m.u. 53: 53: Total charge 0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 53: 53: The Gromos43a1 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (247 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 89 donors and 98 acceptors were found. 53: There are 129 hydrogen bonds 53: Will use HISE for residue 31 53: Will use HISE for residue 51 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS25 HIS31 HIS51 53: SG14 NE264 NE2226 53: HIS31 NE264 1.921 53: HIS51 NE2226 1.498 2.650 53: CYS80 SG477 0.207 1.984 1.570 53: Linking CYS-25 SG-14 and CYS-80 SG-477... 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 146 virtual sites 53: Added 10 dummy masses 53: Added 29 new constraints 53: 53: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 972 pairs 53: Before cleaning: 1256 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 53: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 53: 53: chain #res #atoms 53: 53: 1 'A' 58 488 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 'A' (488 atoms, 58 residues) 53: 53: Identified residue ASN24 as a starting terminus. 53: 53: Identified residue ARG81 as a ending terminus. 53: Start terminus ASN-24: NH3+ 53: End terminus ARG-81: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 58 residues with 635 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 655, now 650 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 321 dihedrals, 350 impropers, 955 angles 53: 972 pairs, 650 bonds and 137 virtual sites 53: 53: Total mass 6908.582 a.m.u. 53: 53: Total charge -6.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 53: 53: The Gromos43a1 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (206 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 25 donors and 23 acceptors were found. 53: There are 41 hydrogen bonds 53: Will use HISE for residue 8 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS3 HIS8 53: SG9 NE251 53: HIS8 NE251 1.055 53: MET12 SD83 0.763 0.990 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 267 pairs 53: Before cleaning: 305 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 53: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 128 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (128 atoms, 16 residues) 53: 53: Identified residue ALA2 as a starting terminus. 53: 53: Identified residue SER17 as a ending terminus. 53: Start terminus ALA-2: NH3+ 53: End terminus SER-17: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 165 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 172, now 167 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 90 dihedrals, 77 impropers, 241 angles 53: 267 pairs, 167 bonds and 0 virtual sites 53: 53: Total mass 1846.116 a.m.u. 53: 53: Total charge 0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 53: 53: The Gromos43a1 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (228 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 30 donors and 22 acceptors were found. 53: There are 36 hydrogen bonds 53: Will use HISE for residue 29 53: Will use HISE for residue 32 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS27 HIS29 53: SG90 NE2111 53: HIS29 NE2111 0.987 53: HIS32 NE2135 1.590 1.155 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 273 pairs 53: Before cleaning: 429 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 53: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 149 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (149 atoms, 16 residues) 53: 53: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue THR18 as a starting terminus. 53: 53: Identified residue PHE33 as a ending terminus. 53: Start terminus THR-18: NH3+ 53: End terminus PHE-33: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 202 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 216, now 211 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 93 dihedrals, 134 impropers, 316 angles 53: 273 pairs, 211 bonds and 0 virtual sites 53: 53: Total mass 2088.361 a.m.u. 53: 53: Total charge 1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 53: 53: The Gromos43a1 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (491 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 22 acceptors were found. 53: There are 26 hydrogen bonds 53: Will use HISE for residue 45 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS45 53: NE295 53: MET46 SD102 1.078 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 242 pairs 53: Before cleaning: 349 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 53: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 132 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (132 atoms, 16 residues) 53: 53: Identified residue ALA34 as a starting terminus. 53: 53: Identified residue ALA49 as a ending terminus. 53: Start terminus ALA-34: NH3+ 53: End terminus ALA-49: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 168 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 179, now 174 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 81 dihedrals, 102 impropers, 260 angles 53: 242 pairs, 174 bonds and 0 virtual sites 53: 53: Total mass 1861.132 a.m.u. 53: 53: Total charge -1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 53: 53: The Gromos43a1 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (145 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 21 acceptors were found. 53: There are 30 hydrogen bonds 53: Will use HISE for residue 60 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS60 53: NE285 53: CYS62 SG98 0.803 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 232 pairs 53: Before cleaning: 299 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 53: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 117 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (117 atoms, 16 residues) 53: 53: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue LYS50 as a starting terminus. 53: 53: Identified residue PRO65 as a ending terminus. 53: Start terminus LYS-50: NH3+ 53: End terminus PRO-65: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 150 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 159, now 154 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 78 dihedrals, 80 impropers, 227 angles 53: 232 pairs, 154 bonds and 0 virtual sites 53: 53: Total mass 1662.887 a.m.u. 53: 53: Total charge 0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 53: 53: The Gromos43a1 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (100 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 89 donors and 98 acceptors were found. 53: There are 129 hydrogen bonds 53: Will use HISE for residue 31 53: Will use HISE for residue 51 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS25 HIS31 HIS51 53: SG14 NE264 NE2226 53: HIS31 NE264 1.921 53: HIS51 NE2226 1.498 2.650 53: CYS80 SG477 0.207 1.984 1.570 53: Linking CYS-25 SG-14 and CYS-80 SG-477... 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 972 pairs 53: Before cleaning: 1256 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 53: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 53: 53: chain #res #atoms 53: 53: 1 'A' 58 488 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 'A' (488 atoms, 58 residues) 53: 53: Identified residue ASN24 as a starting terminus. 53: 53: Identified residue ARG81 as a ending terminus. 53: Start terminus ASN-24: NH3+ 53: End terminus ARG-81: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 58 residues with 635 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 655, now 650 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 321 dihedrals, 350 impropers, 955 angles 53: 972 pairs, 650 bonds and 0 virtual sites 53: 53: Total mass 6908.582 a.m.u. 53: 53: Total charge -6.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 53: 53: The Gromos43a1 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (498 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 25 donors and 23 acceptors were found. 53: There are 41 hydrogen bonds 53: Will use HISE for residue 8 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS3 HIS8 53: SG9 NE251 53: HIS8 NE251 1.055 53: MET12 SD83 0.763 0.990 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 37 virtual sites 53: Added 4 dummy masses 53: Added 8 new constraints 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 267 pairs 53: Before cleaning: 305 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 53: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 128 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (128 atoms, 16 residues) 53: 53: Identified residue ALA2 as a starting terminus. 53: 53: Identified residue SER17 as a ending terminus. 53: Start terminus ALA-2: NH3+ 53: End terminus SER-17: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 165 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 172, now 167 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 90 dihedrals, 77 impropers, 241 angles 53: 267 pairs, 167 bonds and 37 virtual sites 53: 53: Total mass 1846.116 a.m.u. 53: 53: Total charge 0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 53: 53: The Gromos43a1 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (266 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 30 donors and 22 acceptors were found. 53: There are 36 hydrogen bonds 53: Will use HISE for residue 29 53: Will use HISE for residue 32 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS27 HIS29 53: SG90 NE2111 53: HIS29 NE2111 0.987 53: HIS32 NE2135 1.590 1.155 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 53 virtual sites 53: Added 4 dummy masses 53: Added 10 new constraints 53: 53: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 273 pairs 53: Before cleaning: 429 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 53: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 149 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (149 atoms, 16 residues) 53: 53: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue THR18 as a starting terminus. 53: 53: Identified residue PHE33 as a ending terminus. 53: Start terminus THR-18: NH3+ 53: End terminus PHE-33: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 202 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 216, now 211 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 93 dihedrals, 134 impropers, 316 angles 53: 273 pairs, 211 bonds and 51 virtual sites 53: 53: Total mass 2088.361 a.m.u. 53: 53: Total charge 1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 53: 53: The Gromos43a1 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (248 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 22 acceptors were found. 53: There are 26 hydrogen bonds 53: Will use HISE for residue 45 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS45 53: NE295 53: MET46 SD102 1.078 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 36 virtual sites 53: Added 4 dummy masses 53: Added 8 new constraints 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 242 pairs 53: Before cleaning: 349 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 53: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 132 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (132 atoms, 16 residues) 53: 53: Identified residue ALA34 as a starting terminus. 53: 53: Identified residue ALA49 as a ending terminus. 53: Start terminus ALA-34: NH3+ 53: End terminus ALA-49: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 168 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 179, now 174 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 81 dihedrals, 102 impropers, 260 angles 53: 242 pairs, 174 bonds and 36 virtual sites 53: 53: Total mass 1861.132 a.m.u. 53: 53: Total charge -1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 53: 53: The Gromos43a1 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (238 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 21 acceptors were found. 53: There are 30 hydrogen bonds 53: Will use HISE for residue 60 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS60 53: NE285 53: CYS62 SG98 0.803 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 33 virtual sites 53: Added 4 dummy masses 53: Added 10 new constraints 53: 53: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 232 pairs 53: Before cleaning: 299 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 53: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 117 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (117 atoms, 16 residues) 53: 53: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue LYS50 as a starting terminus. 53: 53: Identified residue PRO65 as a ending terminus. 53: Start terminus LYS-50: NH3+ 53: End terminus PRO-65: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 150 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 159, now 154 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 78 dihedrals, 80 impropers, 227 angles 53: 232 pairs, 154 bonds and 31 virtual sites 53: 53: Total mass 1662.887 a.m.u. 53: 53: Total charge 0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 53: 53: The Gromos43a1 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (428 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 89 donors and 98 acceptors were found. 53: There are 129 hydrogen bonds 53: Will use HISE for residue 31 53: Will use HISE for residue 51 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS25 HIS31 HIS51 53: SG14 NE264 NE2226 53: HIS31 NE264 1.921 53: HIS51 NE2226 1.498 2.650 53: CYS80 SG477 0.207 1.984 1.570 53: Linking CYS-25 SG-14 and CYS-80 SG-477... 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 146 virtual sites 53: Added 10 dummy masses 53: Added 29 new constraints 53: 53: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 972 pairs 53: Before cleaning: 1256 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 53: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 53: 53: chain #res #atoms 53: 53: 1 'A' 58 488 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 'A' (488 atoms, 58 residues) 53: 53: Identified residue ASN24 as a starting terminus. 53: 53: Identified residue ARG81 as a ending terminus. 53: Start terminus ASN-24: NH3+ 53: End terminus ARG-81: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 58 residues with 635 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 655, now 650 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 321 dihedrals, 350 impropers, 955 angles 53: 972 pairs, 650 bonds and 137 virtual sites 53: 53: Total mass 6908.582 a.m.u. 53: 53: Total charge -6.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 53: 53: The Gromos43a1 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (167 ms) 53: [----------] 20 tests from G43a1/Pdb2gmxTest (6328 ms total) 53: 53: [----------] 20 tests from G53a6/Pdb2gmxTest 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 25 donors and 23 acceptors were found. 53: There are 41 hydrogen bonds 53: Will use HISE for residue 8 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS3 HIS8 53: SG9 NE251 53: HIS8 NE251 1.055 53: MET12 SD83 0.763 0.990 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 267 pairs 53: Before cleaning: 312 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 53: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 128 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (128 atoms, 16 residues) 53: 53: Identified residue ALA2 as a starting terminus. 53: 53: Identified residue SER17 as a ending terminus. 53: Start terminus ALA-2: NH3+ 53: End terminus SER-17: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 167 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 174, now 169 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 90 dihedrals, 79 impropers, 245 angles 53: 267 pairs, 169 bonds and 0 virtual sites 53: 53: Total mass 1846.116 a.m.u. 53: 53: Total charge 0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 53: 53: The Gromos53a6 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (232 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 30 donors and 22 acceptors were found. 53: There are 36 hydrogen bonds 53: Will use HISE for residue 29 53: Will use HISE for residue 32 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS27 HIS29 53: SG90 NE2111 53: HIS29 NE2111 0.987 53: HIS32 NE2135 1.590 1.155 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 273 pairs 53: Before cleaning: 443 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 53: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 149 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (149 atoms, 16 residues) 53: 53: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue THR18 as a starting terminus. 53: 53: Identified residue PHE33 as a ending terminus. 53: Start terminus THR-18: NH3+ 53: End terminus PHE-33: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 206 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 220, now 215 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 93 dihedrals, 138 impropers, 324 angles 53: 273 pairs, 215 bonds and 0 virtual sites 53: 53: Total mass 2088.361 a.m.u. 53: 53: Total charge 1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 53: 53: The Gromos53a6 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (65 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 22 acceptors were found. 53: There are 26 hydrogen bonds 53: Will use HISE for residue 45 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS45 53: NE295 53: MET46 SD102 1.078 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 242 pairs 53: Before cleaning: 356 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 53: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 132 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (132 atoms, 16 residues) 53: 53: Identified residue ALA34 as a starting terminus. 53: 53: Identified residue ALA49 as a ending terminus. 53: Start terminus ALA-34: NH3+ 53: End terminus ALA-49: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 170 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 181, now 176 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 81 dihedrals, 104 impropers, 264 angles 53: 242 pairs, 176 bonds and 0 virtual sites 53: 53: Total mass 1861.132 a.m.u. 53: 53: Total charge -1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 53: 53: The Gromos53a6 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (86 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 21 acceptors were found. 53: There are 30 hydrogen bonds 53: Will use HISE for residue 60 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS60 53: NE285 53: CYS62 SG98 0.803 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 232 pairs 53: Before cleaning: 306 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 53: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 117 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (117 atoms, 16 residues) 53: 53: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue LYS50 as a starting terminus. 53: 53: Identified residue PRO65 as a ending terminus. 53: Start terminus LYS-50: NH3+ 53: End terminus PRO-65: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 152 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 161, now 156 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 78 dihedrals, 82 impropers, 231 angles 53: 232 pairs, 156 bonds and 0 virtual sites 53: 53: Total mass 1662.887 a.m.u. 53: 53: Total charge -0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 53: 53: The Gromos53a6 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (110 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 89 donors and 98 acceptors were found. 53: There are 129 hydrogen bonds 53: Will use HISE for residue 31 53: Will use HISE for residue 51 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS25 HIS31 HIS51 53: SG14 NE264 NE2226 53: HIS31 NE264 1.921 53: HIS51 NE2226 1.498 2.650 53: CYS80 SG477 0.207 1.984 1.570 53: Linking CYS-25 SG-14 and CYS-80 SG-477... 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 972 pairs 53: Before cleaning: 1270 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 53: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 53: 53: chain #res #atoms 53: 53: 1 'A' 58 488 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 'A' (488 atoms, 58 residues) 53: 53: Identified residue ASN24 as a starting terminus. 53: 53: Identified residue ARG81 as a ending terminus. 53: Start terminus ASN-24: NH3+ 53: End terminus ARG-81: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 58 residues with 639 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 659, now 654 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 321 dihedrals, 354 impropers, 963 angles 53: 972 pairs, 654 bonds and 0 virtual sites 53: 53: Total mass 6908.582 a.m.u. 53: 53: Total charge -6.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 53: 53: The Gromos53a6 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (106 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 25 donors and 23 acceptors were found. 53: There are 41 hydrogen bonds 53: Will use HISE for residue 8 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS3 HIS8 53: SG9 NE251 53: HIS8 NE251 1.055 53: MET12 SD83 0.763 0.990 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 39 virtual sites 53: Added 4 dummy masses 53: Added 8 new constraints 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 267 pairs 53: Before cleaning: 312 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 53: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 128 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (128 atoms, 16 residues) 53: 53: Identified residue ALA2 as a starting terminus. 53: 53: Identified residue SER17 as a ending terminus. 53: Start terminus ALA-2: NH3+ 53: End terminus SER-17: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 167 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 174, now 169 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 90 dihedrals, 79 impropers, 245 angles 53: 267 pairs, 169 bonds and 39 virtual sites 53: 53: Total mass 1846.116 a.m.u. 53: 53: Total charge 0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 53: 53: The Gromos53a6 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (62 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 30 donors and 22 acceptors were found. 53: There are 36 hydrogen bonds 53: Will use HISE for residue 29 53: Will use HISE for residue 32 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS27 HIS29 53: SG90 NE2111 53: HIS29 NE2111 0.987 53: HIS32 NE2135 1.590 1.155 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 57 virtual sites 53: Added 4 dummy masses 53: Added 10 new constraints 53: 53: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 273 pairs 53: Before cleaning: 443 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 53: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 149 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (149 atoms, 16 residues) 53: 53: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue THR18 as a starting terminus. 53: 53: Identified residue PHE33 as a ending terminus. 53: Start terminus THR-18: NH3+ 53: End terminus PHE-33: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 206 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 220, now 215 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 93 dihedrals, 138 impropers, 324 angles 53: 273 pairs, 215 bonds and 55 virtual sites 53: 53: Total mass 2088.361 a.m.u. 53: 53: Total charge 1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 53: 53: The Gromos53a6 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (63 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 22 acceptors were found. 53: There are 26 hydrogen bonds 53: Will use HISE for residue 45 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS45 53: NE295 53: MET46 SD102 1.078 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 38 virtual sites 53: Added 4 dummy masses 53: Added 8 new constraints 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 242 pairs 53: Before cleaning: 356 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 53: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 132 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (132 atoms, 16 residues) 53: 53: Identified residue ALA34 as a starting terminus. 53: 53: Identified residue ALA49 as a ending terminus. 53: Start terminus ALA-34: NH3+ 53: End terminus ALA-49: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 170 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 181, now 176 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 81 dihedrals, 104 impropers, 264 angles 53: 242 pairs, 176 bonds and 38 virtual sites 53: 53: Total mass 1861.132 a.m.u. 53: 53: Total charge -1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 53: 53: The Gromos53a6 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (118 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 21 acceptors were found. 53: There are 30 hydrogen bonds 53: Will use HISE for residue 60 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS60 53: NE285 53: CYS62 SG98 0.803 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 35 virtual sites 53: Added 4 dummy masses 53: Added 10 new constraints 53: 53: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 232 pairs 53: Before cleaning: 306 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 53: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 117 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (117 atoms, 16 residues) 53: 53: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue LYS50 as a starting terminus. 53: 53: Identified residue PRO65 as a ending terminus. 53: Start terminus LYS-50: NH3+ 53: End terminus PRO-65: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 152 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 161, now 156 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 78 dihedrals, 82 impropers, 231 angles 53: 232 pairs, 156 bonds and 33 virtual sites 53: 53: Total mass 1662.887 a.m.u. 53: 53: Total charge -0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 53: 53: The Gromos53a6 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (185 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 89 donors and 98 acceptors were found. 53: There are 129 hydrogen bonds 53: Will use HISE for residue 31 53: Will use HISE for residue 51 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS25 HIS31 HIS51 53: SG14 NE264 NE2226 53: HIS31 NE264 1.921 53: HIS51 NE2226 1.498 2.650 53: CYS80 SG477 0.207 1.984 1.570 53: Linking CYS-25 SG-14 and CYS-80 SG-477... 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 150 virtual sites 53: Added 10 dummy masses 53: Added 29 new constraints 53: 53: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 972 pairs 53: Before cleaning: 1270 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 53: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 53: 53: chain #res #atoms 53: 53: 1 'A' 58 488 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 'A' (488 atoms, 58 residues) 53: 53: Identified residue ASN24 as a starting terminus. 53: 53: Identified residue ARG81 as a ending terminus. 53: Start terminus ASN-24: NH3+ 53: End terminus ARG-81: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 58 residues with 639 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 659, now 654 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 321 dihedrals, 354 impropers, 963 angles 53: 972 pairs, 654 bonds and 141 virtual sites 53: 53: Total mass 6908.582 a.m.u. 53: 53: Total charge -6.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 53: 53: The Gromos53a6 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (127 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 25 donors and 23 acceptors were found. 53: There are 41 hydrogen bonds 53: Will use HISE for residue 8 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS3 HIS8 53: SG9 NE251 53: HIS8 NE251 1.055 53: MET12 SD83 0.763 0.990 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 267 pairs 53: Before cleaning: 312 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 53: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 128 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (128 atoms, 16 residues) 53: 53: Identified residue ALA2 as a starting terminus. 53: 53: Identified residue SER17 as a ending terminus. 53: Start terminus ALA-2: NH3+ 53: End terminus SER-17: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 167 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 174, now 169 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 90 dihedrals, 79 impropers, 245 angles 53: 267 pairs, 169 bonds and 0 virtual sites 53: 53: Total mass 1846.116 a.m.u. 53: 53: Total charge 0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 53: 53: The Gromos53a6 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (69 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 30 donors and 22 acceptors were found. 53: There are 36 hydrogen bonds 53: Will use HISE for residue 29 53: Will use HISE for residue 32 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS27 HIS29 53: SG90 NE2111 53: HIS29 NE2111 0.987 53: HIS32 NE2135 1.590 1.155 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 273 pairs 53: Before cleaning: 443 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 53: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 149 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (149 atoms, 16 residues) 53: 53: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue THR18 as a starting terminus. 53: 53: Identified residue PHE33 as a ending terminus. 53: Start terminus THR-18: NH3+ 53: End terminus PHE-33: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 206 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 220, now 215 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 93 dihedrals, 138 impropers, 324 angles 53: 273 pairs, 215 bonds and 0 virtual sites 53: 53: Total mass 2088.361 a.m.u. 53: 53: Total charge 1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 53: 53: The Gromos53a6 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (187 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 22 acceptors were found. 53: There are 26 hydrogen bonds 53: Will use HISE for residue 45 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS45 53: NE295 53: MET46 SD102 1.078 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 242 pairs 53: Before cleaning: 356 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 53: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 132 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (132 atoms, 16 residues) 53: 53: Identified residue ALA34 as a starting terminus. 53: 53: Identified residue ALA49 as a ending terminus. 53: Start terminus ALA-34: NH3+ 53: End terminus ALA-49: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 170 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 181, now 176 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 81 dihedrals, 104 impropers, 264 angles 53: 242 pairs, 176 bonds and 0 virtual sites 53: 53: Total mass 1861.132 a.m.u. 53: 53: Total charge -1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 53: 53: The Gromos53a6 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (279 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 21 acceptors were found. 53: There are 30 hydrogen bonds 53: Will use HISE for residue 60 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS60 53: NE285 53: CYS62 SG98 0.803 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 232 pairs 53: Before cleaning: 306 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 53: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 117 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (117 atoms, 16 residues) 53: 53: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue LYS50 as a starting terminus. 53: 53: Identified residue PRO65 as a ending terminus. 53: Start terminus LYS-50: NH3+ 53: End terminus PRO-65: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 152 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 161, now 156 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 78 dihedrals, 82 impropers, 231 angles 53: 232 pairs, 156 bonds and 0 virtual sites 53: 53: Total mass 1662.887 a.m.u. 53: 53: Total charge -0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 53: 53: The Gromos53a6 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (408 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 89 donors and 98 acceptors were found. 53: There are 129 hydrogen bonds 53: Will use HISE for residue 31 53: Will use HISE for residue 51 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS25 HIS31 HIS51 53: SG14 NE264 NE2226 53: HIS31 NE264 1.921 53: HIS51 NE2226 1.498 2.650 53: CYS80 SG477 0.207 1.984 1.570 53: Linking CYS-25 SG-14 and CYS-80 SG-477... 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 972 pairs 53: Before cleaning: 1270 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 53: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 53: 53: chain #res #atoms 53: 53: 1 'A' 58 488 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 'A' (488 atoms, 58 residues) 53: 53: Identified residue ASN24 as a starting terminus. 53: 53: Identified residue ARG81 as a ending terminus. 53: Start terminus ASN-24: NH3+ 53: End terminus ARG-81: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 58 residues with 639 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 659, now 654 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 321 dihedrals, 354 impropers, 963 angles 53: 972 pairs, 654 bonds and 0 virtual sites 53: 53: Total mass 6908.582 a.m.u. 53: 53: Total charge -6.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 53: 53: The Gromos53a6 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (157 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 25 donors and 23 acceptors were found. 53: There are 41 hydrogen bonds 53: Will use HISE for residue 8 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS3 HIS8 53: SG9 NE251 53: HIS8 NE251 1.055 53: MET12 SD83 0.763 0.990 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 39 virtual sites 53: Added 4 dummy masses 53: Added 8 new constraints 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 267 pairs 53: Before cleaning: 312 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 53: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 128 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (128 atoms, 16 residues) 53: 53: Identified residue ALA2 as a starting terminus. 53: 53: Identified residue SER17 as a ending terminus. 53: Start terminus ALA-2: NH3+ 53: End terminus SER-17: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 167 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 174, now 169 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 90 dihedrals, 79 impropers, 245 angles 53: 267 pairs, 169 bonds and 39 virtual sites 53: 53: Total mass 1846.116 a.m.u. 53: 53: Total charge 0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 53: 53: The Gromos53a6 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (505 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 30 donors and 22 acceptors were found. 53: There are 36 hydrogen bonds 53: Will use HISE for residue 29 53: Will use HISE for residue 32 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS27 HIS29 53: SG90 NE2111 53: HIS29 NE2111 0.987 53: HIS32 NE2135 1.590 1.155 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 57 virtual sites 53: Added 4 dummy masses 53: Added 10 new constraints 53: 53: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 273 pairs 53: Before cleaning: 443 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 53: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 149 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (149 atoms, 16 residues) 53: 53: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue THR18 as a starting terminus. 53: 53: Identified residue PHE33 as a ending terminus. 53: Start terminus THR-18: NH3+ 53: End terminus PHE-33: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 206 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 220, now 215 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 93 dihedrals, 138 impropers, 324 angles 53: 273 pairs, 215 bonds and 55 virtual sites 53: 53: Total mass 2088.361 a.m.u. 53: 53: Total charge 1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 53: 53: The Gromos53a6 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (522 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 22 acceptors were found. 53: There are 26 hydrogen bonds 53: Will use HISE for residue 45 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS45 53: NE295 53: MET46 SD102 1.078 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 38 virtual sites 53: Added 4 dummy masses 53: Added 8 new constraints 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 242 pairs 53: Before cleaning: 356 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 53: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 132 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (132 atoms, 16 residues) 53: 53: Identified residue ALA34 as a starting terminus. 53: 53: Identified residue ALA49 as a ending terminus. 53: Start terminus ALA-34: NH3+ 53: End terminus ALA-49: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 170 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 181, now 176 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 81 dihedrals, 104 impropers, 264 angles 53: 242 pairs, 176 bonds and 38 virtual sites 53: 53: Total mass 1861.132 a.m.u. 53: 53: Total charge -1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 53: 53: The Gromos53a6 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (327 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 21 acceptors were found. 53: There are 30 hydrogen bonds 53: Will use HISE for residue 60 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS60 53: NE285 53: CYS62 SG98 0.803 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 35 virtual sites 53: Added 4 dummy masses 53: Added 10 new constraints 53: 53: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 232 pairs 53: Before cleaning: 306 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 53: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 117 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (117 atoms, 16 residues) 53: 53: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue LYS50 as a starting terminus. 53: 53: Identified residue PRO65 as a ending terminus. 53: Start terminus LYS-50: NH3+ 53: End terminus PRO-65: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 152 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 161, now 156 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 78 dihedrals, 82 impropers, 231 angles 53: 232 pairs, 156 bonds and 33 virtual sites 53: 53: Total mass 1662.887 a.m.u. 53: 53: Total charge -0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 53: 53: The Gromos53a6 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (119 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 89 donors and 98 acceptors were found. 53: There are 129 hydrogen bonds 53: Will use HISE for residue 31 53: Will use HISE for residue 51 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS25 HIS31 HIS51 53: SG14 NE264 NE2226 53: HIS31 NE264 1.921 53: HIS51 NE2226 1.498 2.650 53: CYS80 SG477 0.207 1.984 1.570 53: Linking CYS-25 SG-14 and CYS-80 SG-477... 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 150 virtual sites 53: Added 10 dummy masses 53: Added 29 new constraints 53: 53: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 972 pairs 53: Before cleaning: 1270 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 53: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 53: 53: chain #res #atoms 53: 53: 1 'A' 58 488 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 'A' (488 atoms, 58 residues) 53: 53: Identified residue ASN24 as a starting terminus. 53: 53: Identified residue ARG81 as a ending terminus. 53: Start terminus ASN-24: NH3+ 53: End terminus ARG-81: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 58 residues with 639 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 659, now 654 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 321 dihedrals, 354 impropers, 963 angles 53: 972 pairs, 654 bonds and 141 virtual sites 53: 53: Total mass 6908.582 a.m.u. 53: 53: Total charge -6.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 53: 53: The Gromos53a6 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (92 ms) 53: [----------] 20 tests from G53a6/Pdb2gmxTest (3827 ms total) 53: 53: [----------] Global test environment tear-down 53: [==========] 40 tests from 2 test suites ran. (10156 ms total) 53: [ PASSED ] 40 tests. 53/90 Test #53: Pdb2gmx2Test .............................. Passed 10.18 sec test 54 Start 54: Pdb2gmx3Test 54: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/pdb2gmx3-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/Pdb2gmx3Test.xml" 54: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/gmxpreprocess/tests 54: Test timeout computed to be: 1920 54: [==========] Running 39 tests from 6 test suites. 54: [----------] Global test environment set-up. 54: [----------] 10 tests from Amber/Pdb2gmxTest 54: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 54: Before cleaning: 653 pairs 54: Before cleaning: 691 dihedrals 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 128 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 (128 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 252 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 255, now 254 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 691 dihedrals, 51 impropers, 457 angles 54: 650 pairs, 254 bonds and 0 virtual sites 54: 54: Total mass 1846.132 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 54: 54: The Amber99sb-ildn force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (66 ms) 54: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 30 donors and 22 acceptors were found. 54: There are 36 hydrogen bonds 54: Will use HISE for residue 29 54: Will use HISE for residue 32 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS27 HIS29 54: SG90 NE2111 54: HIS29 NE2111 0.987 54: HIS32 NE2135 1.590 1.155 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 54: Before cleaning: 748 pairs 54: Before cleaning: 788 dihedrals 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 149 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 (149 atoms, 16 residues) 54: 54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue PHE33 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 281 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 291, now 290 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 788 dihedrals, 72 impropers, 516 angles 54: 736 pairs, 290 bonds and 0 virtual sites 54: 54: Total mass 2088.366 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 54: 54: The Amber99sb-ildn force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (60 ms) 54: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 22 acceptors were found. 54: There are 26 hydrogen bonds 54: Will use HISE for residue 45 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS45 54: NE295 54: MET46 SD102 1.078 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 54: Before cleaning: 676 pairs 54: Before cleaning: 727 dihedrals 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 132 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 (132 atoms, 16 residues) 54: 54: Identified residue ALA34 as a starting terminus. 54: 54: Identified residue ALA49 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 262, now 261 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 727 dihedrals, 56 impropers, 472 angles 54: 667 pairs, 261 bonds and 0 virtual sites 54: 54: Total mass 1861.124 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 54: 54: The Amber99sb-ildn force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (56 ms) 54: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 21 acceptors were found. 54: There are 30 hydrogen bonds 54: Will use HISE for residue 60 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS60 54: NE285 54: CYS62 SG98 0.803 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 54: Before cleaning: 603 pairs 54: Before cleaning: 634 dihedrals 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 117 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 (117 atoms, 16 residues) 54: 54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue LYS50 as a starting terminus. 54: 54: Identified residue PRO65 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 228 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 233, now 232 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 634 dihedrals, 48 impropers, 419 angles 54: 597 pairs, 232 bonds and 0 virtual sites 54: 54: Total mass 1662.888 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 54: 54: The Amber99sb-ildn force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (56 ms) 54: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 89 donors and 98 acceptors were found. 54: There are 129 hydrogen bonds 54: Will use HISE for residue 31 54: Will use HISE for residue 51 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS25 HIS31 HIS51 54: SG14 NE264 NE2226 54: HIS31 NE264 1.921 54: HIS51 NE2226 1.498 2.650 54: CYS80 SG477 0.207 1.984 1.570 54: Linking CYS-25 SG-14 and CYS-80 SG-477... 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 54: Before cleaning: 2499 pairs 54: Before cleaning: 2631 dihedrals 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 58 488 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 'A' (488 atoms, 58 residues) 54: 54: Identified residue ASN24 as a starting terminus. 54: 54: Identified residue ARG81 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 58 residues with 936 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 952, now 951 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2631 dihedrals, 208 impropers, 1704 angles 54: 2469 pairs, 951 bonds and 0 virtual sites 54: 54: Total mass 6908.576 a.m.u. 54: 54: Total charge -6.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 54: 54: The Amber99sb-ildn force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (187 ms) 54: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 54: Marked 124 virtual sites 54: Added 16 dummy masses 54: Added 26 new constraints 54: Before cleaning: 653 pairs 54: Before cleaning: 691 dihedrals 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 128 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 (128 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 252 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 255, now 254 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 691 dihedrals, 51 impropers, 457 angles 54: 650 pairs, 254 bonds and 130 virtual sites 54: 54: Total mass 1846.132 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 54: 54: The Amber99sb-ildn force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (94 ms) 54: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 30 donors and 22 acceptors were found. 54: There are 36 hydrogen bonds 54: Will use HISE for residue 29 54: Will use HISE for residue 32 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS27 HIS29 54: SG90 NE2111 54: HIS29 NE2111 0.987 54: HIS32 NE2135 1.590 1.155 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 54: Marked 132 virtual sites 54: Added 10 dummy masses 54: Added 19 new constraints 54: Before cleaning: 748 pairs 54: Before cleaning: 788 dihedrals 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 149 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 (149 atoms, 16 residues) 54: 54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue PHE33 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 281 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 291, now 290 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 788 dihedrals, 72 impropers, 516 angles 54: 736 pairs, 290 bonds and 133 virtual sites 54: 54: Total mass 2088.366 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 54: 54: The Amber99sb-ildn force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (261 ms) 54: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 22 acceptors were found. 54: There are 26 hydrogen bonds 54: Will use HISE for residue 45 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS45 54: NE295 54: MET46 SD102 1.078 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 54: Marked 123 virtual sites 54: Added 22 dummy masses 54: Added 35 new constraints 54: Before cleaning: 676 pairs 54: Before cleaning: 727 dihedrals 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 132 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 (132 atoms, 16 residues) 54: 54: Identified residue ALA34 as a starting terminus. 54: 54: Identified residue ALA49 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 262, now 261 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 727 dihedrals, 56 impropers, 472 angles 54: 667 pairs, 261 bonds and 132 virtual sites 54: 54: Total mass 1861.124 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 54: 54: The Amber99sb-ildn force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (88 ms) 54: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 21 acceptors were found. 54: There are 30 hydrogen bonds 54: Will use HISE for residue 60 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS60 54: NE285 54: CYS62 SG98 0.803 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 54: Marked 111 virtual sites 54: Added 18 dummy masses 54: Added 31 new constraints 54: Before cleaning: 603 pairs 54: Before cleaning: 634 dihedrals 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 117 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 (117 atoms, 16 residues) 54: 54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue LYS50 as a starting terminus. 54: 54: Identified residue PRO65 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 228 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 233, now 232 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 634 dihedrals, 48 impropers, 419 angles 54: 597 pairs, 232 bonds and 116 virtual sites 54: 54: Total mass 1662.888 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 54: 54: The Amber99sb-ildn force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (58 ms) 54: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 89 donors and 98 acceptors were found. 54: There are 129 hydrogen bonds 54: Will use HISE for residue 31 54: Will use HISE for residue 51 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS25 HIS31 HIS51 54: SG14 NE264 NE2226 54: HIS31 NE264 1.921 54: HIS51 NE2226 1.498 2.650 54: CYS80 SG477 0.207 1.984 1.570 54: Linking CYS-25 SG-14 and CYS-80 SG-477... 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 54: Marked 447 virtual sites 54: Added 58 dummy masses 54: Added 101 new constraints 54: Before cleaning: 2499 pairs 54: Before cleaning: 2631 dihedrals 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 58 488 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 'A' (488 atoms, 58 residues) 54: 54: Identified residue ASN24 as a starting terminus. 54: 54: Identified residue ARG81 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 58 residues with 936 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 952, now 951 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2631 dihedrals, 208 impropers, 1704 angles 54: 2469 pairs, 951 bonds and 462 virtual sites 54: 54: Total mass 6908.576 a.m.u. 54: 54: Total charge -6.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 54: 54: The Amber99sb-ildn force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (126 ms) 54: [----------] 10 tests from Amber/Pdb2gmxTest (1057 ms total) 54: 54: [----------] 1 test from AmberTip4p/Pdb2gmxTest 54: [ RUN ] AmberTip4p/Pdb2gmxTest.Runs/ff_amber99sbildn_tip4p_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/tip4p.pdb... 54: Read 'TIP4p ice to test that MW is handled correctly', 4 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 0 chains and 1 blocks of water and 2 residues with 4 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 2 4 (only water) 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 (4 atoms, 2 residues) 54: 54: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 2 residues with 8 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 4, now 4 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 0 dihedrals, 0 impropers, 2 angles 54: 0 pairs, 4 bonds and 0 virtual sites 54: 54: Total mass 36.032 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/tip4p.pdb. 54: 54: The Amber99sb-ildn force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] AmberTip4p/Pdb2gmxTest.Runs/ff_amber99sbildn_tip4p_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full (26 ms) 54: [----------] 1 test from AmberTip4p/Pdb2gmxTest (26 ms total) 54: 54: [----------] 12 tests from Charmm/Pdb2gmxTest 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 653 pairs 54: Before cleaning: 663 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 128 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 (128 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 252 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 254, now 254 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 14 cmap torsion pairs 54: 54: There are 663 dihedrals, 48 impropers, 457 angles 54: 650 pairs, 254 bonds and 0 virtual sites 54: 54: Total mass 1846.115 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (42 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 30 donors and 22 acceptors were found. 54: There are 36 hydrogen bonds 54: Will use HISE for residue 29 54: Will use HISE for residue 32 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS27 HIS29 54: SG90 NE2111 54: HIS29 NE2111 0.987 54: HIS32 NE2135 1.590 1.155 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 748 pairs 54: Before cleaning: 778 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 149 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 (149 atoms, 16 residues) 54: 54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue PHE33 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus PHE-33: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 281 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 290, now 290 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 14 cmap torsion pairs 54: 54: There are 778 dihedrals, 49 impropers, 516 angles 54: 736 pairs, 290 bonds and 0 virtual sites 54: 54: Total mass 2088.361 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (50 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 22 acceptors were found. 54: There are 26 hydrogen bonds 54: Will use HISE for residue 45 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS45 54: NE295 54: MET46 SD102 1.078 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 676 pairs 54: Before cleaning: 696 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 132 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 (132 atoms, 16 residues) 54: 54: Identified residue ALA34 as a starting terminus. 54: 54: Identified residue ALA49 as a ending terminus. 54: Start terminus ALA-34: NH3+ 54: End terminus ALA-49: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 261, now 261 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 14 cmap torsion pairs 54: 54: There are 696 dihedrals, 39 impropers, 472 angles 54: 667 pairs, 261 bonds and 0 virtual sites 54: 54: Total mass 1861.130 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (42 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 21 acceptors were found. 54: There are 30 hydrogen bonds 54: Will use HISE for residue 60 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS60 54: NE285 54: CYS62 SG98 0.803 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 603 pairs 54: Before cleaning: 618 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 117 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 (117 atoms, 16 residues) 54: 54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue LYS50 as a starting terminus. 54: 54: Identified residue PRO65 as a ending terminus. 54: Start terminus LYS-50: NH3+ 54: End terminus PRO-65: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 228 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 232, now 232 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 14 cmap torsion pairs 54: 54: There are 618 dihedrals, 38 impropers, 419 angles 54: 597 pairs, 232 bonds and 0 virtual sites 54: 54: Total mass 1662.885 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (41 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 89 donors and 98 acceptors were found. 54: There are 129 hydrogen bonds 54: Will use HISE for residue 31 54: Will use HISE for residue 51 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS25 HIS31 HIS51 54: SG14 NE264 NE2226 54: HIS31 NE264 1.921 54: HIS51 NE2226 1.498 2.650 54: CYS80 SG477 0.207 1.984 1.570 54: Linking CYS-25 SG-14 and CYS-80 SG-477... 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 2499 pairs 54: Before cleaning: 2524 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 58 488 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (488 atoms, 58 residues) 54: 54: Identified residue ASN24 as a starting terminus. 54: 54: Identified residue ARG81 as a ending terminus. 54: Start terminus ASN-24: NH3+ 54: End terminus ARG-81: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 58 residues with 936 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 951, now 951 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 56 cmap torsion pairs 54: 54: There are 2524 dihedrals, 149 impropers, 1704 angles 54: 2469 pairs, 951 bonds and 0 virtual sites 54: 54: Total mass 6908.566 a.m.u. 54: 54: Total charge -6.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (102 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_monomerpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 39 pairs 54: Before cleaning: 39 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/monomer.pdb... 54: Read 'GLU', 9 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 1 residues with 9 atoms 54: 54: chain #res #atoms 54: 54: 1 'X' 1 9 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'X' (9 atoms, 1 residues) 54: 54: Identified residue GLU1 as a starting terminus. 54: 54: Identified residue GLU1 as a ending terminus. 54: Start terminus GLU-1: NH3+ 54: End terminus GLU-1: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 1 residues with 18 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 17, now 17 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 39 dihedrals, 2 impropers, 30 angles 54: 39 pairs, 17 bonds and 0 virtual sites 54: 54: Total mass 146.123 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/monomer.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_monomerpdb_format_gro_match_file (27 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Marked 124 virtual sites 54: Added 16 dummy masses 54: Added 26 new constraints 54: Before cleaning: 653 pairs 54: Before cleaning: 663 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 128 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 (128 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 252 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 254, now 254 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 14 cmap torsion pairs 54: 54: There are 663 dihedrals, 48 impropers, 457 angles 54: 650 pairs, 254 bonds and 130 virtual sites 54: 54: Total mass 1846.115 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (44 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 30 donors and 22 acceptors were found. 54: There are 36 hydrogen bonds 54: Will use HISE for residue 29 54: Will use HISE for residue 32 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS27 HIS29 54: SG90 NE2111 54: HIS29 NE2111 0.987 54: HIS32 NE2135 1.590 1.155 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Marked 132 virtual sites 54: Added 10 dummy masses 54: Added 19 new constraints 54: Before cleaning: 748 pairs 54: Before cleaning: 778 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 149 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 (149 atoms, 16 residues) 54: 54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue PHE33 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus PHE-33: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 281 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 290, now 290 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 14 cmap torsion pairs 54: 54: There are 778 dihedrals, 49 impropers, 516 angles 54: 736 pairs, 290 bonds and 133 virtual sites 54: 54: Total mass 2088.361 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (48 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 22 acceptors were found. 54: There are 26 hydrogen bonds 54: Will use HISE for residue 45 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS45 54: NE295 54: MET46 SD102 1.078 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Marked 123 virtual sites 54: Added 22 dummy masses 54: Added 35 new constraints 54: Before cleaning: 676 pairs 54: Before cleaning: 696 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 132 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 (132 atoms, 16 residues) 54: 54: Identified residue ALA34 as a starting terminus. 54: 54: Identified residue ALA49 as a ending terminus. 54: Start terminus ALA-34: NH3+ 54: End terminus ALA-49: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 261, now 261 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 14 cmap torsion pairs 54: 54: There are 696 dihedrals, 39 impropers, 472 angles 54: 667 pairs, 261 bonds and 132 virtual sites 54: 54: Total mass 1861.130 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (47 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 21 acceptors were found. 54: There are 30 hydrogen bonds 54: Will use HISE for residue 60 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS60 54: NE285 54: CYS62 SG98 0.803 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Marked 111 virtual sites 54: Added 18 dummy masses 54: Added 31 new constraints 54: Before cleaning: 603 pairs 54: Before cleaning: 618 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 117 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 (117 atoms, 16 residues) 54: 54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue LYS50 as a starting terminus. 54: 54: Identified residue PRO65 as a ending terminus. 54: Start terminus LYS-50: NH3+ 54: End terminus PRO-65: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 228 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 232, now 232 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 14 cmap torsion pairs 54: 54: There are 618 dihedrals, 38 impropers, 419 angles 54: 597 pairs, 232 bonds and 116 virtual sites 54: 54: Total mass 1662.885 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (47 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 89 donors and 98 acceptors were found. 54: There are 129 hydrogen bonds 54: Will use HISE for residue 31 54: Will use HISE for residue 51 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS25 HIS31 HIS51 54: SG14 NE264 NE2226 54: HIS31 NE264 1.921 54: HIS51 NE2226 1.498 2.650 54: CYS80 SG477 0.207 1.984 1.570 54: Linking CYS-25 SG-14 and CYS-80 SG-477... 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Marked 447 virtual sites 54: Added 58 dummy masses 54: Added 101 new constraints 54: Before cleaning: 2499 pairs 54: Before cleaning: 2524 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 58 488 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (488 atoms, 58 residues) 54: 54: Identified residue ASN24 as a starting terminus. 54: 54: Identified residue ARG81 as a ending terminus. 54: Start terminus ASN-24: NH3+ 54: End terminus ARG-81: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 58 residues with 936 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 951, now 951 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 56 cmap torsion pairs 54: 54: There are 2524 dihedrals, 149 impropers, 1704 angles 54: 2469 pairs, 951 bonds and 462 virtual sites 54: 54: Total mass 6908.566 a.m.u. 54: 54: Total charge -6.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (129 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_monomerpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Marked 8 virtual sites 54: Added 2 dummy masses 54: Added 3 new constraints 54: Before cleaning: 39 pairs 54: Before cleaning: 39 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/monomer.pdb... 54: Read 'GLU', 9 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 1 residues with 9 atoms 54: 54: chain #res #atoms 54: 54: 1 'X' 1 9 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'X' (9 atoms, 1 residues) 54: 54: Identified residue GLU1 as a starting terminus. 54: 54: Identified residue GLU1 as a ending terminus. 54: Start terminus GLU-1: NH3+ 54: End terminus GLU-1: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 1 residues with 18 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 17, now 17 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 39 dihedrals, 2 impropers, 30 angles 54: 39 pairs, 17 bonds and 9 virtual sites 54: 54: Total mass 146.123 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/monomer.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_monomerpdb_format_gro_match_file (26 ms) 54: [----------] 12 tests from Charmm/Pdb2gmxTest (652 ms total) 54: 54: [----------] 8 tests from ChainSep/Pdb2gmxTest 54: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_all_chainTerpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 651 pairs 54: Before cleaning: 661 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on changing chain id only (ignoring TER records). 54: 54: Merged chains into joint molecule definitions at 2 places. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 16 127 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (127 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue GLU5 as a ending terminus. 54: 54: Identified residue PHE6 as a starting terminus. 54: 54: Identified residue MET12 as a ending terminus. 54: 54: Identified residue ASN13 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus GLU-5: COO- 54: Start terminus PHE-6: NH3+ 54: End terminus MET-12: COO- 54: Start terminus ASN-13: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 258 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 258, now 258 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 10 cmap torsion pairs 54: 54: There are 661 dihedrals, 46 impropers, 463 angles 54: 648 pairs, 258 bonds and 0 virtual sites 54: 54: Total mass 1882.146 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_all_chainTerpdb_format_gro_match_file (44 ms) 54: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_chainTerpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 123 pairs 54: Before cleaning: 123 dihedrals 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 10 donors and 7 acceptors were found. 54: There are 7 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS8 54: NE223 54: MET12 SD55 0.990 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 317 pairs 54: Before cleaning: 322 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 211 pairs 54: Before cleaning: 216 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on changing chain id only (ignoring TER records). 54: 54: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 4 28 54: 54: 2 'B' 7 58 54: 54: 3 'C' 5 41 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (28 atoms, 4 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue GLU5 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus GLU-5: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 4 residues with 51 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 50, now 50 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2 cmap torsion pairs 54: 54: There are 123 dihedrals, 9 impropers, 88 angles 54: 123 pairs, 50 bonds and 0 virtual sites 54: 54: Total mass 434.421 a.m.u. 54: 54: Total charge -2.000 e 54: 54: Writing topology 54: 54: Processing chain 2 'B' (58 atoms, 7 residues) 54: 54: Identified residue PHE6 as a starting terminus. 54: 54: Identified residue MET12 as a ending terminus. 54: Start terminus PHE-6: NH3+ 54: End terminus MET-12: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 7 residues with 124 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 125, now 125 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 5 cmap torsion pairs 54: 54: There are 322 dihedrals, 19 impropers, 227 angles 54: 314 pairs, 125 bonds and 0 virtual sites 54: 54: Total mass 846.083 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Processing chain 3 'C' (41 atoms, 5 residues) 54: 54: Identified residue ASN13 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ASN-13: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 5 residues with 83 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 83, now 83 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 3 cmap torsion pairs 54: 54: There are 216 dihedrals, 18 impropers, 148 angles 54: 211 pairs, 83 bonds and 0 virtual sites 54: 54: Total mass 601.643 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Including chain 1 in system: 51 atoms 4 residues 54: 54: Including chain 2 in system: 124 atoms 7 residues 54: 54: Including chain 3 in system: 83 atoms 5 residues 54: 54: Now there are 258 atoms and 16 residues 54: 54: Total mass in system 1882.146 a.m.u. 54: 54: Total charge in system 0.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_chainTerpdb_format_gro_match_file (39 ms) 54: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_all_chainTerpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 651 pairs 54: Before cleaning: 661 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records only (ignoring chain id). 54: 54: Merged chains into joint molecule definitions at 2 places. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 16 127 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (127 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue ILE9 as a ending terminus. 54: 54: Identified residue LYS10 as a starting terminus. 54: 54: Identified residue MET12 as a ending terminus. 54: 54: Identified residue ASN13 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus ILE-9: COO- 54: Start terminus LYS-10: NH3+ 54: End terminus MET-12: COO- 54: Start terminus ASN-13: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 258 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 258, now 258 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 10 cmap torsion pairs 54: 54: There are 661 dihedrals, 46 impropers, 463 angles 54: 648 pairs, 258 bonds and 0 virtual sites 54: 54: Total mass 1882.146 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_all_chainTerpdb_format_gro_match_file (44 ms) 54: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_chainTerpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 10 donors and 12 acceptors were found. 54: There are 13 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 54: SG9 54: HIS8 NE251 1.055 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 288 pairs 54: Before cleaning: 293 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 152 pairs 54: Before cleaning: 152 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 211 pairs 54: Before cleaning: 216 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records only (ignoring chain id). 54: 54: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 8 61 54: 54: 2 'B' 3 25 54: 54: 3 'C' 5 41 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (61 atoms, 8 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue ILE9 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus ILE-9: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 8 residues with 114 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 115, now 115 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 6 cmap torsion pairs 54: 54: There are 293 dihedrals, 23 impropers, 203 angles 54: 285 pairs, 115 bonds and 0 virtual sites 54: 54: Total mass 888.952 a.m.u. 54: 54: Total charge -2.000 e 54: 54: Writing topology 54: 54: Processing chain 2 'B' (25 atoms, 3 residues) 54: 54: Identified residue LYS10 as a starting terminus. 54: 54: Identified residue MET12 as a ending terminus. 54: Start terminus LYS-10: NH3+ 54: End terminus MET-12: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 3 residues with 61 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 60, now 60 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 1 cmap torsion pairs 54: 54: There are 152 dihedrals, 5 impropers, 112 angles 54: 152 pairs, 60 bonds and 0 virtual sites 54: 54: Total mass 391.552 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Processing chain 3 'C' (41 atoms, 5 residues) 54: 54: Identified residue ASN13 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ASN-13: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 5 residues with 83 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 83, now 83 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 3 cmap torsion pairs 54: 54: There are 216 dihedrals, 18 impropers, 148 angles 54: 211 pairs, 83 bonds and 0 virtual sites 54: 54: Total mass 601.643 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Including chain 1 in system: 114 atoms 8 residues 54: 54: Including chain 2 in system: 61 atoms 3 residues 54: 54: Including chain 3 in system: 83 atoms 5 residues 54: 54: Now there are 258 atoms and 16 residues 54: 54: Total mass in system 1882.146 a.m.u. 54: 54: Total charge in system 0.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_chainTerpdb_format_gro_match_file (43 ms) 54: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_chainTerpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 650 pairs 54: Before cleaning: 660 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: Merged chains into joint molecule definitions at 3 places. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 16 127 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (127 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue GLU5 as a ending terminus. 54: 54: Identified residue PHE6 as a starting terminus. 54: 54: Identified residue ILE9 as a ending terminus. 54: 54: Identified residue LYS10 as a starting terminus. 54: 54: Identified residue MET12 as a ending terminus. 54: 54: Identified residue ASN13 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus GLU-5: COO- 54: Start terminus PHE-6: NH3+ 54: End terminus ILE-9: COO- 54: Start terminus LYS-10: NH3+ 54: End terminus MET-12: COO- 54: Start terminus ASN-13: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 261 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 260, now 260 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 8 cmap torsion pairs 54: 54: There are 660 dihedrals, 45 impropers, 466 angles 54: 647 pairs, 260 bonds and 0 virtual sites 54: 54: Total mass 1900.162 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_chainTerpdb_format_gro_match_file (59 ms) 54: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_chainTerpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 54: 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 123 pairs 54: Before cleaning: 123 dihedrals 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 6 donors and 4 acceptors were found. 54: There are 3 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 164 pairs 54: Before cleaning: 169 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 152 pairs 54: Before cleaning: 152 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 211 pairs 54: Before cleaning: 216 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 54: 54: There are 4 chains and 0 blocks of water and 16 residues with 127 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 4 28 54: 54: 2 'B' 4 33 54: 54: 3 'B' 3 25 54: 54: 4 'C' 5 41 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (28 atoms, 4 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue GLU5 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus GLU-5: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 4 residues with 51 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 50, now 50 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2 cmap torsion pairs 54: 54: There are 123 dihedrals, 9 impropers, 88 angles 54: 123 pairs, 50 bonds and 0 virtual sites 54: 54: Total mass 434.421 a.m.u. 54: 54: Total charge -2.000 e 54: 54: Writing topology 54: 54: Processing chain 2 'B' (33 atoms, 4 residues) 54: 54: Identified residue PHE6 as a starting terminus. 54: 54: Identified residue ILE9 as a ending terminus. 54: Start terminus PHE-6: NH3+ 54: End terminus ILE-9: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 4 residues with 66 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 67, now 67 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2 cmap torsion pairs 54: 54: There are 169 dihedrals, 13 impropers, 118 angles 54: 161 pairs, 67 bonds and 0 virtual sites 54: 54: Total mass 472.547 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Processing chain 3 'B' (25 atoms, 3 residues) 54: 54: Identified residue LYS10 as a starting terminus. 54: 54: Identified residue MET12 as a ending terminus. 54: Start terminus LYS-10: NH3+ 54: End terminus MET-12: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 3 residues with 61 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 60, now 60 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 1 cmap torsion pairs 54: 54: There are 152 dihedrals, 5 impropers, 112 angles 54: 152 pairs, 60 bonds and 0 virtual sites 54: 54: Total mass 391.552 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Processing chain 4 'C' (41 atoms, 5 residues) 54: 54: Identified residue ASN13 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ASN-13: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 5 residues with 83 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 83, now 83 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 3 cmap torsion pairs 54: 54: There are 216 dihedrals, 18 impropers, 148 angles 54: 211 pairs, 83 bonds and 0 virtual sites 54: 54: Total mass 601.643 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Including chain 1 in system: 51 atoms 4 residues 54: 54: Including chain 2 in system: 66 atoms 4 residues 54: 54: Including chain 3 in system: 61 atoms 3 residues 54: 54: Including chain 4 in system: 83 atoms 5 residues 54: 54: Now there are 261 atoms and 16 residues 54: 54: Total mass in system 1900.162 a.m.u. 54: 54: Total charge in system 0.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_chainTerpdb_format_gro_match_file (55 ms) 54: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_all_chainTerpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 652 pairs 54: Before cleaning: 662 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records and chain id changing. 54: 54: Merged chains into joint molecule definitions at 1 places. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 16 127 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (127 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue MET12 as a ending terminus. 54: 54: Identified residue ASN13 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus MET-12: COO- 54: Start terminus ASN-13: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 256, now 256 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 12 cmap torsion pairs 54: 54: There are 662 dihedrals, 47 impropers, 460 angles 54: 649 pairs, 256 bonds and 0 virtual sites 54: 54: Total mass 1864.131 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_all_chainTerpdb_format_gro_match_file (46 ms) 54: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_chainTerpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 14 donors and 15 acceptors were found. 54: There are 20 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 441 pairs 54: Before cleaning: 446 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 211 pairs 54: Before cleaning: 216 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records and chain id changing. 54: 54: There are 2 chains and 0 blocks of water and 16 residues with 127 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 11 86 54: 54: 2 'C' 5 41 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (86 atoms, 11 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue MET12 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus MET-12: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 11 residues with 172 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 173, now 173 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 9 cmap torsion pairs 54: 54: There are 446 dihedrals, 29 impropers, 312 angles 54: 438 pairs, 173 bonds and 0 virtual sites 54: 54: Total mass 1262.488 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Processing chain 2 'C' (41 atoms, 5 residues) 54: 54: Identified residue ASN13 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ASN-13: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 5 residues with 83 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 83, now 83 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 3 cmap torsion pairs 54: 54: There are 216 dihedrals, 18 impropers, 148 angles 54: 211 pairs, 83 bonds and 0 virtual sites 54: 54: Total mass 601.643 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Including chain 1 in system: 172 atoms 11 residues 54: 54: Including chain 2 in system: 83 atoms 5 residues 54: 54: Now there are 255 atoms and 16 residues 54: 54: Total mass in system 1864.131 a.m.u. 54: 54: Total charge in system 0.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_chainTerpdb_format_gro_match_file (183 ms) 54: [----------] 8 tests from ChainSep/Pdb2gmxTest (518 ms total) 54: 54: [----------] 4 tests from ChainChanges/Pdb2gmxTest 54: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_fragmentspdb_format_pdb_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 83 pairs 54: Before cleaning: 83 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 145 pairs 54: Before cleaning: 150 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/fragments.pdb... 54: Read 'Fragments of peptides and ions', 47 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on changing chain id only (ignoring TER records). 54: 54: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 3 19 54: 54: 2 'B' 3 28 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (19 atoms, 3 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue ASP4 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus ASP-4: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 3 residues with 36 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 35, now 35 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 1 cmap torsion pairs 54: 54: There are 83 dihedrals, 6 impropers, 61 angles 54: 83 pairs, 35 bonds and 0 virtual sites 54: 54: Total mass 306.314 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Processing chain 2 'B' (28 atoms, 3 residues) 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue TRP20 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus TRP-20: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 3 residues with 57 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 58, now 58 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 1 cmap torsion pairs 54: 54: There are 150 dihedrals, 5 impropers, 103 angles 54: 142 pairs, 58 bonds and 0 virtual sites 54: 54: Total mass 404.468 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Including chain 1 in system: 36 atoms 3 residues 54: 54: Including chain 2 in system: 57 atoms 3 residues 54: 54: Now there are 93 atoms and 6 residues 54: 54: Total mass in system 710.782 a.m.u. 54: 54: Total charge in system -1.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/fragments.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_fragmentspdb_format_pdb_match_file (196 ms) 54: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_fragmentspdb_format_pdb_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 83 pairs 54: Before cleaning: 83 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 145 pairs 54: Before cleaning: 150 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/fragments.pdb... 54: Read 'Fragments of peptides and ions', 47 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records only (ignoring chain id). 54: 54: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 3 19 54: 54: 2 'B' 3 28 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (19 atoms, 3 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue ASP4 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus ASP-4: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 3 residues with 36 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 35, now 35 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 1 cmap torsion pairs 54: 54: There are 83 dihedrals, 6 impropers, 61 angles 54: 83 pairs, 35 bonds and 0 virtual sites 54: 54: Total mass 306.314 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Processing chain 2 'B' (28 atoms, 3 residues) 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue TRP20 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus TRP-20: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 3 residues with 57 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 58, now 58 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 1 cmap torsion pairs 54: 54: There are 150 dihedrals, 5 impropers, 103 angles 54: 142 pairs, 58 bonds and 0 virtual sites 54: 54: Total mass 404.468 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Including chain 1 in system: 36 atoms 3 residues 54: 54: Including chain 2 in system: 57 atoms 3 residues 54: 54: Now there are 93 atoms and 6 residues 54: 54: Total mass in system 710.782 a.m.u. 54: 54: Total charge in system -1.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/fragments.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_fragmentspdb_format_pdb_match_file (42 ms) 54: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_fragmentspdb_format_pdb_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 83 pairs 54: Before cleaning: 83 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 145 pairs 54: Before cleaning: 150 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/fragments.pdb... 54: Read 'Fragments of peptides and ions', 47 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 3 19 54: 54: 2 'B' 3 28 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (19 atoms, 3 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue ASP4 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus ASP-4: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 3 residues with 36 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 35, now 35 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 1 cmap torsion pairs 54: 54: There are 83 dihedrals, 6 impropers, 61 angles 54: 83 pairs, 35 bonds and 0 virtual sites 54: 54: Total mass 306.314 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Processing chain 2 'B' (28 atoms, 3 residues) 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue TRP20 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus TRP-20: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 3 residues with 57 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 58, now 58 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 1 cmap torsion pairs 54: 54: There are 150 dihedrals, 5 impropers, 103 angles 54: 142 pairs, 58 bonds and 0 virtual sites 54: 54: Total mass 404.468 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Including chain 1 in system: 36 atoms 3 residues 54: 54: Including chain 2 in system: 57 atoms 3 residues 54: 54: Now there are 93 atoms and 6 residues 54: 54: Total mass in system 710.782 a.m.u. 54: 54: Total charge in system -1.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/fragments.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_fragmentspdb_format_pdb_match_file (30 ms) 54: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_fragmentspdb_format_pdb_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 83 pairs 54: Before cleaning: 83 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 145 pairs 54: Before cleaning: 150 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/fragments.pdb... 54: Read 'Fragments of peptides and ions', 47 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records and chain id changing. 54: 54: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 3 19 54: 54: 2 'B' 3 28 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (19 atoms, 3 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue ASP4 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus ASP-4: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 3 residues with 36 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 35, now 35 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 1 cmap torsion pairs 54: 54: There are 83 dihedrals, 6 impropers, 61 angles 54: 83 pairs, 35 bonds and 0 virtual sites 54: 54: Total mass 306.314 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Processing chain 2 'B' (28 atoms, 3 residues) 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue TRP20 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus TRP-20: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 3 residues with 57 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 58, now 58 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 1 cmap torsion pairs 54: 54: There are 150 dihedrals, 5 impropers, 103 angles 54: 142 pairs, 58 bonds and 0 virtual sites 54: 54: Total mass 404.468 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Including chain 1 in system: 36 atoms 3 residues 54: 54: Including chain 2 in system: 57 atoms 3 residues 54: 54: Now there are 93 atoms and 6 residues 54: 54: Total mass in system 710.782 a.m.u. 54: 54: Total charge in system -1.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/fragments.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_fragmentspdb_format_pdb_match_file (31 ms) 54: [----------] 4 tests from ChainChanges/Pdb2gmxTest (300 ms total) 54: 54: [----------] 4 tests from Cyclic/Pdb2gmxTest 54: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycrnapdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: WARNING: all CONECT records are ignored 54: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 54: 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 6040 pairs 54: Before cleaning: 6605 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 6040 pairs 54: Before cleaning: 6605 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb... 54: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 54: 54: Moved all the water blocks to the end 54: 54: There are 3 chains and 2 blocks of water and 175 residues with 3087 atoms 54: 54: chain #res #atoms 54: 54: 1 'P' 71 1527 54: 54: 2 'Q' 71 1527 54: 54: 3 'Q' 7 7 54: 54: 4 ' ' 10 10 (only water) 54: 54: 5 ' ' 16 16 (only water) 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'P' (1527 atoms, 71 residues) 54: 54: Identified residue G1 as a starting terminus. 54: 54: Identified residue U71 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 71 residues with 2297 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 2481, now 2481 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 6605 dihedrals, 183 impropers, 4434 angles 54: 5827 pairs, 2481 bonds and 0 virtual sites 54: 54: Total mass 22984.514 a.m.u. 54: 54: Total charge -71.000 e 54: 54: Writing topology 54: 54: Processing chain 2 'Q' (1527 atoms, 71 residues) 54: 54: Identified residue G1 as a starting terminus. 54: 54: Identified residue U71 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 71 residues with 2297 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 2481, now 2481 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 6605 dihedrals, 183 impropers, 4434 angles 54: 5827 pairs, 2481 bonds and 0 virtual sites 54: 54: Total mass 22984.514 a.m.u. 54: 54: Total charge -71.000 e 54: 54: Writing topology 54: 54: Processing chain 3 'Q' (7 atoms, 7 residues) 54: 54: Residue MG72 has type 'Ion', assuming it is not linked into a chain. 54: 54: Residue MG73 has type 'Ion', assuming it is not linked into a chain. 54: 54: Residue MG74 has type 'Ion', assuming it is not linked into a chain. 54: 54: Residue MG75 has type 'Ion', assuming it is not linked into a chain. 54: 54: Residue MG76 has type 'Ion', assuming it is not linked into a chain. 54: 54: Disabling further notes about ions. 54: 54: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 7 residues with 7 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: No bonds 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 0 dihedrals, 0 impropers, 0 angles 54: 0 pairs, 0 bonds and 0 virtual sites 54: 54: Total mass 170.135 a.m.u. 54: 54: Total charge 14.000 e 54: 54: Writing topology 54: 54: Processing chain 4 (10 atoms, 10 residues) 54: 54: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 10 residues with 30 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 30, now 30 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 0 dihedrals, 0 impropers, 30 angles 54: 0 pairs, 30 bonds and 0 virtual sites 54: 54: Total mass 180.154 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Processing chain 5 (16 atoms, 16 residues) 54: 54: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 48 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 48, now 48 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 0 dihedrals, 0 impropers, 48 angles 54: 0 pairs, 48 bonds and 0 virtual sites 54: 54: Total mass 288.246 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Including chain 1 in system: 2297 atoms 71 residues 54: 54: Including chain 2 in system: 2297 atoms 71 residues 54: 54: Including chain 3 in system: 7 atoms 7 residues 54: 54: Including chain 4 in system: 30 atoms 10 residues 54: 54: Including chain 5 in system: 48 atoms 16 residues 54: 54: Now there are 4679 atoms and 175 residues 54: 54: Total mass in system 46607.563 a.m.u. 54: 54: Total charge in system -128.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycrnapdb_format_gro_match_file (384 ms) 54: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycprotpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 2325 pairs 54: Before cleaning: 2325 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb... 54: Read 'CARNOCYCLIN-A', 413 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 60 413 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (413 atoms, 60 residues) 54: 54: Identified residue LEU1 as a starting terminus. 54: 54: Identified residue LEU60 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 60 residues with 878 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 880, now 880 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 60 cmap torsion pairs 54: 54: There are 2325 dihedrals, 137 impropers, 1614 angles 54: 2319 pairs, 880 bonds and 0 virtual sites 54: 54: Total mass 5866.087 a.m.u. 54: 54: Total charge 4.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycprotpdb_format_gro_match_file (94 ms) 54: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycrnapdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: WARNING: all CONECT records are ignored 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 12080 pairs 54: Before cleaning: 13210 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb... 54: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: Moved all the water blocks to the end 54: 54: Merged chains into joint molecule definitions at 2 places. 54: 54: There are 1 chains and 2 blocks of water and 175 residues with 3087 atoms 54: 54: chain #res #atoms 54: 54: 1 'P' 149 3061 54: 54: 2 ' ' 10 10 (only water) 54: 54: 3 ' ' 16 16 (only water) 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'P' (3061 atoms, 149 residues) 54: 54: Identified residue G1 as a starting terminus. 54: 54: Identified residue U71 as a ending terminus. 54: 54: Identified residue G1 as a starting terminus. 54: 54: Identified residue U71 as a ending terminus. 54: 54: Residue MG72 has type 'Ion', assuming it is not linked into a chain. 54: 54: Residue MG73 has type 'Ion', assuming it is not linked into a chain. 54: 54: Residue MG74 has type 'Ion', assuming it is not linked into a chain. 54: 54: Residue MG75 has type 'Ion', assuming it is not linked into a chain. 54: 54: Residue MG76 has type 'Ion', assuming it is not linked into a chain. 54: 54: Disabling further notes about ions. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 149 residues with 4601 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 4962, now 4962 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 13210 dihedrals, 366 impropers, 8868 angles 54: 11654 pairs, 4962 bonds and 0 virtual sites 54: 54: Total mass 46139.162 a.m.u. 54: 54: Total charge -128.000 e 54: 54: Writing topology 54: 54: Processing chain 2 (10 atoms, 10 residues) 54: 54: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 10 residues with 30 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 30, now 30 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 0 dihedrals, 0 impropers, 30 angles 54: 0 pairs, 30 bonds and 0 virtual sites 54: 54: Total mass 180.154 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Processing chain 3 (16 atoms, 16 residues) 54: 54: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 48 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 48, now 48 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 0 dihedrals, 0 impropers, 48 angles 54: 0 pairs, 48 bonds and 0 virtual sites 54: 54: Total mass 288.246 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Including chain 1 in system: 4601 atoms 149 residues 54: 54: Including chain 2 in system: 30 atoms 10 residues 54: 54: Including chain 3 in system: 48 atoms 16 residues 54: 54: Now there are 4679 atoms and 175 residues 54: 54: Total mass in system 46607.563 a.m.u. 54: 54: Total charge in system -128.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycrnapdb_format_gro_match_file (610 ms) 54: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycprotpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 54: Before cleaning: 2325 pairs 54: Before cleaning: 2325 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb... 54: Read 'CARNOCYCLIN-A', 413 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 60 413 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (413 atoms, 60 residues) 54: 54: Identified residue LEU1 as a starting terminus. 54: 54: Identified residue LEU60 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 60 residues with 878 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 880, now 880 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 60 cmap torsion pairs 54: 54: There are 2325 dihedrals, 137 impropers, 1614 angles 54: 2319 pairs, 880 bonds and 0 virtual sites 54: 54: Total mass 5866.087 a.m.u. 54: 54: Total charge 4.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycprotpdb_format_gro_match_file (100 ms) 54: [----------] 4 tests from Cyclic/Pdb2gmxTest (1190 ms total) 54: 54: [----------] Global test environment tear-down 54: [==========] 39 tests from 6 test suites ran. (3747 ms total) 54: [ PASSED ] 39 tests. 54/90 Test #54: Pdb2gmx3Test .............................. Passed 3.79 sec test 55 Start 55: CorrelationsTest 55: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/correlations-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/CorrelationsTest.xml" 55: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/correlationfunctions/tests 55: Test timeout computed to be: 30 55: [==========] Running 21 tests from 3 test suites. 55: [----------] Global test environment set-up. 55: [----------] 10 tests from AutocorrTest 55: [ RUN ] AutocorrTest.EacNormal 55: [ OK ] AutocorrTest.EacNormal (93 ms) 55: [ RUN ] AutocorrTest.EacNoNormalize 55: [ OK ] AutocorrTest.EacNoNormalize (62 ms) 55: [ RUN ] AutocorrTest.EacCos 55: [ OK ] AutocorrTest.EacCos (131 ms) 55: [ RUN ] AutocorrTest.EacVector 55: [ OK ] AutocorrTest.EacVector (179 ms) 55: [ RUN ] AutocorrTest.EacRcross 55: [ OK ] AutocorrTest.EacRcross (9 ms) 55: [ RUN ] AutocorrTest.EacP0 55: [ OK ] AutocorrTest.EacP0 (177 ms) 55: [ RUN ] AutocorrTest.EacP1 55: [ OK ] AutocorrTest.EacP1 (188 ms) 55: [ RUN ] AutocorrTest.EacP2 55: [ OK ] AutocorrTest.EacP2 (399 ms) 55: [ RUN ] AutocorrTest.EacP3 55: [ OK ] AutocorrTest.EacP3 (7 ms) 55: [ RUN ] AutocorrTest.EacP4 55: [ OK ] AutocorrTest.EacP4 (204 ms) 55: [----------] 10 tests from AutocorrTest (1456 ms total) 55: 55: [----------] 10 tests from ExpfitTest 55: [ RUN ] ExpfitTest.EffnEXP1 55: [ OK ] ExpfitTest.EffnEXP1 (0 ms) 55: [ RUN ] ExpfitTest.EffnEXP2 55: [ OK ] ExpfitTest.EffnEXP2 (0 ms) 55: [ RUN ] ExpfitTest.EffnEXPEXP 55: [ OK ] ExpfitTest.EffnEXPEXP (1 ms) 55: [ RUN ] ExpfitTest.EffnEXP5 55: [ OK ] ExpfitTest.EffnEXP5 (4 ms) 55: [ RUN ] ExpfitTest.EffnEXP7 55: [ OK ] ExpfitTest.EffnEXP7 (4 ms) 55: [ RUN ] ExpfitTest.EffnEXP9 55: [ OK ] ExpfitTest.EffnEXP9 (40 ms) 55: [ RUN ] ExpfitTest.EffnERF 55: [ OK ] ExpfitTest.EffnERF (2 ms) 55: [ RUN ] ExpfitTest.EffnERREST 55: [ OK ] ExpfitTest.EffnERREST (2 ms) 55: [ RUN ] ExpfitTest.EffnVAC 55: [ OK ] ExpfitTest.EffnVAC (9 ms) 55: [ RUN ] ExpfitTest.EffnPRES 55: [ OK ] ExpfitTest.EffnPRES (17 ms) 55: [----------] 10 tests from ExpfitTest (83 ms total) 55: 55: [----------] 1 test from ManyAutocorrelationTest 55: [ RUN ] ManyAutocorrelationTest.Empty 55: [ OK ] ManyAutocorrelationTest.Empty (0 ms) 55: [----------] 1 test from ManyAutocorrelationTest (0 ms total) 55: 55: [----------] Global test environment tear-down 55: [==========] 21 tests from 3 test suites ran. (1545 ms total) 55: [ PASSED ] 21 tests. 55/90 Test #55: CorrelationsTest .......................... Passed 1.58 sec test 56 Start 56: AnalysisDataUnitTests 56: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/analysisdata-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/AnalysisDataUnitTests.xml" 56: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/analysisdata/tests 56: Test timeout computed to be: 30 56: [==========] Running 69 tests from 14 test suites. 56: [----------] Global test environment set-up. 56: [----------] 3 tests from AnalysisDataInitializationTest 56: [ RUN ] AnalysisDataInitializationTest.BasicInitialization 56: [ OK ] AnalysisDataInitializationTest.BasicInitialization (0 ms) 56: [ RUN ] AnalysisDataInitializationTest.ChecksMultiColumnModules 56: [ OK ] AnalysisDataInitializationTest.ChecksMultiColumnModules (0 ms) 56: [ RUN ] AnalysisDataInitializationTest.ChecksMultipointModules 56: [ OK ] AnalysisDataInitializationTest.ChecksMultipointModules (0 ms) 56: [----------] 3 tests from AnalysisDataInitializationTest (0 ms total) 56: 56: [----------] 8 tests from AnalysisDataCommonTest/0, where TypeParam = gmx::test::(anonymous namespace)::SimpleInputData 56: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly 56: [ OK ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames 56: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 56: [ RUN ] AnalysisDataCommonTest/0.FullStorageWorks 56: [ OK ] AnalysisDataCommonTest/0.FullStorageWorks (0 ms) 56: [ RUN ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData 56: [ OK ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData (0 ms) 56: [ RUN ] AnalysisDataCommonTest/0.LimitedStorageWorks 56: [ OK ] AnalysisDataCommonTest/0.LimitedStorageWorks (0 ms) 56: [----------] 8 tests from AnalysisDataCommonTest/0 (2 ms total) 56: 56: [----------] 8 tests from AnalysisDataCommonTest/1, where TypeParam = gmx::test::(anonymous namespace)::DataSetsInputData 56: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly 56: [ OK ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames 56: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 56: [ RUN ] AnalysisDataCommonTest/1.FullStorageWorks 56: [ OK ] AnalysisDataCommonTest/1.FullStorageWorks (0 ms) 56: [ RUN ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData 56: [ OK ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData (0 ms) 56: [ RUN ] AnalysisDataCommonTest/1.LimitedStorageWorks 56: [ OK ] AnalysisDataCommonTest/1.LimitedStorageWorks (0 ms) 56: [----------] 8 tests from AnalysisDataCommonTest/1 (2 ms total) 56: 56: [----------] 8 tests from AnalysisDataCommonTest/2, where TypeParam = gmx::test::(anonymous namespace)::MultipointInputData 56: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly 56: [ OK ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames 56: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 56: [ RUN ] AnalysisDataCommonTest/2.FullStorageWorks 56: [ OK ] AnalysisDataCommonTest/2.FullStorageWorks (0 ms) 56: [ RUN ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData 56: [ OK ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData (0 ms) 56: [ RUN ] AnalysisDataCommonTest/2.LimitedStorageWorks 56: [ OK ] AnalysisDataCommonTest/2.LimitedStorageWorks (0 ms) 56: [----------] 8 tests from AnalysisDataCommonTest/2 (3 ms total) 56: 56: [----------] 8 tests from AnalysisDataCommonTest/3, where TypeParam = gmx::test::(anonymous namespace)::MultipointDataSetsInputData 56: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly 56: [ OK ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames 56: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 56: [ RUN ] AnalysisDataCommonTest/3.FullStorageWorks 56: [ OK ] AnalysisDataCommonTest/3.FullStorageWorks (0 ms) 56: [ RUN ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData 56: [ OK ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData (0 ms) 56: [ RUN ] AnalysisDataCommonTest/3.LimitedStorageWorks 56: [ OK ] AnalysisDataCommonTest/3.LimitedStorageWorks (0 ms) 56: [----------] 8 tests from AnalysisDataCommonTest/3 (3 ms total) 56: 56: [----------] 4 tests from AnalysisArrayDataTest 56: [ RUN ] AnalysisArrayDataTest.CallsModuleCorrectly 56: [ OK ] AnalysisArrayDataTest.CallsModuleCorrectly (0 ms) 56: [ RUN ] AnalysisArrayDataTest.StorageWorks 56: [ OK ] AnalysisArrayDataTest.StorageWorks (0 ms) 56: [ RUN ] AnalysisArrayDataTest.CanSetXAxis 56: [ OK ] AnalysisArrayDataTest.CanSetXAxis (0 ms) 56: [ RUN ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount 56: [ OK ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount (0 ms) 56: [----------] 4 tests from AnalysisArrayDataTest (0 ms total) 56: 56: [----------] 6 tests from AverageModuleTest 56: [ RUN ] AverageModuleTest.BasicTest 56: [ OK ] AverageModuleTest.BasicTest (0 ms) 56: [ RUN ] AverageModuleTest.HandlesMultipointData 56: [ OK ] AverageModuleTest.HandlesMultipointData (0 ms) 56: [ RUN ] AverageModuleTest.HandlesMultipleDataSets 56: [ OK ] AverageModuleTest.HandlesMultipleDataSets (0 ms) 56: [ RUN ] AverageModuleTest.HandlesDataSetAveraging 56: [ OK ] AverageModuleTest.HandlesDataSetAveraging (0 ms) 56: [ RUN ] AverageModuleTest.CanCustomizeXAxis 56: [ OK ] AverageModuleTest.CanCustomizeXAxis (0 ms) 56: [ RUN ] AverageModuleTest.CanCustomizeNonUniformXAxis 56: [ OK ] AverageModuleTest.CanCustomizeNonUniformXAxis (0 ms) 56: [----------] 6 tests from AverageModuleTest (4 ms total) 56: 56: [----------] 2 tests from FrameAverageModuleTest 56: [ RUN ] FrameAverageModuleTest.BasicTest 56: [ OK ] FrameAverageModuleTest.BasicTest (0 ms) 56: [ RUN ] FrameAverageModuleTest.HandlesMultipleDataSets 56: [ OK ] FrameAverageModuleTest.HandlesMultipleDataSets (0 ms) 56: [----------] 2 tests from FrameAverageModuleTest (1 ms total) 56: 56: [----------] 7 tests from AnalysisHistogramSettingsTest 56: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBins 56: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBins (0 ms) 56: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins 56: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins (0 ms) 56: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount 56: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount (0 ms) 56: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth 56: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth (0 ms) 56: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins 56: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins (0 ms) 56: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins 56: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins (0 ms) 56: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange 56: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange (0 ms) 56: [----------] 7 tests from AnalysisHistogramSettingsTest (0 ms total) 56: 56: [----------] 2 tests from SimpleHistogramModuleTest 56: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectly 56: [ OK ] SimpleHistogramModuleTest.ComputesCorrectly (0 ms) 56: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll 56: [ OK ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll (0 ms) 56: [----------] 2 tests from SimpleHistogramModuleTest (1 ms total) 56: 56: [----------] 3 tests from WeightedHistogramModuleTest 56: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectly 56: [ OK ] WeightedHistogramModuleTest.ComputesCorrectly (0 ms) 56: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll 56: [ OK ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll (0 ms) 56: [ RUN ] WeightedHistogramModuleTest.HandlesMultipleDataSets 56: [ OK ] WeightedHistogramModuleTest.HandlesMultipleDataSets (1 ms) 56: [----------] 3 tests from WeightedHistogramModuleTest (2 ms total) 56: 56: [----------] 3 tests from BinAverageModuleTest 56: [ RUN ] BinAverageModuleTest.ComputesCorrectly 56: [ OK ] BinAverageModuleTest.ComputesCorrectly (0 ms) 56: [ RUN ] BinAverageModuleTest.ComputesCorrectlyWithAll 56: [ OK ] BinAverageModuleTest.ComputesCorrectlyWithAll (0 ms) 56: [ RUN ] BinAverageModuleTest.HandlesMultipleDataSets 56: [ OK ] BinAverageModuleTest.HandlesMultipleDataSets (0 ms) 56: [----------] 3 tests from BinAverageModuleTest (2 ms total) 56: 56: [----------] 4 tests from AbstractAverageHistogramTest 56: [ RUN ] AbstractAverageHistogramTest.ClonesCorrectly 56: [ OK ] AbstractAverageHistogramTest.ClonesCorrectly (0 ms) 56: [ RUN ] AbstractAverageHistogramTest.ComputesCumulativeHistogram 56: [ OK ] AbstractAverageHistogramTest.ComputesCumulativeHistogram (0 ms) 56: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth 56: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth (0 ms) 56: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins 56: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins (0 ms) 56: [----------] 4 tests from AbstractAverageHistogramTest (3 ms total) 56: 56: [----------] 3 tests from LifetimeModuleTest 56: [ RUN ] LifetimeModuleTest.BasicTest 56: [ OK ] LifetimeModuleTest.BasicTest (0 ms) 56: [ RUN ] LifetimeModuleTest.CumulativeTest 56: [ OK ] LifetimeModuleTest.CumulativeTest (0 ms) 56: [ RUN ] LifetimeModuleTest.HandlesMultipleDataSets 56: [ OK ] LifetimeModuleTest.HandlesMultipleDataSets (0 ms) 56: [----------] 3 tests from LifetimeModuleTest (1 ms total) 56: 56: [----------] Global test environment tear-down 56: [==========] 69 tests from 14 test suites ran. (30 ms total) 56: [ PASSED ] 69 tests. 56/90 Test #56: AnalysisDataUnitTests ..................... Passed 0.06 sec test 57 Start 57: CoordinateIOTests 57: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/coordinateio-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/CoordinateIOTests.xml" 57: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/coordinateio/tests 57: Test timeout computed to be: 30 57: [==========] Running 67 tests from 20 test suites. 57: [----------] Global test environment set-up. 57: [----------] 1 test from OutputSelectorDeathTest 57: [ RUN ] OutputSelectorDeathTest.RejectsBadSelection 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] OutputSelectorDeathTest.RejectsBadSelection (4 ms) 57: [----------] 1 test from OutputSelectorDeathTest (4 ms total) 57: 57: [----------] 5 tests from TrajectoryFrameWriterTest 57: [ RUN ] TrajectoryFrameWriterTest.RejectsWrongFiletype 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] TrajectoryFrameWriterTest.RejectsWrongFiletype (1 ms) 57: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms (1 ms) 57: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms (1 ms) 57: [ RUN ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms (3 ms) 57: [ RUN ] TrajectoryFrameWriterTest.TNGOutputWorks 57: [ OK ] TrajectoryFrameWriterTest.TNGOutputWorks (0 ms) 57: [----------] 5 tests from TrajectoryFrameWriterTest (9 ms total) 57: 57: [----------] 5 tests from OutputAdapterContainer 57: [ RUN ] OutputAdapterContainer.MakeEmpty 57: [ OK ] OutputAdapterContainer.MakeEmpty (0 ms) 57: [ RUN ] OutputAdapterContainer.AddAdapter 57: [ OK ] OutputAdapterContainer.AddAdapter (0 ms) 57: [ RUN ] OutputAdapterContainer.RejectBadAdapter 57: [ OK ] OutputAdapterContainer.RejectBadAdapter (0 ms) 57: [ RUN ] OutputAdapterContainer.RejectDuplicateAdapter 57: [ OK ] OutputAdapterContainer.RejectDuplicateAdapter (0 ms) 57: [ RUN ] OutputAdapterContainer.AcceptMultipleAdapters 57: [ OK ] OutputAdapterContainer.AcceptMultipleAdapters (0 ms) 57: [----------] 5 tests from OutputAdapterContainer (0 ms total) 57: 57: [----------] 3 tests from RegisterFrameConverterTest 57: [ RUN ] RegisterFrameConverterTest.NoConverterWorks 57: [ OK ] RegisterFrameConverterTest.NoConverterWorks (0 ms) 57: [ RUN ] RegisterFrameConverterTest.RegistrationWorks 57: [ OK ] RegisterFrameConverterTest.RegistrationWorks (0 ms) 57: [ RUN ] RegisterFrameConverterTest.NewConverterCanInvalidateGuarantees 57: [ OK ] RegisterFrameConverterTest.NewConverterCanInvalidateGuarantees (0 ms) 57: [----------] 3 tests from RegisterFrameConverterTest (0 ms total) 57: 57: [----------] 5 tests from FlagTest 57: [ RUN ] FlagTest.CanSetSimpleFlag 57: [ OK ] FlagTest.CanSetSimpleFlag (0 ms) 57: [ RUN ] FlagTest.CanAddNewBox 57: [ OK ] FlagTest.CanAddNewBox (0 ms) 57: [ RUN ] FlagTest.SetsImplicitPrecisionChange 57: [ OK ] FlagTest.SetsImplicitPrecisionChange (0 ms) 57: [ RUN ] FlagTest.SetsImplicitStartTimeChange 57: [ OK ] FlagTest.SetsImplicitStartTimeChange (0 ms) 57: [ RUN ] FlagTest.SetsImplicitTimeStepChange 57: [ OK ] FlagTest.SetsImplicitTimeStepChange (0 ms) 57: [----------] 5 tests from FlagTest (0 ms total) 57: 57: [----------] 5 tests from SetAtomsTest 57: [ RUN ] SetAtomsTest.RemovesExistingAtoms 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] SetAtomsTest.RemovesExistingAtoms (1 ms) 57: [ RUN ] SetAtomsTest.AddsNewAtoms 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] SetAtomsTest.AddsNewAtoms (1 ms) 57: [ RUN ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable (1 ms) 57: [ RUN ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable (1 ms) 57: [ RUN ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible (1 ms) 57: [----------] 5 tests from SetAtomsTest (8 ms total) 57: 57: [----------] 2 tests from SetBothTimeTest 57: [ RUN ] SetBothTimeTest.StartTimeZeroWorks 57: [ OK ] SetBothTimeTest.StartTimeZeroWorks (0 ms) 57: [ RUN ] SetBothTimeTest.SetStartTimeNonZeroWorks 57: [ OK ] SetBothTimeTest.SetStartTimeNonZeroWorks (0 ms) 57: [----------] 2 tests from SetBothTimeTest (0 ms total) 57: 57: [----------] 2 tests from SetStartTimeTest 57: [ RUN ] SetStartTimeTest.WorksWithNonZeroStart 57: [ OK ] SetStartTimeTest.WorksWithNonZeroStart (0 ms) 57: [ RUN ] SetStartTimeTest.WorksWithZeroStart 57: [ OK ] SetStartTimeTest.WorksWithZeroStart (0 ms) 57: [----------] 2 tests from SetStartTimeTest (0 ms total) 57: 57: [----------] 1 test from SetTimeStepTest 57: [ RUN ] SetTimeStepTest.SetTimeStepWorks 57: [ OK ] SetTimeStepTest.SetTimeStepWorks (0 ms) 57: [----------] 1 test from SetTimeStepTest (0 ms total) 57: 57: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest 57: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 (1 ms) 57: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 (1 ms) 57: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 (1 ms) 57: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 (1 ms) 57: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 (1 ms) 57: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 (1 ms) 57: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest (10 ms total) 57: 57: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles 57: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/0 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/0 (1 ms) 57: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/1 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/1 (1 ms) 57: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/2 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/2 (1 ms) 57: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles (5 ms total) 57: 57: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles 57: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 57: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 (0 ms) 57: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 57: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 (0 ms) 57: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 57: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 (0 ms) 57: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles (0 ms total) 57: 57: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles 57: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/0 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/0 (3 ms) 57: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/1 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/1 (3 ms) 57: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/2 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/2 (3 ms) 57: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/3 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/3 (3 ms) 57: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles (14 ms total) 57: 57: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles 57: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/0 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/0 (1 ms) 57: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/1 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/1 (1 ms) 57: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/2 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/2 (2 ms) 57: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles (5 ms total) 57: 57: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles 57: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 57: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 (0 ms) 57: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 57: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 (0 ms) 57: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 57: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 (0 ms) 57: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles (0 ms total) 57: 57: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles 57: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/0 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/0 (1 ms) 57: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/1 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/1 (1 ms) 57: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles (3 ms total) 57: 57: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles 57: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 57: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 (0 ms) 57: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 57: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 (0 ms) 57: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 57: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 (0 ms) 57: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 57: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 (0 ms) 57: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles (0 ms total) 57: 57: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles 57: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 (1 ms) 57: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 (1 ms) 57: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles (3 ms total) 57: 57: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles 57: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 57: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 (0 ms) 57: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 57: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 (0 ms) 57: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 57: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 (0 ms) 57: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 57: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 (0 ms) 57: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles (0 ms total) 57: 57: [----------] 4 tests from ModuleSupported/NoOptionalOutput 57: [ RUN ] ModuleSupported/NoOptionalOutput.Works/0 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/NoOptionalOutput.Works/0 (1 ms) 57: [ RUN ] ModuleSupported/NoOptionalOutput.Works/1 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/NoOptionalOutput.Works/1 (1 ms) 57: [ RUN ] ModuleSupported/NoOptionalOutput.Works/2 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/NoOptionalOutput.Works/2 (1 ms) 57: [ RUN ] ModuleSupported/NoOptionalOutput.Works/3 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/NoOptionalOutput.Works/3 (1 ms) 57: [----------] 4 tests from ModuleSupported/NoOptionalOutput (6 ms total) 57: 57: [----------] Global test environment tear-down 57: [==========] 67 tests from 20 test suites ran. (73 ms total) 57: [ PASSED ] 67 tests. 57/90 Test #57: CoordinateIOTests ......................... Passed 0.09 sec test 58 Start 58: TrajectoryAnalysisUnitTests 58: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/trajectoryanalysis-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/TrajectoryAnalysisUnitTests.xml" 58: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests 58: Test timeout computed to be: 1920 58: [==========] Running 393 tests from 21 test suites. 58: [----------] Global test environment set-up. 58: [----------] 11 tests from AngleModuleTest 58: [ RUN ] AngleModuleTest.ComputesSimpleAngles 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.ComputesSimpleAngles (2 ms) 58: [ RUN ] AngleModuleTest.ComputesDihedrals 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.ComputesDihedrals (1 ms) 58: [ RUN ] AngleModuleTest.ComputesVectorPairAngles 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.ComputesVectorPairAngles (1 ms) 58: [ RUN ] AngleModuleTest.ComputesVectorPlanePairAngles 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.ComputesVectorPlanePairAngles (1 ms) 58: [ RUN ] AngleModuleTest.ComputesPlaneZAxisAngles 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.ComputesPlaneZAxisAngles (1 ms) 58: [ RUN ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles (2 ms) 58: [ RUN ] AngleModuleTest.ComputesVectorTimeZeroAngles 58: Reading frames from gro file 'Test system for different angles', 33 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.ComputesVectorTimeZeroAngles (3 ms) 58: [ RUN ] AngleModuleTest.ComputesMultipleAngles 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.ComputesMultipleAngles (1 ms) 58: [ RUN ] AngleModuleTest.HandlesDynamicSelections 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.HandlesDynamicSelections (1 ms) 58: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorAngles 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorAngles (1 ms) 58: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles (1 ms) 58: [----------] 11 tests from AngleModuleTest (21 ms total) 58: 58: [----------] 5 tests from ClustsizeTest 58: [ RUN ] ClustsizeTest.NoMolDefaultCutoff 58: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 58: There is one group in the index 58: '', 24 atoms 58: Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Total number of atoms in clusters = 24 58: cmid: 2, cmax: 4, max_size: 6 58: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 58: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolDefaultCutoff (187 ms) 58: [ RUN ] ClustsizeTest.NoMolShortCutoff 58: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 58: There is one group in the index 58: '', 24 atoms 58: Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Total number of atoms in clusters = 24 58: cmid: 1, cmax: 6, max_size: 6 58: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 58: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolShortCutoff (2 ms) 58: [ RUN ] ClustsizeTest.MolDefaultCutoff 58: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 58: '', 24 atoms 58: Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Total number of atoms in clusters = 8 58: cmid: 2, cmax: 4, max_size: 2 58: 50%100%cmid: 2, cmax: 6, max_size: 2 58: 50%100%[ OK ] ClustsizeTest.MolDefaultCutoff (73 ms) 58: [ RUN ] ClustsizeTest.MolShortCutoff 58: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 58: '', 24 atoms 58: Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Total number of atoms in clusters = 8 58: cmid: 1, cmax: 6, max_size: 2 58: 50%100%cmid: 2, cmax: 6, max_size: 2 58: 50%100%[ OK ] ClustsizeTest.MolShortCutoff (5 ms) 58: [ RUN ] ClustsizeTest.MolCSize 58: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 58: '', 24 atoms 58: Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Total number of atoms in clusters = 8 58: cmid: 2, cmax: 4, max_size: 2 58: 50%100%cmid: 2, cmax: 6, max_size: 2 58: 50%100%[ OK ] ClustsizeTest.MolCSize (35 ms) 58: [----------] 5 tests from ClustsizeTest (305 ms total) 58: 58: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest 58: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp 58: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp (1 ms) 58: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory 58: Reading frames from gro file 'Test system', 8 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory (3 ms) 58: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset 58: Reading frames from gro file 'Test system', 8 atoms. 58: Reading frame 0 time 0.000 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset (2 ms) 58: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory 58: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory (0 ms) 58: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest (6 ms total) 58: 58: [----------] 4 tests from ConvertTrjModuleTest 58: [ RUN ] ConvertTrjModuleTest.WritesNormalOutput 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 58: Reading frame 0 time 0.000 Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: [ OK ] ConvertTrjModuleTest.WritesNormalOutput (21 ms) 58: [ RUN ] ConvertTrjModuleTest.WritesAtomSubset 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 58: Reading frame 0 time 0.000 Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: [ OK ] ConvertTrjModuleTest.WritesAtomSubset (15 ms) 58: [ RUN ] ConvertTrjModuleTest.WorksWithAtomAdding 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms 58: Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: [ OK ] ConvertTrjModuleTest.WorksWithAtomAdding (2 ms) 58: [ RUN ] ConvertTrjModuleTest.WorksWithAtomsAndSelection 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms 58: Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: [ OK ] ConvertTrjModuleTest.WorksWithAtomsAndSelection (1 ms) 58: [----------] 4 tests from ConvertTrjModuleTest (41 ms total) 58: 58: [----------] 6 tests from DistanceModuleTest 58: [ RUN ] DistanceModuleTest.ComputesDistances 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: atomname S1 S2: 58: Number of samples: 5 58: Average distance: 1.43246 nm 58: Standard deviation: 0.96700 nm 58: [ OK ] DistanceModuleTest.ComputesDistances (3 ms) 58: [ RUN ] DistanceModuleTest.ComputesMultipleDistances 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: atomname S1 S2: 58: Number of samples: 5 58: Average distance: 1.43246 nm 58: Standard deviation: 0.96700 nm 58: resindex 1 to 4 and atomname CB merge resindex 2 to 5 and atomname CB: 58: Number of samples: 4 58: Average distance: 1.81066 nm 58: Standard deviation: 0.79289 nm 58: [ OK ] DistanceModuleTest.ComputesMultipleDistances (10 ms) 58: [ RUN ] DistanceModuleTest.HandlesDynamicSelections 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: atomname S1 S2 and res_cog x < 2.8: 58: Number of samples: 3 58: Average distance: 1.72076 nm 58: Standard deviation: 1.24839 nm 58: [ OK ] DistanceModuleTest.HandlesDynamicSelections (3 ms) 58: [ RUN ] DistanceModuleTest.HandlesSelectionFromGroup 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: Contacts: 58: Number of samples: 2 58: Average distance: 1.00000 nm 58: Standard deviation: 0.00000 nm 58: [ OK ] DistanceModuleTest.HandlesSelectionFromGroup (7 ms) 58: [ RUN ] DistanceModuleTest.HandlesSelectionFromGroupWithSuccessiveIndices 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: SuccessiveContacts: 58: Number of samples: 2 58: Average distance: 1.00000 nm 58: Standard deviation: 0.00000 nm 58: [ OK ] DistanceModuleTest.HandlesSelectionFromGroupWithSuccessiveIndices (7 ms) 58: [ RUN ] DistanceModuleTest.HandlesSelectionFromLargeGroup 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: ManyContacts: 58: Number of samples: 10 58: Average distance: 1.82913 nm 58: Standard deviation: 0.78478 nm 58: [ OK ] DistanceModuleTest.HandlesSelectionFromLargeGroup (8 ms) 58: [----------] 6 tests from DistanceModuleTest (43 ms total) 58: 58: [----------] 2 tests from ExtractClusterModuleTest 58: [ RUN ] ExtractClusterModuleTest.WorksWithAllAtoms 58: trr version: GMX_trn_file (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 58: Analyzed 26 frames, last time 0.050 58: There are 8 clusters containing 26 structures, highest framenr is 25 58: [ OK ] ExtractClusterModuleTest.WorksWithAllAtoms (3 ms) 58: [ RUN ] ExtractClusterModuleTest.WorksWithAtomSubset 58: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 58: Analyzed 26 frames, last time 0.050 58: There are 8 clusters containing 26 structures, highest framenr is 25 58: [ OK ] ExtractClusterModuleTest.WorksWithAtomSubset (4 ms) 58: [----------] 2 tests from ExtractClusterModuleTest (8 ms total) 58: 58: [----------] 2 tests from FreeVolumeModuleTest 58: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolume 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 58: from the source below. This means the results may be different 58: compared to previous GROMACS versions. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. (1964) 58: DOI: 10.1021/j100785a001 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Could not determine VDW radius for CO2-RM. Set to zero. 58: Could not determine VDW radius for CO2-RM. Set to zero. 58: Could not determine VDW radius for CO2-RM. Set to zero. 58: Could not determine VDW radius for CO2-RM. Set to zero. 58: Could not determine VDW radius for CO2-RM. Set to zero. 58: Could not determine VDW radius for CO2-RM. Set to zero. 58: Could not determine VDW radius for CO2-RM. Set to zero. 58: Could not determine VDW radius for CO2-RM. Set to zero. 58: Could not determine VDW radius for CO2-RM. Set to zero. 58: Could not determine VDW radius for 40 particles. These were set to zero. 58: Reading frame 0 time 0.000 Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: cutoff = 0.18 nm 58: probe_radius = 0 nm 58: seed = 13 58: ninsert = 1000 probes per nm^3 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. (1964) 58: DOI: 10.1021/j100785a001 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: Tuanan C. Lourenco, Mariny F. C. Coelho, Teodorico C. Ramalho, David van der 58: Spoel, Luciano T. Costa 58: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 58: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 58: Environ. Sci. Technol. (2013) 58: DOI: 10.1021/es4020986 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Free volume 38.02 +/- 0.00 % 58: Total volume 68.92 +/- 0.00 nm^3 58: Number of molecules 340 total mass 63491.38 Dalton 58: Average molar mass: 186.74 Dalton 58: Density rho: 1529.71 +/- 0.00 nm^3 58: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 58: Molecular van der Waals volume assuming homogeneity: 0.1256 +/- 0.0000 nm^3 58: Fractional free volume 0.194 +/- 0.000 58: [ OK ] FreeVolumeModuleTest.ComputesFreeVolume (95 ms) 58: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolumeSelection 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 58: from the source below. This means the results may be different 58: compared to previous GROMACS versions. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. (1964) 58: DOI: 10.1021/j100785a001 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Reading frame 0 time 0.000 Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: cutoff = 0.18 nm 58: probe_radius = 0 nm 58: seed = 17 58: ninsert = 1000 probes per nm^3 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. (1964) 58: DOI: 10.1021/j100785a001 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: Tuanan C. Lourenco, Mariny F. C. Coelho, Teodorico C. Ramalho, David van der 58: Spoel, Luciano T. Costa 58: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 58: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 58: Environ. Sci. Technol. (2013) 58: DOI: 10.1021/es4020986 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Free volume 38.48 +/- 0.00 % 58: Total volume 68.92 +/- 0.00 nm^3 58: Number of molecules 340 total mass 63491.38 Dalton 58: Average molar mass: 186.74 Dalton 58: Density rho: 1529.71 +/- 0.00 nm^3 58: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 58: Molecular van der Waals volume assuming homogeneity: 0.1247 +/- 0.0000 nm^3 58: Fractional free volume 0.200 +/- 0.000 58: [ OK ] FreeVolumeModuleTest.ComputesFreeVolumeSelection (97 ms) 58: [----------] 2 tests from FreeVolumeModuleTest (192 ms total) 58: 58: [----------] 13 tests from MsdModuleTest 58: [ RUN ] MsdModuleTest.threeDimensionalDiffusion 58: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 58: Analyzed 10 frames, last time 9.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] MsdModuleTest.threeDimensionalDiffusion (3 ms) 58: [ RUN ] MsdModuleTest.twoDimensionalDiffusion 58: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 58: Analyzed 10 frames, last time 9.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] MsdModuleTest.twoDimensionalDiffusion (2 ms) 58: [ RUN ] MsdModuleTest.oneDimensionalDiffusion 58: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 58: Analyzed 10 frames, last time 9.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] MsdModuleTest.oneDimensionalDiffusion (4 ms) 58: [ RUN ] MsdModuleTest.oneDimensionalDiffusionWithMaxTau 58: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 58: Analyzed 10 frames, last time 9.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] MsdModuleTest.oneDimensionalDiffusionWithMaxTau (6 ms) 58: [ RUN ] MsdModuleTest.multipleGroupsWork 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 58: For energy conservation with LINCS, lincs_iter should be 2 or larger. 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 1818.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 58: NVE simulation: will use the initial temperature of 288.764 K for 58: determining the Verlet buffer size 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 58: There are 9 non-linear virtual site constructions. Their contribution to 58: the energy error is approximated. In most cases this does not affect the 58: error significantly. 58: 58: 58: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 5 NOTEs 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 2.000 58: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 58: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 58: Analyzed 21 frames, last time 40.000 58: Setting the LD random seed to -130026113 58: 58: Generated 2145 of the 2145 non-bonded parameter combinations 58: 58: Generated 2145 of the 2145 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 58: 58: Cleaning up constraints and constant bonded interactions with virtual sites 58: 58: Converted 15 Bonds with virtual sites to connections, 7 left 58: 58: Removed 18 Angles with virtual sites, 21 left 58: 58: Removed 10 Proper Dih.s with virtual sites, 44 left 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 58: 58: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: [ OK ] MsdModuleTest.multipleGroupsWork (42 ms) 58: [ RUN ] MsdModuleTest.subPicosecondTrajectoryWorks 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 58: For energy conservation with LINCS, lincs_iter should be 2 or larger. 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 1818.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 58: NVE simulation: will use the initial temperature of 288.764 K for 58: determining the Verlet buffer size 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 58: There are 9 non-linear virtual site constructions. Their contribution to 58: the energy error is approximated. In most cases this does not affect the 58: error significantly. 58: 58: 58: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 5 NOTEs 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 0.100 58: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 58: Reading frame 2 time 0.200 Reading frame 3 time 0.300 Reading frame 4 time 0.400 Reading frame 5 time 0.500 Reading frame 6 time 0.600 Reading frame 7 time 0.700 Reading frame 8 time 0.800 Reading frame 9 time 0.900 Reading frame 10 time 1.000 Reading frame 11 time 1.100 Reading frame 12 time 1.200 Reading frame 13 time 1.300 Reading frame 14 time 1.400 Reading frame 15 time 1.500 Reading frame 16 time 1.600 Reading frame 17 time 1.700 Reading frame 18 time 1.800 Reading frame 19 time 1.900 Reading frame 20 time 2.000 Last frame 20 time 2.000 58: Analyzed 21 frames, last time 2.000 58: Setting the LD random seed to 1509414879 58: 58: Generated 2145 of the 2145 non-bonded parameter combinations 58: 58: Generated 2145 of the 2145 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 58: 58: Cleaning up constraints and constant bonded interactions with virtual sites 58: 58: Converted 15 Bonds with virtual sites to connections, 7 left 58: 58: Removed 18 Angles with virtual sites, 21 left 58: 58: Removed 10 Proper Dih.s with virtual sites, 44 left 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 58: 58: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: [ OK ] MsdModuleTest.subPicosecondTrajectoryWorks (40 ms) 58: [ RUN ] MsdModuleTest.trestartLessThanDt 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 58: For energy conservation with LINCS, lincs_iter should be 2 or larger. 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 1818.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 58: NVE simulation: will use the initial temperature of 288.764 K for 58: determining the Verlet buffer size 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 58: There are 9 non-linear virtual site constructions. Their contribution to 58: the energy error is approximated. In most cases this does not affect the 58: error significantly. 58: 58: 58: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 5 NOTEs 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Setting the LD random seed to -285212905 58: 58: Generated 2145 of the 2145 non-bonded parameter combinations 58: 58: Generated 2145 of the 2145 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 58: 58: Cleaning up constraints and constant bonded interactions with virtual sites 58: 58: Converted 15 Bonds with virtual sites to connections, 7 left 58: 58: Removed 18 Angles with virtual sites, 21 left 58: 58: Removed 10 Proper Dih.s with virtual sites, 44 left 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 58: 58: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: [ OK ] MsdModuleTest.trestartLessThanDt (29 ms) 58: [ RUN ] MsdModuleTest.trestartGreaterThanDt 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 58: For energy conservation with LINCS, lincs_iter should be 2 or larger. 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 1818.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 58: NVE simulation: will use the initial temperature of 288.764 K for 58: determining the Verlet buffer size 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 58: There are 9 non-linear virtual site constructions. Their contribution to 58: the energy error is approximated. In most cases this does not affect the 58: error significantly. 58: 58: 58: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 5 NOTEs 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 58: Analyzed 21 frames, last time 40.000 58: Setting the LD random seed to -319838473 58: 58: Generated 2145 of the 2145 non-bonded parameter combinations 58: 58: Generated 2145 of the 2145 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 58: 58: Cleaning up constraints and constant bonded interactions with virtual sites 58: 58: Converted 15 Bonds with virtual sites to connections, 7 left 58: 58: Removed 18 Angles with virtual sites, 21 left 58: 58: Removed 10 Proper Dih.s with virtual sites, 44 left 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 58: 58: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: [ OK ] MsdModuleTest.trestartGreaterThanDt (36 ms) 58: [ RUN ] MsdModuleTest.trestartGreaterThanDtAndNotAMultipleOfDt 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 58: For energy conservation with LINCS, lincs_iter should be 2 or larger. 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 1818.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 58: NVE simulation: will use the initial temperature of 288.764 K for 58: determining the Verlet buffer size 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 58: There are 9 non-linear virtual site constructions. Their contribution to 58: the energy error is approximated. In most cases this does not affect the 58: error significantly. 58: 58: 58: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 5 NOTEs 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Setting the LD random seed to -1073947144 58: 58: Generated 2145 of the 2145 non-bonded parameter combinations 58: 58: Generated 2145 of the 2145 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 58: 58: Cleaning up constraints and constant bonded interactions with virtual sites 58: 58: Converted 15 Bonds with virtual sites to connections, 7 left 58: 58: Removed 18 Angles with virtual sites, 21 left 58: 58: Removed 10 Proper Dih.s with virtual sites, 44 left 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 58: 58: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: [ OK ] MsdModuleTest.trestartGreaterThanDtAndNotAMultipleOfDt (29 ms) 58: [ RUN ] MsdModuleTest.molTest 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 58: For energy conservation with LINCS, lincs_iter should be 2 or larger. 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 1818.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 58: NVE simulation: will use the initial temperature of 288.764 K for 58: determining the Verlet buffer size 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 58: There are 9 non-linear virtual site constructions. Their contribution to 58: the energy error is approximated. In most cases this does not affect the 58: error significantly. 58: 58: 58: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 5 NOTEs 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 58: Analyzed 21 frames, last time 40.000 58: Setting the LD random seed to 1456976279 58: 58: Generated 2145 of the 2145 non-bonded parameter combinations 58: 58: Generated 2145 of the 2145 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 58: 58: Cleaning up constraints and constant bonded interactions with virtual sites 58: 58: Converted 15 Bonds with virtual sites to connections, 7 left 58: 58: Removed 18 Angles with virtual sites, 21 left 58: 58: Removed 10 Proper Dih.s with virtual sites, 44 left 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 58: 58: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: [ OK ] MsdModuleTest.molTest (37 ms) 58: [ RUN ] MsdModuleTest.beginFit 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 58: For energy conservation with LINCS, lincs_iter should be 2 or larger. 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 1818.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 58: NVE simulation: will use the initial temperature of 288.764 K for 58: determining the Verlet buffer size 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 58: There are 9 non-linear virtual site constructions. Their contribution to 58: the energy error is approximated. In most cases this does not affect the 58: error significantly. 58: 58: 58: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 5 NOTEs 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 2.000 58: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 58: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 58: Analyzed 21 frames, last time 40.000 58: Setting the LD random seed to 2142108603 58: 58: Generated 2145 of the 2145 non-bonded parameter combinations 58: 58: Generated 2145 of the 2145 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 58: 58: Cleaning up constraints and constant bonded interactions with virtual sites 58: 58: Converted 15 Bonds with virtual sites to connections, 7 left 58: 58: Removed 18 Angles with virtual sites, 21 left 58: 58: Removed 10 Proper Dih.s with virtual sites, 44 left 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 58: 58: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: [ OK ] MsdModuleTest.beginFit (37 ms) 58: [ RUN ] MsdModuleTest.endFit 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 58: For energy conservation with LINCS, lincs_iter should be 2 or larger. 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 1818.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 58: NVE simulation: will use the initial temperature of 288.764 K for 58: determining the Verlet buffer size 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 58: There are 9 non-linear virtual site constructions. Their contribution to 58: the energy error is approximated. In most cases this does not affect the 58: error significantly. 58: 58: 58: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 5 NOTEs 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 2.000 58: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 58: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 58: Analyzed 21 frames, last time 40.000 58: Setting the LD random seed to 1929248572 58: 58: Generated 2145 of the 2145 non-bonded parameter combinations 58: 58: Generated 2145 of the 2145 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 58: 58: Cleaning up constraints and constant bonded interactions with virtual sites 58: 58: Converted 15 Bonds with virtual sites to connections, 7 left 58: 58: Removed 18 Angles with virtual sites, 21 left 58: 58: Removed 10 Proper Dih.s with virtual sites, 44 left 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 58: 58: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: [ OK ] MsdModuleTest.endFit (40 ms) 58: [ RUN ] MsdModuleTest.notEnoughPointsForFitErrorEstimate 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 58: For energy conservation with LINCS, lincs_iter should be 2 or larger. 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 1818.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 58: NVE simulation: will use the initial temperature of 288.764 K for 58: determining the Verlet buffer size 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 58: There are 9 non-linear virtual site constructions. Their contribution to 58: the energy error is approximated. In most cases this does not affect the 58: error significantly. 58: 58: 58: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 5 NOTEs 58: NOTE: You provided an index file 58: /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_solvated.ndx 58: (with -n), but it was not used by any selection. 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 2.000 58: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 58: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 58: Analyzed 21 frames, last time 40.000 58: Setting the LD random seed to 2140143613 58: 58: Generated 2145 of the 2145 non-bonded parameter combinations 58: 58: Generated 2145 of the 2145 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 58: 58: Cleaning up constraints and constant bonded interactions with virtual sites 58: 58: Converted 15 Bonds with virtual sites to connections, 7 left 58: 58: Removed 18 Angles with virtual sites, 21 left 58: 58: Removed 10 Proper Dih.s with virtual sites, 44 left 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 58: 58: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: [ OK ] MsdModuleTest.notEnoughPointsForFitErrorEstimate (36 ms) 58: [----------] 13 tests from MsdModuleTest (349 ms total) 58: 58: [----------] 9 tests from PairDistanceModuleTest 58: [ RUN ] PairDistanceModuleTest.ComputesAllDistances 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] PairDistanceModuleTest.ComputesAllDistances (2 ms) 58: [ RUN ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff (3 ms) 58: [ RUN ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff (2 ms) 58: [ RUN ] PairDistanceModuleTest.ComputesMaxDistance 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] PairDistanceModuleTest.ComputesMaxDistance (2 ms) 58: [ RUN ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff (2 ms) 58: [ RUN ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff (2 ms) 58: [ RUN ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff (2 ms) 58: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten (2 ms) 58: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup (2 ms) 58: [----------] 9 tests from PairDistanceModuleTest (25 ms total) 58: 58: [----------] 5 tests from RdfModuleTest 58: [ RUN ] RdfModuleTest.BasicTest 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] RdfModuleTest.BasicTest (26 ms) 58: [ RUN ] RdfModuleTest.SelectionsSolelyFromIndexFileWork 58: Reading frames from gro file '216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984', 648 atoms. 58: Reading frame 0 time 0.000 Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: [ OK ] RdfModuleTest.SelectionsSolelyFromIndexFileWork (19 ms) 58: [ RUN ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork (23 ms) 58: [ RUN ] RdfModuleTest.CalculatesSurf 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] RdfModuleTest.CalculatesSurf (10 ms) 58: [ RUN ] RdfModuleTest.CalculatesXY 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] RdfModuleTest.CalculatesXY (25 ms) 58: [----------] 5 tests from RdfModuleTest (106 ms total) 58: 58: [----------] 5 tests from SasaModuleTest 58: [ RUN ] SasaModuleTest.BasicTest 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 58: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 58: of Surface Area and Volume and to Dot Surface Contouring of Molecular 58: Assemblies 58: J. Comp. Chem. (1995) 58: DOI: 10.1002/jcc.540160303 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 58: from the source below. This means the results may be different 58: compared to previous GROMACS versions. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. (1964) 58: DOI: 10.1021/j100785a001 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Analyzed topology coordinates 58: [ OK ] SasaModuleTest.BasicTest (12 ms) 58: [ RUN ] SasaModuleTest.HandlesSelectedResidues 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 58: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 58: of Surface Area and Volume and to Dot Surface Contouring of Molecular 58: Assemblies 58: J. Comp. Chem. (1995) 58: DOI: 10.1002/jcc.540160303 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 58: from the source below. This means the results may be different 58: compared to previous GROMACS versions. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. (1964) 58: DOI: 10.1021/j100785a001 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Analyzed topology coordinates 58: [ OK ] SasaModuleTest.HandlesSelectedResidues (7 ms) 58: [ RUN ] SasaModuleTest.WritesConnollySurfaceWithSolute 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 58: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 58: of Surface Area and Volume and to Dot Surface Contouring of Molecular 58: Assemblies 58: J. Comp. Chem. (1995) 58: DOI: 10.1002/jcc.540160303 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 58: from the source below. This means the results may be different 58: compared to previous GROMACS versions. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. (1964) 58: DOI: 10.1021/j100785a001 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Analyzed topology coordinates 58: [ OK ] SasaModuleTest.WritesConnollySurfaceWithSolute (5 ms) 58: [ RUN ] SasaModuleTest.HandlesDynamicOutputGroup 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 58: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 58: of Surface Area and Volume and to Dot Surface Contouring of Molecular 58: Assemblies 58: J. Comp. Chem. (1995) 58: DOI: 10.1002/jcc.540160303 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 58: from the source below. This means the results may be different 58: compared to previous GROMACS versions. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. (1964) 58: DOI: 10.1021/j100785a001 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Analyzed topology coordinates 58: [ OK ] SasaModuleTest.HandlesDynamicOutputGroup (9 ms) 58: [ RUN ] SasaModuleTest.HandlesDynamicCalculationGroup 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 58: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 58: of Surface Area and Volume and to Dot Surface Contouring of Molecular 58: Assemblies 58: J. Comp. Chem. (1995) 58: DOI: 10.1002/jcc.540160303 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 58: from the source below. This means the results may be different 58: compared to previous GROMACS versions. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. (1964) 58: DOI: 10.1021/j100785a001 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Analyzed topology coordinates 58: [ OK ] SasaModuleTest.HandlesDynamicCalculationGroup (8 ms) 58: [----------] 5 tests from SasaModuleTest (46 ms total) 58: 58: [----------] 8 tests from SelectModuleTest 58: [ RUN ] SelectModuleTest.BasicTest 58: Reading frames from gro file 'Test system', 15 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] SelectModuleTest.BasicTest (5 ms) 58: [ RUN ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput 58: Reading frames from gro file 'Test system', 15 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput (3 ms) 58: [ RUN ] SelectModuleTest.HandlesPDBOutputWithPDBInput 58: Reading frames from gro file 'Test system', 15 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] SelectModuleTest.HandlesPDBOutputWithPDBInput (3 ms) 58: [ RUN ] SelectModuleTest.HandlesMaxPDBOutput 58: Reading frames from gro file 'Test system', 15 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] SelectModuleTest.HandlesMaxPDBOutput (3 ms) 58: [ RUN ] SelectModuleTest.HandlesSelectedPDBOutput 58: Reading frames from gro file 'Test system', 15 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] SelectModuleTest.HandlesSelectedPDBOutput (3 ms) 58: [ RUN ] SelectModuleTest.NormalizesSizes 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] SelectModuleTest.NormalizesSizes (2 ms) 58: [ RUN ] SelectModuleTest.WritesResidueNumbers 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] SelectModuleTest.WritesResidueNumbers (2 ms) 58: [ RUN ] SelectModuleTest.WritesResidueIndices 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] SelectModuleTest.WritesResidueIndices (2 ms) 58: [----------] 8 tests from SelectModuleTest (27 ms total) 58: 58: [----------] 10 tests from SurfaceAreaTest 58: [ RUN ] SurfaceAreaTest.ComputesSinglePoint 58: [ OK ] SurfaceAreaTest.ComputesSinglePoint (0 ms) 58: [ RUN ] SurfaceAreaTest.ComputesTwoPoints 58: [ OK ] SurfaceAreaTest.ComputesTwoPoints (0 ms) 58: [ RUN ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius 58: [ OK ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius (0 ms) 58: [ RUN ] SurfaceAreaTest.SurfacePoints12 58: [ OK ] SurfaceAreaTest.SurfacePoints12 (0 ms) 58: [ RUN ] SurfaceAreaTest.SurfacePoints32 58: [ OK ] SurfaceAreaTest.SurfacePoints32 (0 ms) 58: [ RUN ] SurfaceAreaTest.SurfacePoints42 58: [ OK ] SurfaceAreaTest.SurfacePoints42 (0 ms) 58: [ RUN ] SurfaceAreaTest.SurfacePoints122 58: [ OK ] SurfaceAreaTest.SurfacePoints122 (0 ms) 58: [ RUN ] SurfaceAreaTest.Computes100Points 58: [ OK ] SurfaceAreaTest.Computes100Points (0 ms) 58: [ RUN ] SurfaceAreaTest.Computes100PointsWithRectangularPBC 58: [ OK ] SurfaceAreaTest.Computes100PointsWithRectangularPBC (2 ms) 58: [ RUN ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC 58: [ OK ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC (3 ms) 58: [----------] 10 tests from SurfaceAreaTest (11 ms total) 58: 58: [----------] 4 tests from TopologyInformation 58: [ RUN ] TopologyInformation.CantWorkWithoutReadingAFile 58: [ OK ] TopologyInformation.CantWorkWithoutReadingAFile (0 ms) 58: [ RUN ] TopologyInformation.WorksWithGroFile 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] TopologyInformation.WorksWithGroFile (2 ms) 58: [ RUN ] TopologyInformation.WorksWithPdbFile 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] TopologyInformation.WorksWithPdbFile (2 ms) 58: [ RUN ] TopologyInformation.WorksWithTprFromPdbFile 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file lysozyme.top, line 1465]: 58: System has non-zero total charge: 2.000000 58: Total charge should normally be an integer. See 58: https://manual.gromacs.org/current/user-guide/floating-point.html 58: for discussion on how close it should be to an integer. 58: 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 465.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 58: NVE simulation with an initial temperature of zero: will use a Verlet 58: buffer of 10%. Check your energy drift! 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 4 NOTEs 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 58: Setting the LD random seed to -723566659 58: 58: Generated 330891 of the 330891 non-bonded parameter combinations 58: 58: Generated 330891 of the 330891 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 58: 58: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 58: Analysing residue names: 58: There are: 10 Protein residues 58: Analysing Protein... 58: 58: This run will generate roughly 0 Mb of data 58: [ OK ] TopologyInformation.WorksWithTprFromPdbFile (757 ms) 58: [----------] 4 tests from TopologyInformation (762 ms total) 58: 58: [----------] 4 tests from TrajectoryModuleTest 58: [ RUN ] TrajectoryModuleTest.BasicTest 58: Reading frames from gro file 'Test system', 15 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] TrajectoryModuleTest.BasicTest (3 ms) 58: [ RUN ] TrajectoryModuleTest.PlotsXOnly 58: Reading frames from gro file 'Test system', 15 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] TrajectoryModuleTest.PlotsXOnly (2 ms) 58: [ RUN ] TrajectoryModuleTest.HandlesNoVelocities 58: Reading frames from gro file 'Test system', 15 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] TrajectoryModuleTest.HandlesNoVelocities (4 ms) 58: [ RUN ] TrajectoryModuleTest.HandlesNoForces 58: Reading frames from gro file 'Test system', 15 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] TrajectoryModuleTest.HandlesNoForces (2 ms) 58: [----------] 4 tests from TrajectoryModuleTest (12 ms total) 58: 58: [----------] 5 tests from UnionFinderTest 58: [ RUN ] UnionFinderTest.WorksEmpty 58: [ OK ] UnionFinderTest.WorksEmpty (0 ms) 58: [ RUN ] UnionFinderTest.BasicMerges 58: [ OK ] UnionFinderTest.BasicMerges (0 ms) 58: [ RUN ] UnionFinderTest.LargerMerges 58: [ OK ] UnionFinderTest.LargerMerges (0 ms) 58: [ RUN ] UnionFinderTest.LongRightMerge 58: [ OK ] UnionFinderTest.LongRightMerge (0 ms) 58: [ RUN ] UnionFinderTest.LongLeftMerge 58: [ OK ] UnionFinderTest.LongLeftMerge (0 ms) 58: [----------] 5 tests from UnionFinderTest (0 ms total) 58: 58: [----------] 1 test from MappedUnionFinderTest 58: [ RUN ] MappedUnionFinderTest.BasicMerges 58: [ OK ] MappedUnionFinderTest.BasicMerges (0 ms) 58: [----------] 1 test from MappedUnionFinderTest (0 ms total) 58: 58: [----------] 192 tests from MoleculeTests/DsspModuleTest 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/0 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/0 (27 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/1 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/1 (27 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/2 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/2 (27 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/3 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/3 (29 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/4 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/4 (28 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/5 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/5 (27 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/6 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/6 (27 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/7 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/7 (27 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/8 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/8 (29 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/9 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/9 (27 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/10 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/10 (27 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/11 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/11 (27 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/12 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/12 (27 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/13 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/13 (27 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/14 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/14 (29 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/15 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/15 (29 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/16 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/16 (28 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/17 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/17 (26 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/18 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/18 (29 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/19 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/19 (28 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/20 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/20 (28 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/21 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/21 (36 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/22 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/22 (27 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/23 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/23 (27 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/24 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/24 (27 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/25 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/25 (27 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/26 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/26 (27 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/27 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/27 (27 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/28 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/28 (25 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/29 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/29 (28 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/30 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/30 (29 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/31 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/31 (30 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/32 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/32 (28 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/33 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/33 (27 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/34 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/34 (29 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/35 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/35 (28 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/36 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/36 (29 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/37 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/37 (28 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/38 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/38 (30 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/39 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/39 (28 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/40 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/40 (28 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/41 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/41 (29 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/42 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/42 (31 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/43 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/43 (29 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/44 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/44 (33 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/45 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/45 (35 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/46 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/46 (52 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/47 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/47 (31 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/48 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/48 (28 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/49 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/49 (27 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/50 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/50 (28 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/51 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/51 (29 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/52 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/52 (26 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/53 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/53 (34 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/54 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/54 (37 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/55 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/55 (45 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/56 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/56 (38 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/57 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/57 (42 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/58 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/58 (54 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/59 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/59 (54 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/60 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/60 (29 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/61 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/61 (29 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/62 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/62 (34 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/63 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/63 (28 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/64 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/64 (25 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/65 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/65 (27 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/66 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/66 (25 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/67 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/67 (26 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/68 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/68 (27 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/69 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/69 (25 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/70 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/70 (25 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/71 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/71 (22 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/72 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/72 (26 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/73 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/73 (27 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/74 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/74 (26 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/75 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/75 (25 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/76 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/76 (31 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/77 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/77 (23 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/78 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/78 (24 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/79 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/79 (25 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/80 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/80 (21 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/81 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/81 (25 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/82 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/82 (28 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/83 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/83 (24 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/84 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/84 (23 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/85 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/85 (29 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/86 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/86 (25 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/87 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/87 (27 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/88 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/88 (26 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/89 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/89 (26 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/90 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/90 (26 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/91 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/91 (28 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/92 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/92 (25 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/93 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/93 (27 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/94 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/94 (30 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/95 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/95 (28 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/96 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/96 (26 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/97 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/97 (25 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/98 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/98 (27 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/99 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/99 (24 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/100 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/100 (26 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/101 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/101 (25 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/102 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/102 (25 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/103 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/103 (30 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/104 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/104 (29 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/105 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/105 (29 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/106 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/106 (27 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/107 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/107 (27 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/108 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/108 (25 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/109 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/109 (31 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/110 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/110 (25 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/111 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/111 (22 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/112 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/112 (23 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/113 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/113 (23 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/114 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/114 (26 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/115 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/115 (24 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/116 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/116 (23 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/117 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/117 (24 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/118 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/118 (23 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/119 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/119 (22 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/120 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/120 (24 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/121 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/121 (24 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/122 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/122 (21 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/123 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/123 (19 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/124 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/124 (21 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/125 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/125 (20 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/126 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/126 (22 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/127 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/127 (26 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/128 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/128 (17 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/129 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/129 (20 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/130 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/130 (17 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/131 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/131 (19 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/132 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/132 (17 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/133 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/133 (20 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/134 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/134 (19 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/135 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/135 (19 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/136 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/136 (16 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/137 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/137 (17 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/138 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/138 (18 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/139 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/139 (17 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/140 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/140 (17 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/141 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/141 (18 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/142 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/142 (18 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/143 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/143 (18 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/144 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/144 (18 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/145 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/145 (20 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/146 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/146 (16 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/147 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/147 (18 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/148 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/148 (20 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/149 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/149 (19 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/150 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/150 (17 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/151 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/151 (16 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/152 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/152 (20 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/153 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/153 (18 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/154 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/154 (17 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/155 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/155 (18 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/156 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/156 (19 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/157 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/157 (17 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/158 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/158 (18 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/159 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/159 (19 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/160 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/160 (33 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/161 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/161 (19 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/162 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/162 (19 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/163 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/163 (22 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/164 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/164 (17 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/165 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/165 (17 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/166 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/166 (16 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/167 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/167 (18 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/168 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/168 (17 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/169 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/169 (18 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/170 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/170 (17 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/171 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/171 (18 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/172 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/172 (25 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/173 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/173 (18 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/174 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/174 (18 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/175 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/175 (19 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/176 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/176 (18 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/177 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/177 (17 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/178 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/178 (19 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/179 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/179 (19 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/180 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/180 (19 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/181 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/181 (24 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/182 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/182 (21 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/183 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/183 (17 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/184 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/184 (18 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/185 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/185 (18 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/186 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/186 (19 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/187 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/187 (20 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/188 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/188 (18 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/189 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/189 (18 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/190 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/190 (19 ms) 58: [ RUN ] MoleculeTests/DsspModuleTest.Works/191 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features 58: Biopolymers (1983) 58: DOI: 10.1002/bip.360221211 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c01344 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTest.Works/191 (18 ms) 58: [----------] 192 tests from MoleculeTests/DsspModuleTest (4854 ms total) 58: 58: [----------] 3 tests from GyrateTests/GyrateModuleTest 58: [ RUN ] GyrateTests/GyrateModuleTest.Works/0 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: [ OK ] GyrateTests/GyrateModuleTest.Works/0 (9 ms) 58: [ RUN ] GyrateTests/GyrateModuleTest.Works/1 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: [ OK ] GyrateTests/GyrateModuleTest.Works/1 (9 ms) 58: [ RUN ] GyrateTests/GyrateModuleTest.Works/2 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: [ OK ] GyrateTests/GyrateModuleTest.Works/2 (8 ms) 58: [----------] 3 tests from GyrateTests/GyrateModuleTest (27 ms total) 58: 58: [----------] 96 tests from HBondTests/HbondModuleTest 58: [ RUN ] HBondTests/HbondModuleTest.Works/0 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 56 acceptors and 27 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/0 (15 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/1 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 29 acceptors and 27 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/1 (21 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/2 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 56 acceptors and 4 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/2 (16 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/3 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 29 acceptors and 4 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/3 (16 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/4 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 56 acceptors and 27 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/4 (17 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/5 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 29 acceptors and 27 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/5 (25 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/6 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 56 acceptors and 4 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/6 (15 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/7 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 29 acceptors and 4 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/7 (16 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/8 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 56 acceptors and 27 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/8 (18 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/9 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 29 acceptors and 27 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/9 (18 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/10 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 56 acceptors and 4 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/10 (15 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/11 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 29 acceptors and 4 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/11 (16 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/12 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 56 acceptors and 27 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/12 (18 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/13 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 29 acceptors and 27 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/13 (16 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/14 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 56 acceptors and 4 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/14 (14 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/15 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 29 acceptors and 4 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/15 (16 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/16 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 56 acceptors and 27 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/16 (18 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/17 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 29 acceptors and 27 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/17 (21 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/18 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 56 acceptors and 4 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/18 (20 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/19 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 29 acceptors and 4 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/19 (21 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/20 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 56 acceptors and 27 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/20 (26 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/21 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 29 acceptors and 27 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/21 (27 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/22 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 56 acceptors and 4 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/22 (23 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/23 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 29 acceptors and 4 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/23 (20 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/24 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 56 acceptors and 27 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/24 (20 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/25 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 29 acceptors and 27 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/25 (19 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/26 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 56 acceptors and 4 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/26 (18 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/27 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 29 acceptors and 4 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/27 (20 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/28 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 56 acceptors and 27 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/28 (20 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/29 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 29 acceptors and 27 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/29 (16 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/30 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 56 acceptors and 4 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/30 (18 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/31 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: Selection 'Protein' has 29 acceptors and 4 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/31 (16 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/32 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 56 acceptors and 27 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/32 (86 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/33 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 29 acceptors and 27 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/33 (91 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/34 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 56 acceptors and 4 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/34 (84 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/35 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 29 acceptors and 4 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/35 (70 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/36 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 56 acceptors and 27 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/36 (187 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/37 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 29 acceptors and 27 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/37 (80 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/38 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 56 acceptors and 4 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/38 (96 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/39 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 29 acceptors and 4 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/39 (83 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/40 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 56 acceptors and 27 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/40 (88 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/41 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 29 acceptors and 27 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/41 (80 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/42 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 56 acceptors and 4 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/42 (85 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/43 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 29 acceptors and 4 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/43 (79 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/44 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 56 acceptors and 27 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/44 (84 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/45 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 29 acceptors and 27 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/45 (84 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/46 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 56 acceptors and 4 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/46 (84 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/47 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 29 acceptors and 4 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/47 (81 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/48 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 56 acceptors and 27 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/48 (89 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/49 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 29 acceptors and 27 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/49 (84 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/50 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 56 acceptors and 4 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/50 (82 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/51 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 29 acceptors and 4 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/51 (82 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/52 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 56 acceptors and 27 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/52 (87 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/53 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 29 acceptors and 27 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/53 (86 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/54 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 56 acceptors and 4 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/54 (86 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/55 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 29 acceptors and 4 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/55 (83 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/56 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 56 acceptors and 27 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/56 (84 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/57 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 29 acceptors and 27 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/57 (96 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/58 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 56 acceptors and 4 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/58 (85 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/59 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 29 acceptors and 4 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/59 (83 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/60 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 56 acceptors and 27 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/60 (89 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/61 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 29 acceptors and 27 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/61 (87 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/62 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 56 acceptors and 4 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/62 (81 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/63 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Selection 'Protein' has 29 acceptors and 4 donors. 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/63 (76 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/64 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/64 (81 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/65 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/65 (81 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/66 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/66 (98 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/67 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/67 (93 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/68 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/68 (87 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/69 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/69 (85 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/70 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/70 (90 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/71 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/71 (80 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/72 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/72 (88 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/73 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/73 (91 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/74 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/74 (90 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/75 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/75 (91 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/76 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/76 (91 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/77 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/77 (90 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/78 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/78 (96 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/79 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/79 (90 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/80 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/80 (83 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/81 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/81 (88 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/82 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/82 (76 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/83 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/83 (85 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/84 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/84 (84 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/85 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/85 (69 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/86 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/86 (72 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/87 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/87 (89 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/88 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/88 (89 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/89 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/89 (98 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/90 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/90 (98 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/91 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/91 (91 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/92 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/92 (87 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/93 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/93 (89 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/94 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/94 (90 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/95 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: Selection 'Water' has 1160 acceptors and 1160 donors. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 58: Memory Limitation 58: Journal of Chemical Information and Modeling (2024) 58: DOI: 10.1021/acs.jcim.3c02087 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] HBondTests/HbondModuleTest.Works/95 (91 ms) 58: [----------] 96 tests from HBondTests/HbondModuleTest (7110 ms total) 58: 58: [----------] 4 tests from MoleculeTests/ScatteringModule 58: [ RUN ] MoleculeTests/ScatteringModule.DirectMode/0 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 58: Method for calculating small-angle neutron scattering spectra using all-atom 58: molecular dynamics trajectories 58: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 58: DOI: 10.1134/S1027451013060372 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/ScatteringModule.DirectMode/0 (15 ms) 58: [ RUN ] MoleculeTests/ScatteringModule.DirectMode/1 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 58: Method for calculating small-angle neutron scattering spectra using all-atom 58: molecular dynamics trajectories 58: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 58: DOI: 10.1134/S1027451013060372 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: D. T. Cromer, J. B. Mann 58: X-ray scattering factors computed from numerical Hartree-Fock wave functions 58: Acta Cryst. A (1968) 58: DOI: 10.1107/S0567739468000550 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/ScatteringModule.DirectMode/1 (390 ms) 58: [ RUN ] MoleculeTests/ScatteringModule.MCMode/0 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 58: Method for calculating small-angle neutron scattering spectra using all-atom 58: molecular dynamics trajectories 58: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 58: DOI: 10.1134/S1027451013060372 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/ScatteringModule.MCMode/0 (11 ms) 58: [ RUN ] MoleculeTests/ScatteringModule.MCMode/1 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 58: Method for calculating small-angle neutron scattering spectra using all-atom 58: molecular dynamics trajectories 58: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 58: DOI: 10.1134/S1027451013060372 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: D. T. Cromer, J. B. Mann 58: X-ray scattering factors computed from numerical Hartree-Fock wave functions 58: Acta Cryst. A (1968) 58: DOI: 10.1107/S0567739468000550 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/ScatteringModule.MCMode/1 (88 ms) 58: [----------] 4 tests from MoleculeTests/ScatteringModule (509 ms total) 58: 58: [----------] Global test environment tear-down 58: [==========] 393 tests from 21 test suites ran. (14461 ms total) 58: [ PASSED ] 393 tests. 58/90 Test #58: TrajectoryAnalysisUnitTests ............... Passed 14.50 sec test 59 Start 59: EnergyAnalysisUnitTests 59: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/energyanalysis-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/EnergyAnalysisUnitTests.xml" 59: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/energyanalysis/tests 59: Test timeout computed to be: 30 59: [==========] Running 12 tests from 5 test suites. 59: [----------] Global test environment set-up. 59: [----------] 2 tests from EnergyTermTest 59: [ RUN ] EnergyTermTest.ConstructWorks 59: [ OK ] EnergyTermTest.ConstructWorks (0 ms) 59: [ RUN ] EnergyTermTest.AddFrameWorks 59: [ OK ] EnergyTermTest.AddFrameWorks (0 ms) 59: [----------] 2 tests from EnergyTermTest (0 ms total) 59: 59: [----------] 1 test from DhdlTest 59: [ RUN ] DhdlTest.ExtractDhdl 59: Opened /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/dhdl.edr as double precision energy file 59: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/dhdl.tpr, VERSION 2016-dev-20160810-e3ded7f (double precision) 59: Note: file tpx version 110, software tpx version 137 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Reading energy frame 6 time 0.060 Reading energy frame 7 time 0.070 Reading energy frame 8 time 0.080 Reading energy frame 9 time 0.090 Reading energy frame 10 time 0.100 Reading energy frame 11 time 0.110 Reading energy frame 12 time 0.120 Reading energy frame 13 time 0.130 Reading energy frame 14 time 0.140 Reading energy frame 15 time 0.150 Reading energy frame 16 time 0.160 Reading energy frame 17 time 0.170 Reading energy frame 18 time 0.180 Reading energy frame 19 time 0.190 Reading energy frame 20 time 0.200 Reading energy frame 30 time 0.300 Reading energy frame 40 time 0.400 Reading energy frame 50 time 0.500 Reading energy frame 60 time 0.600 Reading energy frame 70 time 0.700 Reading energy frame 80 time 0.800 Reading energy frame 90 time 0.900 Reading energy frame 100 time 1.000 Last energy frame read 100 time 1.000 59: 59: 59: Wrote 8 lambda values with 101 samples as 808 dH data blocks to /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary/DhdlTest_ExtractDhdl_dhdl.xvg 59: [ OK ] DhdlTest.ExtractDhdl (9 ms) 59: [----------] 1 test from DhdlTest (9 ms total) 59: 59: [----------] 1 test from OriresTest 59: [ RUN ] OriresTest.ExtractOrires 59: Opened /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/orires.edr as single precision energy file 59: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/orires.tpr, VERSION 2017-dev-20170725-fea8651 (single precision) 59: Note: file tpx version 111, software tpx version 137 59: Found 7 orientation restraints with 1 experimentsSelect the orientation restraint labels you want (-1 is all) 59: End your selection with 0 59: Selecting all 7 orientation restraints 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Reading energy frame 3 time 0.006 Reading energy frame 4 time 0.008 Reading energy frame 5 time 0.010 Reading energy frame 6 time 0.012 Reading energy frame 7 time 0.014 Reading energy frame 8 time 0.016 Reading energy frame 9 time 0.018 Reading energy frame 10 time 0.020 Last energy frame read 10 time 0.020 59: [ OK ] OriresTest.ExtractOrires (12 ms) 59: [----------] 1 test from OriresTest (12 ms total) 59: 59: [----------] 5 tests from EnergyTest 59: [ RUN ] EnergyTest.ExtractEnergy 59: Opened /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 59: 59: Select the terms you want from the following list by 59: selecting either (part of) the name or the number or a combination. 59: End your selection with an empty line or a zero. 59: ------------------------------------------------------------------- 59: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 59: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 59: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 59: 13 Box-Z 14 Volume 15 Density 16 pV 59: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 59: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 59: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 59: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 59: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 59: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 59: 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 59: 59: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 59: All statistics are over 5001 points 59: 59: Energy Average Err.Est. RMSD Tot-Drift 59: ------------------------------------------------------------------------------- 59: Potential -34142.2 39 228.993 -62.8906 (kJ/mol) 59: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 59: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 59: [ OK ] EnergyTest.ExtractEnergy (2 ms) 59: [ RUN ] EnergyTest.ExtractEnergyByNumber 59: Opened /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 59: 59: Select the terms you want from the following list by 59: selecting either (part of) the name or the number or a combination. 59: End your selection with an empty line or a zero. 59: ------------------------------------------------------------------- 59: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 59: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 59: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 59: 13 Box-Z 14 Volume 15 Density 16 pV 59: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 59: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 59: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 59: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 59: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 59: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 59: 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 59: 59: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 59: All statistics are over 5001 points 59: 59: Energy Average Err.Est. RMSD Tot-Drift 59: ------------------------------------------------------------------------------- 59: Coul. recip. 302.771 2.8 17.5152 12.5403 (kJ/mol) 59: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 59: Pres. DC -268.49 3 8.52175 13.2804 (bar) 59: [ OK ] EnergyTest.ExtractEnergyByNumber (3 ms) 59: [ RUN ] EnergyTest.ExtractEnergyMixed 59: Opened /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 59: 59: Select the terms you want from the following list by 59: selecting either (part of) the name or the number or a combination. 59: End your selection with an empty line or a zero. 59: ------------------------------------------------------------------- 59: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 59: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 59: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 59: 13 Box-Z 14 Volume 15 Density 16 pV 59: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 59: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 59: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 59: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 59: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 59: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 59: 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 59: 59: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 4 data sets 59: All statistics are over 5001 points 59: 59: Energy Average Err.Est. RMSD Tot-Drift 59: ------------------------------------------------------------------------------- 59: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 59: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 59: Box-Z 2.92457 0.0054 0.0151558 0.0234974 (nm) 59: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 59: [ OK ] EnergyTest.ExtractEnergyMixed (2 ms) 59: [ RUN ] EnergyTest.ExtractEnergyWithNumberInName 59: Opened /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/ener_numberInName.edr as single precision energy file 59: 59: Select the terms you want from the following list by 59: selecting either (part of) the name or the number or a combination. 59: End your selection with an empty line or a zero. 59: ------------------------------------------------------------------- 59: 1 Bond 2 Angle 3 Proper-Dih. 4 Per.-Imp.-Dih. 59: 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 Coulomb-(SR) 59: 9 Coul.-recip. 10 Potential 11 Kinetic-En. 12 Total-Energy 59: 13 Conserved-En. 14 Temperature 15 Pressure 16 Constr.-rmsd 59: 17 Vir-XX 18 Vir-XY 19 Vir-XZ 20 Vir-YX 59: 21 Vir-YY 22 Vir-YZ 23 Vir-ZX 24 Vir-ZY 59: 25 Vir-ZZ 26 Pres-XX 27 Pres-XY 28 Pres-XZ 59: 29 Pres-YX 30 Pres-YY 31 Pres-YZ 32 Pres-ZX 59: 33 Pres-ZY 34 Pres-ZZ 35 #Surf*SurfTen 36 2CosZ*Vel-X 59: 37 1/Viscosity 38 T-System 39 Lamb-System 59: 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Last energy frame read 2 time 0.004 59: 59: Statistics over 3 steps [ 0.0000 through 0.0040 ps ], 1 data sets 59: All statistics are over 3 points (frames) 59: 59: Energy Average Err.Est. RMSD Tot-Drift 59: ------------------------------------------------------------------------------- 59: 1/Viscosity 57767.2 -- 10666.2 -25998 (m s/kg) 59: [ OK ] EnergyTest.ExtractEnergyWithNumberInName (1 ms) 59: [ RUN ] EnergyTest.ExtractEnergyWithNumberInNameAndAlsoByNumber 59: Opened /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/ener_numberInName.edr as single precision energy file 59: 59: Select the terms you want from the following list by 59: selecting either (part of) the name or the number or a combination. 59: End your selection with an empty line or a zero. 59: ------------------------------------------------------------------- 59: 1 Bond 2 Angle 3 Proper-Dih. 4 Per.-Imp.-Dih. 59: 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 Coulomb-(SR) 59: 9 Coul.-recip. 10 Potential 11 Kinetic-En. 12 Total-Energy 59: 13 Conserved-En. 14 Temperature 15 Pressure 16 Constr.-rmsd 59: 17 Vir-XX 18 Vir-XY 19 Vir-XZ 20 Vir-YX 59: 21 Vir-YY 22 Vir-YZ 23 Vir-ZX 24 Vir-ZY 59: 25 Vir-ZZ 26 Pres-XX 27 Pres-XY 28 Pres-XZ 59: 29 Pres-YX 30 Pres-YY 31 Pres-YZ 32 Pres-ZX 59: 33 Pres-ZY 34 Pres-ZZ 35 #Surf*SurfTen 36 2CosZ*Vel-X 59: 37 1/Viscosity 38 T-System 39 Lamb-System 59: 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Last energy frame read 2 time 0.004 59: 59: Statistics over 3 steps [ 0.0000 through 0.0040 ps ], 2 data sets 59: All statistics are over 3 points (frames) 59: 59: Energy Average Err.Est. RMSD Tot-Drift 59: ------------------------------------------------------------------------------- 59: LJ (SR) -14.1095 -- 0.384124 0.932214 (kJ/mol) 59: 1/Viscosity 57767.2 -- 10666.2 -25998 (m s/kg) 59: [ OK ] EnergyTest.ExtractEnergyWithNumberInNameAndAlsoByNumber (0 ms) 59: [----------] 5 tests from EnergyTest (10 ms total) 59: 59: [----------] 3 tests from ViscosityTest 59: [ RUN ] ViscosityTest.EinsteinViscosity 59: Opened /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 59: 59: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 59: All statistics are over 5001 points 59: 59: Energy Average Err.Est. RMSD Tot-Drift 59: ------------------------------------------------------------------------------- 59: Pres-XX 20.2092 65 717.193 185.978 (bar) 59: Pres-XY -47.7351 39 372.522 207.456 (bar) 59: Pres-XZ 11.477 31 379.79 6.80818 (bar) 59: Pres-YX -47.7106 39 372.525 207.5 (bar) 59: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 59: Pres-YZ -41.3534 45 401.216 114.663 (bar) 59: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 59: Pres-ZY -41.3119 45 401.196 114.743 (bar) 59: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 59: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 59: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 59: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 59: 59: Computing shear viscosity using the Einstein relation with 6 start points separated by 0.2 ps 59: [ OK ] ViscosityTest.EinsteinViscosity (213 ms) 59: [ RUN ] ViscosityTest.EinsteinViscosityIntegral 59: Opened /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 59: 59: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 59: All statistics are over 5001 points 59: 59: Energy Average Err.Est. RMSD Tot-Drift 59: ------------------------------------------------------------------------------- 59: Pres-XX 20.2092 65 717.193 185.978 (bar) 59: Pres-XY -47.7351 39 372.522 207.456 (bar) 59: Pres-XZ 11.477 31 379.79 6.80818 (bar) 59: Pres-YX -47.7106 39 372.525 207.5 (bar) 59: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 59: Pres-YZ -41.3534 45 401.216 114.663 (bar) 59: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 59: Pres-ZY -41.3119 45 401.196 114.743 (bar) 59: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 59: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 59: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 59: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 59: 59: Computing shear viscosity using the Einstein relation with 6 start points separated by 0.2 ps 59: [ OK ] ViscosityTest.EinsteinViscosityIntegral (306 ms) 59: [ RUN ] ViscosityTest.EinsteinViscosityDefaultArguments 59: Opened /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 59: 59: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 59: All statistics are over 5001 points 59: 59: Energy Average Err.Est. RMSD Tot-Drift 59: ------------------------------------------------------------------------------- 59: Pres-XX 20.2092 65 717.193 185.978 (bar) 59: Pres-XY -47.7351 39 372.522 207.456 (bar) 59: Pres-XZ 11.477 31 379.79 6.80818 (bar) 59: Pres-YX -47.7106 39 372.525 207.5 (bar) 59: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 59: Pres-YZ -41.3534 45 401.216 114.663 (bar) 59: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 59: Pres-ZY -41.3119 45 401.196 114.743 (bar) 59: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 59: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 59: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 59: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 59: 59: Computing shear viscosity using the Einstein relation with 6 start points separated by 0.2 ps 59: [ OK ] ViscosityTest.EinsteinViscosityDefaultArguments (315 ms) 59: [----------] 3 tests from ViscosityTest (835 ms total) 59: 59: [----------] Global test environment tear-down 59: [==========] 12 tests from 5 test suites ran. (869 ms total) 59: [ PASSED ] 12 tests. 59/90 Test #59: EnergyAnalysisUnitTests ................... Passed 0.89 sec test 60 Start 60: ToolUnitTests 60: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/tool-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/ToolUnitTests.xml" 60: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests 60: Test timeout computed to be: 1920 60: [==========] Running 63 tests from 8 test suites. 60: [----------] Global test environment set-up. 60: [----------] 2 tests from DumpTest 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file lysozyme.top, line 1465]: 60: System has non-zero total charge: 2.000000 60: Total charge should normally be an integer. See 60: https://manual.gromacs.org/current/user-guide/floating-point.html 60: for discussion on how close it should be to an integer. 60: 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 465.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 60: NVE simulation with an initial temperature of zero: will use a Verlet 60: buffer of 10%. Check your energy drift! 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 NOTEs 60: Setting the LD random seed to -385969153 60: 60: Generated 330891 of the 330891 non-bonded parameter combinations 60: 60: Generated 330891 of the 330891 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 60: Analysing residue names: 60: There are: 10 Protein residues 60: Analysing Protein... 60: 60: This run will generate roughly 0 Mb of data 60: [ RUN ] DumpTest.WorksWithTpr 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 60: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr: 60: inputrec: 60: integrator = md 60: tinit = 0 60: dt = 0.001 60: nsteps = 0 60: init-step = 0 60: simulation-part = 1 60: mts = false 60: mass-repartition-factor = 1 60: comm-mode = Linear 60: nstcomm = 100 60: bd-fric = 0 60: ld-seed = -385969153 60: emtol = 10 60: emstep = 0.01 60: niter = 20 60: fcstep = 0 60: nstcgsteep = 1000 60: nbfgscorr = 10 60: rtpi = 0.05 60: nstxout = 0 60: nstvout = 0 60: nstfout = 0 60: nstlog = 1000 60: nstcalcenergy = 100 60: nstenergy = 1000 60: nstxout-compressed = 0 60: compressed-x-precision = 1000 60: cutoff-scheme = Verlet 60: nstlist = 10 60: pbc = xyz 60: periodic-molecules = false 60: verlet-buffer-tolerance = -1 60: verlet-buffer-pressure-tolerance = 0.5 60: rlist = 1.1 60: coulombtype = Cut-off 60: coulomb-modifier = Potential-shift 60: rcoulomb-switch = 0 60: rcoulomb = 1 60: epsilon-r = 1 60: epsilon-rf = inf 60: vdw-type = Cut-off 60: vdw-modifier = Potential-shift 60: rvdw-switch = 0 60: rvdw = 1 60: DispCorr = No 60: table-extension = 1 60: fourierspacing = 0.12 60: fourier-nx = 0 60: fourier-ny = 0 60: fourier-nz = 0 60: pme-order = 4 60: ewald-rtol = 1e-05 60: ewald-rtol-lj = 0.001 60: lj-pme-comb-rule = Geometric 60: ewald-geometry = 3d 60: epsilon-surface = 0 60: ensemble-temperature-setting = not available 60: tcoupl = No 60: nsttcouple = -1 60: nh-chain-length = 0 60: print-nose-hoover-chain-variables = false 60: pcoupl = No 60: refcoord-scaling = No 60: posres-com: not available 60: posres-comB: not available 60: QMMM = false 60: qm-opts: 60: ngQM = 0 60: constraint-algorithm = Lincs 60: continuation = false 60: Shake-SOR = false 60: shake-tol = 0.0001 60: lincs-order = 4 60: lincs-iter = 1 60: lincs-warnangle = 30 60: nwall = 0 60: wall-type = 9-3 60: wall-r-linpot = -1 60: wall-atomtype[0] = -1 60: wall-atomtype[1] = -1 60: wall-density[0] = 0 60: wall-density[1] = 0 60: wall-ewald-zfac = 3 60: pull = false 60: awh = false 60: rotation = false 60: interactiveMD = false 60: disre = No 60: disre-weighting = Conservative 60: disre-mixed = false 60: dr-fc = 1000 60: dr-tau = 0 60: nstdisreout = 100 60: orire-fc = 0 60: orire-tau = 0 60: nstorireout = 100 60: free-energy = no 60: cos-acceleration = 0 60: deform (3x3): 60: deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: simulated-tempering = false 60: swapcoords = no 60: userint1 = 0 60: userint2 = 0 60: userint3 = 0 60: userint4 = 0 60: userreal1 = 0 60: userreal2 = 0 60: userreal3 = 0 60: userreal4 = 0 60: applied-forces: 60: electric-field: 60: x: 60: E0 = 0 60: omega = 0 60: t0 = 0 60: sigma = 0 60: y: 60: E0 = 0 60: omega = 0 60: t0 = 0 60: sigma = 0 60: z: 60: E0 = 0 60: omega = 0 60: t0 = 0 60: sigma = 0 60: density-guided-simulation: 60: active = false 60: group = protein 60: similarity-measure = inner-product 60: atom-spreading-weight = unity 60: force-constant = 1e+09 60: gaussian-transform-spreading-width = 0.2 60: gaussian-transform-spreading-range-in-multiples-of-width = 4 60: reference-density-filename = reference.mrc 60: nst = 1 60: normalize-densities = true 60: adaptive-force-scaling = false 60: adaptive-force-scaling-time-constant = 4 60: shift-vector = 60: transformation-matrix = 60: qmmm-cp2k: 60: active = false 60: qmgroup = System 60: qmmethod = PBE 60: qmfilenames = 60: qmcharge = 0 60: qmmultiplicity = 1 60: colvars: 60: active = false 60: configfile = 60: seed = -1 60: nnpot: 60: active = false 60: modelfile = model.pt 60: input-group = System 60: model-input1 = 60: model-input2 = 60: model-input3 = 60: model-input4 = 60: grpopts: 60: nrdf: 465 60: ref-t: 0 60: tau-t: 0 60: annealing: No 60: annealing-npoints: 0 60: acc: 0 0 0 60: nfreeze: N N N 60: energygrp-flags[ 0]: 0 60: header: 60: bIr = present 60: bBox = present 60: bTop = present 60: bX = present 60: bV = present 60: bF = not present 60: natoms = 156 60: lambda = 0.000000e+00 60: buffer size = 57082 60: topology: 60: name="First 10 residues from 1AKI" 60: #atoms = 156 60: #molblock = 1 60: molblock (0): 60: moltype = 0 "Protein_chain_B" 60: #molecules = 1 60: #posres_xA = 0 60: #posres_xB = 0 60: bIntermolecularInteractions = false 60: ffparams: 60: atnr=10 60: ntypes=212 60: functype[0]=LJ_SR, c6= 3.35274678e-03, c12= 3.95094442e-06 60: functype[1]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[2]=LJ_SR, c6= 2.60916961e-03, c12= 3.84022374e-06 60: functype[3]=LJ_SR, c6= 6.41072082e-04, c12= 3.43856290e-07 60: functype[4]=LJ_SR, c6= 4.04775915e-03, c12= 7.32754594e-06 60: functype[5]=LJ_SR, c6= 2.81521126e-03, c12= 2.50631820e-06 60: functype[6]=LJ_SR, c6= 2.80388560e-03, c12= 4.30621225e-06 60: functype[7]=LJ_SR, c6= 5.81477529e-04, c12= 2.82897505e-07 60: functype[8]=LJ_SR, c6= 6.03335344e-04, c12= 2.35915461e-07 60: functype[9]=LJ_SR, c6= 7.20490366e-03, c12= 1.15394674e-05 60: functype[10]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[11]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[12]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[13]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[14]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[15]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[16]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[17]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[18]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[19]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[20]=LJ_SR, c6= 2.60916961e-03, c12= 3.84022374e-06 60: functype[21]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[22]=LJ_SR, c6= 2.03050409e-03, c12= 3.73260587e-06 60: functype[23]=LJ_SR, c6= 4.98894161e-04, c12= 3.34220112e-07 60: functype[24]=LJ_SR, c6= 3.15004110e-03, c12= 7.12219987e-06 60: functype[25]=LJ_SR, c6= 2.19084952e-03, c12= 2.43608151e-06 60: functype[26]=LJ_SR, c6= 2.18203568e-03, c12= 4.18553559e-06 60: functype[27]=LJ_SR, c6= 4.52516577e-04, c12= 2.74969627e-07 60: functype[28]=LJ_SR, c6= 4.69526733e-04, c12= 2.29304201e-07 60: functype[29]=LJ_SR, c6= 5.60698940e-03, c12= 1.12160870e-05 60: functype[30]=LJ_SR, c6= 6.41072082e-04, c12= 3.43856290e-07 60: functype[31]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[32]=LJ_SR, c6= 4.98894161e-04, c12= 3.34220112e-07 60: functype[33]=LJ_SR, c6= 1.22578125e-04, c12= 2.99263000e-08 60: functype[34]=LJ_SR, c6= 7.73964023e-04, c12= 6.37726703e-07 60: functype[35]=LJ_SR, c6= 5.38290978e-04, c12= 2.18128423e-07 60: functype[36]=LJ_SR, c6= 5.36125420e-04, c12= 3.74775753e-07 60: functype[37]=LJ_SR, c6= 1.11183168e-04, c12= 2.46209706e-08 60: functype[38]=LJ_SR, c6= 1.15362558e-04, c12= 2.05320568e-08 60: functype[39]=LJ_SR, c6= 1.37763538e-03, c12= 1.00429619e-06 60: functype[40]=LJ_SR, c6= 4.04775915e-03, c12= 7.32754594e-06 60: functype[41]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[42]=LJ_SR, c6= 3.15004110e-03, c12= 7.12219987e-06 60: functype[43]=LJ_SR, c6= 7.73964023e-04, c12= 6.37726703e-07 60: functype[44]=LJ_SR, c6= 4.88684509e-03, c12= 1.35898974e-05 60: functype[45]=LJ_SR, c6= 3.39879445e-03, c12= 4.64829665e-06 60: functype[46]=LJ_SR, c6= 3.38512102e-03, c12= 7.98643684e-06 60: functype[47]=LJ_SR, c6= 7.02015733e-04, c12= 5.24670621e-07 60: functype[48]=LJ_SR, c6= 7.28404594e-04, c12= 4.37536244e-07 60: functype[49]=LJ_SR, c6= 8.69845432e-03, c12= 2.14014596e-05 60: functype[50]=LJ_SR, c6= 2.81521126e-03, c12= 2.50631820e-06 60: functype[51]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[52]=LJ_SR, c6= 2.19084952e-03, c12= 2.43608151e-06 60: functype[53]=LJ_SR, c6= 5.38290978e-04, c12= 2.18128423e-07 60: functype[54]=LJ_SR, c6= 3.39879445e-03, c12= 4.64829665e-06 60: functype[55]=LJ_SR, c6= 2.36385715e-03, c12= 1.58990617e-06 60: functype[56]=LJ_SR, c6= 2.35434729e-03, c12= 2.73168564e-06 60: functype[57]=LJ_SR, c6= 4.88251036e-04, c12= 1.79458653e-07 60: functype[58]=LJ_SR, c6= 5.06604455e-04, c12= 1.49655159e-07 60: functype[59]=LJ_SR, c6= 6.04976375e-03, c12= 7.32016804e-06 60: functype[60]=LJ_SR, c6= 2.80388560e-03, c12= 4.30621225e-06 60: functype[61]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[62]=LJ_SR, c6= 2.18203568e-03, c12= 4.18553559e-06 60: functype[63]=LJ_SR, c6= 5.36125420e-04, c12= 3.74775753e-07 60: functype[64]=LJ_SR, c6= 3.38512102e-03, c12= 7.98643684e-06 60: functype[65]=LJ_SR, c6= 2.35434729e-03, c12= 2.73168564e-06 60: functype[66]=LJ_SR, c6= 2.34487570e-03, c12= 4.69342567e-06 60: functype[67]=LJ_SR, c6= 4.86286790e-04, c12= 3.08335570e-07 60: functype[68]=LJ_SR, c6= 5.04566372e-04, c12= 2.57128914e-07 60: functype[69]=LJ_SR, c6= 6.02542540e-03, c12= 1.25770931e-05 60: functype[70]=LJ_SR, c6= 5.81477529e-04, c12= 2.82897505e-07 60: functype[71]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[72]=LJ_SR, c6= 4.52516577e-04, c12= 2.74969627e-07 60: functype[73]=LJ_SR, c6= 1.11183168e-04, c12= 2.46209706e-08 60: functype[74]=LJ_SR, c6= 7.02015733e-04, c12= 5.24670621e-07 60: functype[75]=LJ_SR, c6= 4.88251036e-04, c12= 1.79458653e-07 60: functype[76]=LJ_SR, c6= 4.86286790e-04, c12= 3.08335570e-07 60: functype[77]=LJ_SR, c6= 1.00847496e-04, c12= 2.02561691e-08 60: functype[78]=LJ_SR, c6= 1.04638366e-04, c12= 1.68921372e-08 60: functype[79]=LJ_SR, c6= 1.24956934e-03, c12= 8.26254733e-07 60: functype[80]=LJ_SR, c6= 6.03335344e-04, c12= 2.35915461e-07 60: functype[81]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[82]=LJ_SR, c6= 4.69526733e-04, c12= 2.29304201e-07 60: functype[83]=LJ_SR, c6= 1.15362558e-04, c12= 2.05320568e-08 60: functype[84]=LJ_SR, c6= 7.28404594e-04, c12= 4.37536244e-07 60: functype[85]=LJ_SR, c6= 5.06604455e-04, c12= 1.49655159e-07 60: functype[86]=LJ_SR, c6= 5.04566372e-04, c12= 2.57128914e-07 60: functype[87]=LJ_SR, c6= 1.04638366e-04, c12= 1.68921372e-08 60: functype[88]=LJ_SR, c6= 1.08571736e-04, c12= 1.40867851e-08 60: functype[89]=LJ_SR, c6= 1.29654081e-03, c12= 6.89034944e-07 60: functype[90]=LJ_SR, c6= 7.20490366e-03, c12= 1.15394674e-05 60: functype[91]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[92]=LJ_SR, c6= 5.60698940e-03, c12= 1.12160870e-05 60: functype[93]=LJ_SR, c6= 1.37763538e-03, c12= 1.00429619e-06 60: functype[94]=LJ_SR, c6= 8.69845432e-03, c12= 2.14014596e-05 60: functype[95]=LJ_SR, c6= 6.04976375e-03, c12= 7.32016804e-06 60: functype[96]=LJ_SR, c6= 6.02542540e-03, c12= 1.25770931e-05 60: functype[97]=LJ_SR, c6= 1.24956934e-03, c12= 8.26254733e-07 60: functype[98]=LJ_SR, c6= 1.29654081e-03, c12= 6.89034944e-07 60: functype[99]=LJ_SR, c6= 1.54830174e-02, c12= 3.37031588e-05 60: functype[100]=BONDS, b0A= 1.01000e-01, cbA= 3.63171e+05, b0B= 1.01000e-01, cbB= 3.63171e+05 60: functype[101]=BONDS, b0A= 1.47100e-01, cbA= 3.07106e+05, b0B= 1.47100e-01, cbB= 3.07106e+05 60: functype[102]=BONDS, b0A= 1.09000e-01, cbA= 2.84512e+05, b0B= 1.09000e-01, cbB= 2.84512e+05 60: functype[103]=BONDS, b0A= 1.52900e-01, cbA= 2.24262e+05, b0B= 1.52900e-01, cbB= 2.24262e+05 60: functype[104]=BONDS, b0A= 1.52200e-01, cbA= 2.65266e+05, b0B= 1.52200e-01, cbB= 2.65266e+05 60: functype[105]=BONDS, b0A= 1.22900e-01, cbA= 4.76976e+05, b0B= 1.22900e-01, cbB= 4.76976e+05 60: functype[106]=BONDS, b0A= 1.33500e-01, cbA= 4.10032e+05, b0B= 1.33500e-01, cbB= 4.10032e+05 60: functype[107]=BONDS, b0A= 1.44900e-01, cbA= 2.82002e+05, b0B= 1.44900e-01, cbB= 2.82002e+05 60: functype[108]=BONDS, b0A= 1.51000e-01, cbA= 2.65266e+05, b0B= 1.51000e-01, cbB= 2.65266e+05 60: functype[109]=BONDS, b0A= 1.40000e-01, cbA= 3.92459e+05, b0B= 1.40000e-01, cbB= 3.92459e+05 60: functype[110]=BONDS, b0A= 1.08000e-01, cbA= 3.07106e+05, b0B= 1.08000e-01, cbB= 3.07106e+05 60: functype[111]=BONDS, b0A= 1.46300e-01, cbA= 2.82002e+05, b0B= 1.46300e-01, cbB= 2.82002e+05 60: functype[112]=BONDS, b0A= 1.34000e-01, cbA= 4.02501e+05, b0B= 1.34000e-01, cbB= 4.02501e+05 60: functype[113]=BONDS, b0A= 1.81000e-01, cbA= 1.85770e+05, b0B= 1.81000e-01, cbB= 1.85770e+05 60: functype[114]=BONDS, b0A= 1.33600e-01, cbA= 2.29283e+05, b0B= 1.33600e-01, cbB= 2.29283e+05 60: functype[115]=BONDS, b0A= 1.25000e-01, cbA= 5.48941e+05, b0B= 1.25000e-01, cbB= 5.48941e+05 60: functype[116]=ANGLES, thA= 1.09500e+02, ctA= 2.92880e+02, thB= 1.09500e+02, ctB= 2.92880e+02 60: functype[117]=ANGLES, thA= 1.11200e+02, ctA= 6.69440e+02, thB= 1.11200e+02, ctB= 6.69440e+02 60: functype[118]=ANGLES, thA= 1.10700e+02, ctA= 3.13800e+02, thB= 1.10700e+02, ctB= 3.13800e+02 60: functype[119]=ANGLES, thA= 1.11100e+02, ctA= 5.27184e+02, thB= 1.11100e+02, ctB= 5.27184e+02 60: functype[120]=ANGLES, thA= 1.12700e+02, ctA= 4.88273e+02, thB= 1.12700e+02, ctB= 4.88273e+02 60: functype[121]=ANGLES, thA= 1.07800e+02, ctA= 2.76144e+02, thB= 1.07800e+02, ctB= 2.76144e+02 60: functype[122]=ANGLES, thA= 1.20400e+02, ctA= 6.69440e+02, thB= 1.20400e+02, ctB= 6.69440e+02 60: functype[123]=ANGLES, thA= 1.16600e+02, ctA= 5.85760e+02, thB= 1.16600e+02, ctB= 5.85760e+02 60: functype[124]=ANGLES, thA= 1.22900e+02, ctA= 6.69440e+02, thB= 1.22900e+02, ctB= 6.69440e+02 60: functype[125]=ANGLES, thA= 1.19800e+02, ctA= 2.92880e+02, thB= 1.19800e+02, ctB= 2.92880e+02 60: functype[126]=ANGLES, thA= 1.21900e+02, ctA= 4.18400e+02, thB= 1.21900e+02, ctB= 4.18400e+02 60: functype[127]=ANGLES, thA= 1.18400e+02, ctA= 3.17984e+02, thB= 1.18400e+02, ctB= 3.17984e+02 60: functype[128]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09700e+02, ctB= 6.69440e+02 60: functype[129]=ANGLES, thA= 1.10100e+02, ctA= 5.27184e+02, thB= 1.10100e+02, ctB= 5.27184e+02 60: functype[130]=ANGLES, thA= 1.14000e+02, ctA= 5.27184e+02, thB= 1.14000e+02, ctB= 5.27184e+02 60: functype[131]=ANGLES, thA= 1.20000e+02, ctA= 5.85760e+02, thB= 1.20000e+02, ctB= 5.85760e+02 60: functype[132]=ANGLES, thA= 1.20000e+02, ctA= 5.27184e+02, thB= 1.20000e+02, ctB= 5.27184e+02 60: functype[133]=ANGLES, thA= 1.20000e+02, ctA= 2.92880e+02, thB= 1.20000e+02, ctB= 2.92880e+02 60: functype[134]=ANGLES, thA= 1.18400e+02, ctA= 2.92880e+02, thB= 1.18400e+02, ctB= 2.92880e+02 60: functype[135]=ANGLES, thA= 1.23200e+02, ctA= 4.18400e+02, thB= 1.23200e+02, ctB= 4.18400e+02 60: functype[136]=ANGLES, thA= 1.08600e+02, ctA= 4.18400e+02, thB= 1.08600e+02, ctB= 4.18400e+02 60: functype[137]=ANGLES, thA= 9.60000e+01, ctA= 3.68192e+02, thB= 9.60000e+01, ctB= 3.68192e+02 60: functype[138]=ANGLES, thA= 1.17000e+02, ctA= 5.85760e+02, thB= 1.17000e+02, ctB= 5.85760e+02 60: functype[139]=ANGLES, thA= 1.26000e+02, ctA= 6.69440e+02, thB= 1.26000e+02, ctB= 6.69440e+02 60: functype[140]=PDIHS, phiA= 1.80000000e+02, cpA= 4.39320000e+01, phiB= 1.80000000e+02, cpB= 4.39320000e+01, mult=2 60: functype[141]=PDIHS, phiA= 1.80000000e+02, cpA= 4.18400000e+00, phiB= 1.80000000e+02, cpB= 4.18400000e+00, mult=2 60: functype[142]=PDIHS, phiA= 1.80000000e+02, cpA= 4.60240000e+00, phiB= 1.80000000e+02, cpB= 4.60240000e+00, mult=2 60: functype[143]=RBDIHS, rbcA[0]= 5.46010000e-01, rbcA[1]= 1.63803000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.18405000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 5.46010000e-01, rbcB[1]= 1.63803000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.18405000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[144]=RBDIHS, rbcA[0]= 7.25920000e-01, rbcA[1]= 2.17777000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.90370000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 7.25920000e-01, rbcB[1]= 2.17777000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.90370000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[145]=RBDIHS, rbcA[0]= 1.27612000e+00, rbcA[1]= 1.16734000e+00, rbcA[2]= 8.95380000e-01, rbcA[3]=-3.33884000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 1.27612000e+00, rbcB[1]= 1.16734000e+00, rbcB[2]= 8.95380000e-01, rbcB[3]=-3.33884000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[146]=RBDIHS, rbcA[0]=-6.91824000e+00, rbcA[1]= 4.67562000e+00, rbcA[2]= 2.24262000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-6.91824000e+00, rbcB[1]= 4.67562000e+00, rbcB[2]= 2.24262000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[147]=RBDIHS, rbcA[0]= 9.70690000e-01, rbcA[1]= 2.91206000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.88275000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 9.70690000e-01, rbcB[1]= 2.91206000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.88275000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[148]=RBDIHS, rbcA[0]= 6.27600000e-01, rbcA[1]= 1.88280000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.51040000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 6.27600000e-01, rbcB[1]= 1.88280000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.51040000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[149]=RBDIHS, rbcA[0]=-1.58990000e-01, rbcA[1]=-4.76980000e-01, rbcA[2]= 0.00000000e+00, rbcA[3]= 6.35960000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-1.58990000e-01, rbcB[1]=-4.76980000e-01, rbcB[2]= 0.00000000e+00, rbcB[3]= 6.35960000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[150]=RBDIHS, rbcA[0]= 1.03637600e+01, rbcA[1]=-6.60654000e+00, rbcA[2]=-1.04934700e+01, rbcA[3]= 6.73624000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 1.03637600e+01, rbcB[1]=-6.60654000e+00, rbcB[2]=-1.04934700e+01, rbcB[3]= 6.73624000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[151]=RBDIHS, rbcA[0]= 5.00825000e+00, rbcA[1]=-1.69870000e+00, rbcA[2]=-3.72380000e-01, rbcA[3]=-2.93716000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 5.00825000e+00, rbcB[1]=-1.69870000e+00, rbcB[2]=-3.72380000e-01, rbcB[3]=-2.93716000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[152]=RBDIHS, rbcA[0]= 2.92880000e+00, rbcA[1]=-1.46440000e+00, rbcA[2]= 2.09200000e-01, rbcA[3]=-1.67360000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 2.92880000e+00, rbcB[1]=-1.46440000e+00, rbcB[2]= 2.09200000e-01, rbcB[3]=-1.67360000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[153]=RBDIHS, rbcA[0]= 5.77183000e+00, rbcA[1]=-2.67148000e+00, rbcA[2]= 9.58140000e-01, rbcA[3]=-4.05848000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 5.77183000e+00, rbcB[1]=-2.67148000e+00, rbcB[2]= 9.58140000e-01, rbcB[3]=-4.05848000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[154]=RBDIHS, rbcA[0]= 8.03330000e-01, rbcA[1]= 2.40999000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.21331000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 8.03330000e-01, rbcB[1]= 2.40999000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.21331000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[155]=RBDIHS, rbcA[0]= 2.05016000e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.05016000e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 2.05016000e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.05016000e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[156]=RBDIHS, rbcA[0]= 3.02879800e+01, rbcA[1]=-4.81160000e+00, rbcA[2]=-2.54763800e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 3.02879800e+01, rbcB[1]=-4.81160000e+00, rbcB[2]=-2.54763800e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[157]=RBDIHS, rbcA[0]= 2.54763800e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.54763800e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 2.54763800e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.54763800e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[158]=RBDIHS, rbcA[0]= 1.57025500e+01, rbcA[1]= 3.17565600e+01, rbcA[2]=-3.66936000e+00, rbcA[3]=-4.37897500e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 1.57025500e+01, rbcB[1]= 3.17565600e+01, rbcB[2]=-3.66936000e+00, rbcB[3]=-4.37897500e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[159]=RBDIHS, rbcA[0]=-1.03574900e+01, rbcA[1]=-2.95871600e+01, rbcA[2]=-1.16734000e+00, rbcA[3]= 4.11119900e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-1.03574900e+01, rbcB[1]=-2.95871600e+01, rbcB[2]=-1.16734000e+00, rbcB[3]= 4.11119900e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[160]=RBDIHS, rbcA[0]= 4.50199000e+00, rbcA[1]= 7.82410000e-01, rbcA[2]=-1.60247000e+00, rbcA[3]=-3.68192000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 4.50199000e+00, rbcB[1]= 7.82410000e-01, rbcB[2]=-1.60247000e+00, rbcB[3]=-3.68192000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[161]=RBDIHS, rbcA[0]= 4.22590000e-01, rbcA[1]= 2.70705000e+00, rbcA[2]=-3.12964000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 4.22590000e-01, rbcB[1]= 2.70705000e+00, rbcB[2]=-3.12964000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[162]=RBDIHS, rbcA[0]=-7.65670000e-01, rbcA[1]= 2.70705000e+00, rbcA[2]= 4.02501000e+00, rbcA[3]=-5.96639000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-7.65670000e-01, rbcB[1]= 2.70705000e+00, rbcB[2]= 4.02501000e+00, rbcB[3]=-5.96639000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[163]=RBDIHS, rbcA[0]= 9.66500000e-01, rbcA[1]= 2.89951000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.86601000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 9.66500000e-01, rbcB[1]= 2.89951000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.86601000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[164]=RBDIHS, rbcA[0]=-4.23421000e+00, rbcA[1]= 7.22159000e+00, rbcA[2]= 1.90790000e+00, rbcA[3]=-4.89528000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-4.23421000e+00, rbcB[1]= 7.22159000e+00, rbcB[2]= 1.90790000e+00, rbcB[3]=-4.89528000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[165]=RBDIHS, rbcA[0]= 3.03340000e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.03340000e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 3.03340000e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.03340000e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[166]=RBDIHS, rbcA[0]= 1.02319700e+01, rbcA[1]= 3.52083000e+00, rbcA[2]=-3.97899000e+00, rbcA[3]=-9.77382000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 1.02319700e+01, rbcB[1]= 3.52083000e+00, rbcB[2]=-3.97899000e+00, rbcB[3]=-9.77382000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[167]=RBDIHS, rbcA[0]= 5.49778000e+00, rbcA[1]= 1.41838000e+00, rbcA[2]=-6.91615000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 5.49778000e+00, rbcB[1]= 1.41838000e+00, rbcB[2]=-6.91615000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[168]=RBDIHS, rbcA[0]=-1.21755000e+00, rbcA[1]=-3.65264000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 4.87018000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-1.21755000e+00, rbcB[1]=-3.65264000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 4.87018000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[169]=RBDIHS, rbcA[0]=-1.26775000e+00, rbcA[1]= 3.02085000e+00, rbcA[2]= 1.74473000e+00, rbcA[3]=-3.49782000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-1.26775000e+00, rbcB[1]= 3.02085000e+00, rbcB[2]= 1.74473000e+00, rbcB[3]=-3.49782000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[170]=RBDIHS, rbcA[0]= 3.80117000e+00, rbcA[1]=-6.95172000e+00, rbcA[2]=-1.01671000e+00, rbcA[3]= 4.16726000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 3.80117000e+00, rbcB[1]=-6.95172000e+00, rbcB[2]=-1.01671000e+00, rbcB[3]= 4.16726000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[171]=RBDIHS, rbcA[0]= 3.70280000e-01, rbcA[1]= 1.11086000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-1.48114000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 3.70280000e-01, rbcB[1]= 1.11086000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-1.48114000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[172]=RBDIHS, rbcA[0]= 3.32042200e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.32042200e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 3.32042200e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.32042200e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[173]=RBDIHS, rbcA[0]= 1.63176000e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-1.63176000e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 1.63176000e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-1.63176000e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[174]=RBDIHS, rbcA[0]= 3.40787000e+00, rbcA[1]=-2.80537000e+00, rbcA[2]=-3.59820000e-01, rbcA[3]=-2.42670000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 3.40787000e+00, rbcB[1]=-2.80537000e+00, rbcB[2]=-3.59820000e-01, rbcB[3]=-2.42670000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[175]=RBDIHS, rbcA[0]=-1.62590200e+01, rbcA[1]= 9.08765000e+00, rbcA[2]= 7.17138000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-1.62590200e+01, rbcB[1]= 9.08765000e+00, rbcB[2]= 7.17138000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[176]=RBDIHS, rbcA[0]= 9.45590000e-01, rbcA[1]= 2.83675000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.78234000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 9.45590000e-01, rbcB[1]= 2.83675000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.78234000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[177]=RBDIHS, rbcA[0]=-1.50624000e+00, rbcA[1]= 5.37225000e+00, rbcA[2]= 1.17989000e+00, rbcA[3]=-5.04590000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-1.50624000e+00, rbcB[1]= 5.37225000e+00, rbcB[2]= 1.17989000e+00, rbcB[3]=-5.04590000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[178]=RBDIHS, rbcA[0]= 1.00416000e+00, rbcA[1]= 3.01248000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-4.01664000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 1.00416000e+00, rbcB[1]= 3.01248000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-4.01664000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[179]=RBDIHS, rbcA[0]= 8.79268000e+00, rbcA[1]=-1.18344400e+01, rbcA[2]= 1.07529000e+00, rbcA[3]= 1.96648000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 8.79268000e+00, rbcB[1]=-1.18344400e+01, rbcB[2]= 1.07529000e+00, rbcB[3]= 1.96648000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[180]=RBDIHS, rbcA[0]=-5.77392000e+00, rbcA[1]= 3.38485000e+00, rbcA[2]= 2.38906000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-5.77392000e+00, rbcB[1]= 3.38485000e+00, rbcB[2]= 2.38906000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[181]=RBDIHS, rbcA[0]=-9.08346000e+00, rbcA[1]= 9.75709000e+00, rbcA[2]= 3.45180000e+00, rbcA[3]=-4.12542000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-9.08346000e+00, rbcB[1]= 9.75709000e+00, rbcB[2]= 3.45180000e+00, rbcB[3]=-4.12542000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[182]=RBDIHS, rbcA[0]=-4.70700000e-01, rbcA[1]=-1.41210000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 1.88280000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-4.70700000e-01, rbcB[1]=-1.41210000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 1.88280000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[183]=RBDIHS, rbcA[0]= 3.43088000e+00, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.43088000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 3.43088000e+00, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.43088000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[184]=RBDIHS, rbcA[0]= 2.57316000e+00, rbcA[1]= 3.49782000e+00, rbcA[2]=-1.10039000e+00, rbcA[3]=-4.97059000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 2.57316000e+00, rbcB[1]= 3.49782000e+00, rbcB[2]=-1.10039000e+00, rbcB[3]=-4.97059000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[185]=RBDIHS, rbcA[0]=-8.22160000e-01, rbcA[1]= 1.12759000e+00, rbcA[2]=-3.05440000e-01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-8.22160000e-01, rbcB[1]= 1.12759000e+00, rbcB[2]=-3.05440000e-01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[186]=LJ14, c6A= 3.20536041e-04, c12A= 1.71928145e-07, c6B= 3.20536041e-04, c12B= 1.71928145e-07 60: functype[187]=LJ14, c6A= 1.30458481e-03, c12A= 1.92011187e-06, c6B= 1.30458481e-03, c12B= 1.92011187e-06 60: functype[188]=LJ14, c6A= 1.40760563e-03, c12A= 1.25315910e-06, c6B= 1.40760563e-03, c12B= 1.25315910e-06 60: functype[189]=LJ14, c6A= 1.67637339e-03, c12A= 1.97547221e-06, c6B= 1.67637339e-03, c12B= 1.97547221e-06 60: functype[190]=LJ14, c6A= 0.00000000e+00, c12A= 0.00000000e+00, c6B= 0.00000000e+00, c12B= 0.00000000e+00 60: functype[191]=LJ14, c6A= 2.49447081e-04, c12A= 1.67110056e-07, c6B= 2.49447081e-04, c12B= 1.67110056e-07 60: functype[192]=LJ14, c6A= 1.01525205e-03, c12A= 1.86630294e-06, c6B= 1.01525205e-03, c12B= 1.86630294e-06 60: functype[193]=LJ14, c6A= 6.12890625e-05, c12A= 1.49631500e-08, c6B= 6.12890625e-05, c12B= 1.49631500e-08 60: functype[194]=LJ14, c6A= 2.69145489e-04, c12A= 1.09064212e-07, c6B= 2.69145489e-04, c12B= 1.09064212e-07 60: functype[195]=LJ14, c6A= 1.09542476e-03, c12A= 1.21804075e-06, c6B= 1.09542476e-03, c12B= 1.21804075e-06 60: functype[196]=LJ14, c6A= 3.86982011e-04, c12A= 3.18863352e-07, c6B= 3.86982011e-04, c12B= 3.18863352e-07 60: functype[197]=LJ14, c6A= 1.57502055e-03, c12A= 3.56109993e-06, c6B= 1.57502055e-03, c12B= 3.56109993e-06 60: functype[198]=LJ14, c6A= 2.44342255e-03, c12A= 6.79494872e-06, c6B= 2.44342255e-03, c12B= 6.79494872e-06 60: functype[199]=LJ14, c6A= 1.40194280e-03, c12A= 2.15310613e-06, c6B= 1.40194280e-03, c12B= 2.15310613e-06 60: functype[200]=LJ14, c6A= 1.09101784e-03, c12A= 2.09276780e-06, c6B= 1.09101784e-03, c12B= 2.09276780e-06 60: functype[201]=LJ14, c6A= 2.68062710e-04, c12A= 1.87387876e-07, c6B= 2.68062710e-04, c12B= 1.87387876e-07 60: functype[202]=LJ14, c6A= 2.26258289e-04, c12A= 1.37484813e-07, c6B= 2.26258289e-04, c12B= 1.37484813e-07 60: functype[203]=LJ14, c6A= 2.43143395e-04, c12A= 1.54167785e-07, c6B= 2.43143395e-04, c12B= 1.54167785e-07 60: functype[204]=LJ14, c6A= 1.17243785e-03, c12A= 2.34671283e-06, c6B= 1.17243785e-03, c12B= 2.34671283e-06 60: functype[205]=LJ14, c6A= 1.69256051e-03, c12A= 3.99321842e-06, c6B= 1.69256051e-03, c12B= 3.99321842e-06 60: functype[206]=LJ14, c6A= 5.04237478e-05, c12A= 1.01280845e-08, c6B= 5.04237478e-05, c12B= 1.01280845e-08 60: functype[207]=LJ14, c6A= 2.34763367e-04, c12A= 1.14652101e-07, c6B= 2.34763367e-04, c12B= 1.14652101e-07 60: functype[208]=LJ14, c6A= 5.76812790e-05, c12A= 1.02660284e-08, c6B= 5.76812790e-05, c12B= 1.02660284e-08 60: functype[209]=LJ14, c6A= 3.60245183e-03, c12A= 5.76973368e-06, c6B= 3.60245183e-03, c12B= 5.76973368e-06 60: functype[210]=LJ14, c6A= 6.88817690e-04, c12A= 5.02148096e-07, c6B= 6.88817690e-04, c12B= 5.02148096e-07 60: functype[211]=LJ14, c6A= 4.34922716e-03, c12A= 1.07007298e-05, c6B= 4.34922716e-03, c12B= 1.07007298e-05 60: reppow = 12 60: fudgeQQ = 0.5 60: cmap 60: moltype (0): 60: name="Protein_chain_B" 60: atoms: 60: atom (156): 60: atom[ 0]={type= 0, typeB= 0, ptype= Atom, m= 1.40027e+01, q=-3.00000e-01, mB= 1.40027e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} 60: atom[ 1]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 60: atom[ 2]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 60: atom[ 3]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 60: atom[ 4]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 2.50000e-01, mB= 1.20110e+01, qB= 2.50000e-01, resind= 0, atomnumber= 6} 60: atom[ 5]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 60: atom[ 6]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 60: atom[ 7]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 60: atom[ 8]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 60: atom[ 9]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 60: atom[ 10]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 60: atom[ 11]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 60: atom[ 12]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 60: atom[ 13]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 60: atom[ 14]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 60: atom[ 15]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 0, atomnumber= 6} 60: atom[ 16]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 60: atom[ 17]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 60: atom[ 18]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-3.00000e-01, mB= 1.40067e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} 60: atom[ 19]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 60: atom[ 20]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 60: atom[ 21]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 60: atom[ 22]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 0, atomnumber= 6} 60: atom[ 23]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 0, atomnumber= 8} 60: atom[ 24]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 1, atomnumber= 7} 60: atom[ 25]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 1, atomnumber= 1} 60: atom[ 26]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 1, atomnumber= 6} 60: atom[ 27]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 60: atom[ 28]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 1, atomnumber= 6} 60: atom[ 29]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 60: atom[ 30]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} 60: atom[ 31]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 60: atom[ 32]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 60: atom[ 33]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 60: atom[ 34]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} 60: atom[ 35]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 60: atom[ 36]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 60: atom[ 37]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 60: atom[ 38]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 1, atomnumber= 6} 60: atom[ 39]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 1, atomnumber= 8} 60: atom[ 40]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 2, atomnumber= 7} 60: atom[ 41]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 2, atomnumber= 1} 60: atom[ 42]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 2, atomnumber= 6} 60: atom[ 43]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 60: atom[ 44]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-03, mB= 1.20110e+01, qB=-5.00000e-03, resind= 2, atomnumber= 6} 60: atom[ 45]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 60: atom[ 46]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 60: atom[ 47]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 60: atom[ 48]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 60: atom[ 49]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 60: atom[ 50]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 60: atom[ 51]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 60: atom[ 52]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 60: atom[ 53]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 60: atom[ 54]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 60: atom[ 55]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 60: atom[ 56]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 60: atom[ 57]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 60: atom[ 58]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 2, atomnumber= 6} 60: atom[ 59]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 2, atomnumber= 8} 60: atom[ 60]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 3, atomnumber= 7} 60: atom[ 61]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 3, atomnumber= 1} 60: atom[ 62]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 8.00000e-02, mB= 1.20110e+01, qB= 8.00000e-02, resind= 3, atomnumber= 6} 60: atom[ 63]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} 60: atom[ 64]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} 60: atom[ 65]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 3, atomnumber= 6} 60: atom[ 66]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 3, atomnumber= 8} 60: atom[ 67]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 4, atomnumber= 7} 60: atom[ 68]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 4, atomnumber= 1} 60: atom[ 69]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 4, atomnumber= 6} 60: atom[ 70]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 60: atom[ 71]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 4, atomnumber= 6} 60: atom[ 72]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 60: atom[ 73]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 60: atom[ 74]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-02, mB= 1.20110e+01, qB=-5.00000e-02, resind= 4, atomnumber= 6} 60: atom[ 75]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 60: atom[ 76]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 60: atom[ 77]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 4, atomnumber= 6} 60: atom[ 78]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 60: atom[ 79]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 60: atom[ 80]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-7.00000e-01, mB= 1.40067e+01, qB=-7.00000e-01, resind= 4, atomnumber= 7} 60: atom[ 81]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.40000e-01, mB= 1.00800e+00, qB= 4.40000e-01, resind= 4, atomnumber= 1} 60: atom[ 82]={type= 8, typeB= 8, ptype= Atom, m= 1.20110e+01, q= 6.40000e-01, mB= 1.20110e+01, qB= 6.40000e-01, resind= 4, atomnumber= 6} 60: atom[ 83]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} 60: atom[ 84]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 60: atom[ 85]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 60: atom[ 86]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} 60: atom[ 87]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 60: atom[ 88]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 60: atom[ 89]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 4, atomnumber= 6} 60: atom[ 90]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 4, atomnumber= 8} 60: atom[ 91]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 5, atomnumber= 7} 60: atom[ 92]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 5, atomnumber= 1} 60: atom[ 93]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 5, atomnumber= 6} 60: atom[ 94]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 60: atom[ 95]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 6.00000e-02, mB= 1.20110e+01, qB= 6.00000e-02, resind= 5, atomnumber= 6} 60: atom[ 96]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 60: atom[ 97]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 60: atom[ 98]={type= 9, typeB= 9, ptype= Atom, m= 3.20600e+01, q=-3.35000e-01, mB= 3.20600e+01, qB=-3.35000e-01, resind= 5, atomnumber= 16} 60: atom[ 99]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 1.55000e-01, mB= 1.00800e+00, qB= 1.55000e-01, resind= 5, atomnumber= 1} 60: atom[ 100]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 5, atomnumber= 6} 60: atom[ 101]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 5, atomnumber= 8} 60: atom[ 102]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 6, atomnumber= 7} 60: atom[ 103]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 6, atomnumber= 1} 60: atom[ 104]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 6, atomnumber= 6} 60: atom[ 105]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 60: atom[ 106]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 6, atomnumber= 6} 60: atom[ 107]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 60: atom[ 108]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 60: atom[ 109]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-2.20000e-01, mB= 1.20110e+01, qB=-2.20000e-01, resind= 6, atomnumber= 6} 60: atom[ 110]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 60: atom[ 111]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 60: atom[ 112]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 7.00000e-01, mB= 1.20110e+01, qB= 7.00000e-01, resind= 6, atomnumber= 6} 60: atom[ 113]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} 60: atom[ 114]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} 60: atom[ 115]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 6, atomnumber= 6} 60: atom[ 116]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 6, atomnumber= 8} 60: atom[ 117]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 7, atomnumber= 7} 60: atom[ 118]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 7, atomnumber= 1} 60: atom[ 119]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 7, atomnumber= 6} 60: atom[ 120]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 60: atom[ 121]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 7, atomnumber= 6} 60: atom[ 122]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 60: atom[ 123]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 60: atom[ 124]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 7, atomnumber= 6} 60: atom[ 125]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 60: atom[ 126]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} 60: atom[ 127]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 60: atom[ 128]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 60: atom[ 129]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 60: atom[ 130]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} 60: atom[ 131]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 60: atom[ 132]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 60: atom[ 133]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 60: atom[ 134]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 7, atomnumber= 6} 60: atom[ 135]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 7, atomnumber= 8} 60: atom[ 136]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 8, atomnumber= 7} 60: atom[ 137]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 8, atomnumber= 1} 60: atom[ 138]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 8, atomnumber= 6} 60: atom[ 139]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 60: atom[ 140]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 8, atomnumber= 6} 60: atom[ 141]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 60: atom[ 142]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 60: atom[ 143]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 60: atom[ 144]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 8, atomnumber= 6} 60: atom[ 145]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 8, atomnumber= 8} 60: atom[ 146]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 9, atomnumber= 7} 60: atom[ 147]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 9, atomnumber= 1} 60: atom[ 148]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 9, atomnumber= 6} 60: atom[ 149]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 60: atom[ 150]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 9, atomnumber= 6} 60: atom[ 151]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 60: atom[ 152]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 60: atom[ 153]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 60: atom[ 154]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 9, atomnumber= 6} 60: atom[ 155]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 9, atomnumber= 8} 60: atom (156): 60: atom[0]={name="N"} 60: atom[1]={name="H1"} 60: atom[2]={name="H2"} 60: atom[3]={name="H3"} 60: atom[4]={name="CA"} 60: atom[5]={name="HA"} 60: atom[6]={name="CB"} 60: atom[7]={name="HB1"} 60: atom[8]={name="HB2"} 60: atom[9]={name="CG"} 60: atom[10]={name="HG1"} 60: atom[11]={name="HG2"} 60: atom[12]={name="CD"} 60: atom[13]={name="HD1"} 60: atom[14]={name="HD2"} 60: atom[15]={name="CE"} 60: atom[16]={name="HE1"} 60: atom[17]={name="HE2"} 60: atom[18]={name="NZ"} 60: atom[19]={name="HZ1"} 60: atom[20]={name="HZ2"} 60: atom[21]={name="HZ3"} 60: atom[22]={name="C"} 60: atom[23]={name="O"} 60: atom[24]={name="N"} 60: atom[25]={name="H"} 60: atom[26]={name="CA"} 60: atom[27]={name="HA"} 60: atom[28]={name="CB"} 60: atom[29]={name="HB"} 60: atom[30]={name="CG1"} 60: atom[31]={name="HG11"} 60: atom[32]={name="HG12"} 60: atom[33]={name="HG13"} 60: atom[34]={name="CG2"} 60: atom[35]={name="HG21"} 60: atom[36]={name="HG22"} 60: atom[37]={name="HG23"} 60: atom[38]={name="C"} 60: atom[39]={name="O"} 60: atom[40]={name="N"} 60: atom[41]={name="H"} 60: atom[42]={name="CA"} 60: atom[43]={name="HA"} 60: atom[44]={name="CB"} 60: atom[45]={name="HB1"} 60: atom[46]={name="HB2"} 60: atom[47]={name="CG"} 60: atom[48]={name="CD1"} 60: atom[49]={name="HD1"} 60: atom[50]={name="CD2"} 60: atom[51]={name="HD2"} 60: atom[52]={name="CE1"} 60: atom[53]={name="HE1"} 60: atom[54]={name="CE2"} 60: atom[55]={name="HE2"} 60: atom[56]={name="CZ"} 60: atom[57]={name="HZ"} 60: atom[58]={name="C"} 60: atom[59]={name="O"} 60: atom[60]={name="N"} 60: atom[61]={name="H"} 60: atom[62]={name="CA"} 60: atom[63]={name="HA1"} 60: atom[64]={name="HA2"} 60: atom[65]={name="C"} 60: atom[66]={name="O"} 60: atom[67]={name="N"} 60: atom[68]={name="H"} 60: atom[69]={name="CA"} 60: atom[70]={name="HA"} 60: atom[71]={name="CB"} 60: atom[72]={name="HB1"} 60: atom[73]={name="HB2"} 60: atom[74]={name="CG"} 60: atom[75]={name="HG1"} 60: atom[76]={name="HG2"} 60: atom[77]={name="CD"} 60: atom[78]={name="HD1"} 60: atom[79]={name="HD2"} 60: atom[80]={name="NE"} 60: atom[81]={name="HE"} 60: atom[82]={name="CZ"} 60: atom[83]={name="NH1"} 60: atom[84]={name="HH11"} 60: atom[85]={name="HH12"} 60: atom[86]={name="NH2"} 60: atom[87]={name="HH21"} 60: atom[88]={name="HH22"} 60: atom[89]={name="C"} 60: atom[90]={name="O"} 60: atom[91]={name="N"} 60: atom[92]={name="H"} 60: atom[93]={name="CA"} 60: atom[94]={name="HA"} 60: atom[95]={name="CB"} 60: atom[96]={name="HB1"} 60: atom[97]={name="HB2"} 60: atom[98]={name="SG"} 60: atom[99]={name="HG"} 60: atom[100]={name="C"} 60: atom[101]={name="O"} 60: atom[102]={name="N"} 60: atom[103]={name="H"} 60: atom[104]={name="CA"} 60: atom[105]={name="HA"} 60: atom[106]={name="CB"} 60: atom[107]={name="HB1"} 60: atom[108]={name="HB2"} 60: atom[109]={name="CG"} 60: atom[110]={name="HG1"} 60: atom[111]={name="HG2"} 60: atom[112]={name="CD"} 60: atom[113]={name="OE1"} 60: atom[114]={name="OE2"} 60: atom[115]={name="C"} 60: atom[116]={name="O"} 60: atom[117]={name="N"} 60: atom[118]={name="H"} 60: atom[119]={name="CA"} 60: atom[120]={name="HA"} 60: atom[121]={name="CB"} 60: atom[122]={name="HB1"} 60: atom[123]={name="HB2"} 60: atom[124]={name="CG"} 60: atom[125]={name="HG"} 60: atom[126]={name="CD1"} 60: atom[127]={name="HD11"} 60: atom[128]={name="HD12"} 60: atom[129]={name="HD13"} 60: atom[130]={name="CD2"} 60: atom[131]={name="HD21"} 60: atom[132]={name="HD22"} 60: atom[133]={name="HD23"} 60: atom[134]={name="C"} 60: atom[135]={name="O"} 60: atom[136]={name="N"} 60: atom[137]={name="H"} 60: atom[138]={name="CA"} 60: atom[139]={name="HA"} 60: atom[140]={name="CB"} 60: atom[141]={name="HB1"} 60: atom[142]={name="HB2"} 60: atom[143]={name="HB3"} 60: atom[144]={name="C"} 60: atom[145]={name="O"} 60: atom[146]={name="N"} 60: atom[147]={name="H"} 60: atom[148]={name="CA"} 60: atom[149]={name="HA"} 60: atom[150]={name="CB"} 60: atom[151]={name="HB1"} 60: atom[152]={name="HB2"} 60: atom[153]={name="HB3"} 60: atom[154]={name="C"} 60: atom[155]={name="O"} 60: type (156): 60: type[0]={name="opls_287",nameB="opls_287"} 60: type[1]={name="opls_290",nameB="opls_290"} 60: type[2]={name="opls_290",nameB="opls_290"} 60: type[3]={name="opls_290",nameB="opls_290"} 60: type[4]={name="opls_293B",nameB="opls_293B"} 60: type[5]={name="opls_140",nameB="opls_140"} 60: type[6]={name="opls_136",nameB="opls_136"} 60: type[7]={name="opls_140",nameB="opls_140"} 60: type[8]={name="opls_140",nameB="opls_140"} 60: type[9]={name="opls_136",nameB="opls_136"} 60: type[10]={name="opls_140",nameB="opls_140"} 60: type[11]={name="opls_140",nameB="opls_140"} 60: type[12]={name="opls_136",nameB="opls_136"} 60: type[13]={name="opls_140",nameB="opls_140"} 60: type[14]={name="opls_140",nameB="opls_140"} 60: type[15]={name="opls_292",nameB="opls_292"} 60: type[16]={name="opls_140",nameB="opls_140"} 60: type[17]={name="opls_140",nameB="opls_140"} 60: type[18]={name="opls_287",nameB="opls_287"} 60: type[19]={name="opls_290",nameB="opls_290"} 60: type[20]={name="opls_290",nameB="opls_290"} 60: type[21]={name="opls_290",nameB="opls_290"} 60: type[22]={name="opls_235",nameB="opls_235"} 60: type[23]={name="opls_236",nameB="opls_236"} 60: type[24]={name="opls_238",nameB="opls_238"} 60: type[25]={name="opls_241",nameB="opls_241"} 60: type[26]={name="opls_224B",nameB="opls_224B"} 60: type[27]={name="opls_140",nameB="opls_140"} 60: type[28]={name="opls_137",nameB="opls_137"} 60: type[29]={name="opls_140",nameB="opls_140"} 60: type[30]={name="opls_135",nameB="opls_135"} 60: type[31]={name="opls_140",nameB="opls_140"} 60: type[32]={name="opls_140",nameB="opls_140"} 60: type[33]={name="opls_140",nameB="opls_140"} 60: type[34]={name="opls_135",nameB="opls_135"} 60: type[35]={name="opls_140",nameB="opls_140"} 60: type[36]={name="opls_140",nameB="opls_140"} 60: type[37]={name="opls_140",nameB="opls_140"} 60: type[38]={name="opls_235",nameB="opls_235"} 60: type[39]={name="opls_236",nameB="opls_236"} 60: type[40]={name="opls_238",nameB="opls_238"} 60: type[41]={name="opls_241",nameB="opls_241"} 60: type[42]={name="opls_224B",nameB="opls_224B"} 60: type[43]={name="opls_140",nameB="opls_140"} 60: type[44]={name="opls_149",nameB="opls_149"} 60: type[45]={name="opls_140",nameB="opls_140"} 60: type[46]={name="opls_140",nameB="opls_140"} 60: type[47]={name="opls_145",nameB="opls_145"} 60: type[48]={name="opls_145",nameB="opls_145"} 60: type[49]={name="opls_146",nameB="opls_146"} 60: type[50]={name="opls_145",nameB="opls_145"} 60: type[51]={name="opls_146",nameB="opls_146"} 60: type[52]={name="opls_145",nameB="opls_145"} 60: type[53]={name="opls_146",nameB="opls_146"} 60: type[54]={name="opls_145",nameB="opls_145"} 60: type[55]={name="opls_146",nameB="opls_146"} 60: type[56]={name="opls_145",nameB="opls_145"} 60: type[57]={name="opls_146",nameB="opls_146"} 60: type[58]={name="opls_235",nameB="opls_235"} 60: type[59]={name="opls_236",nameB="opls_236"} 60: type[60]={name="opls_238",nameB="opls_238"} 60: type[61]={name="opls_241",nameB="opls_241"} 60: type[62]={name="opls_223B",nameB="opls_223B"} 60: type[63]={name="opls_140",nameB="opls_140"} 60: type[64]={name="opls_140",nameB="opls_140"} 60: type[65]={name="opls_235",nameB="opls_235"} 60: type[66]={name="opls_236",nameB="opls_236"} 60: type[67]={name="opls_238",nameB="opls_238"} 60: type[68]={name="opls_241",nameB="opls_241"} 60: type[69]={name="opls_224B",nameB="opls_224B"} 60: type[70]={name="opls_140",nameB="opls_140"} 60: type[71]={name="opls_136",nameB="opls_136"} 60: type[72]={name="opls_140",nameB="opls_140"} 60: type[73]={name="opls_140",nameB="opls_140"} 60: type[74]={name="opls_308",nameB="opls_308"} 60: type[75]={name="opls_140",nameB="opls_140"} 60: type[76]={name="opls_140",nameB="opls_140"} 60: type[77]={name="opls_307",nameB="opls_307"} 60: type[78]={name="opls_140",nameB="opls_140"} 60: type[79]={name="opls_140",nameB="opls_140"} 60: type[80]={name="opls_303",nameB="opls_303"} 60: type[81]={name="opls_304",nameB="opls_304"} 60: type[82]={name="opls_302",nameB="opls_302"} 60: type[83]={name="opls_300",nameB="opls_300"} 60: type[84]={name="opls_301",nameB="opls_301"} 60: type[85]={name="opls_301",nameB="opls_301"} 60: type[86]={name="opls_300",nameB="opls_300"} 60: type[87]={name="opls_301",nameB="opls_301"} 60: type[88]={name="opls_301",nameB="opls_301"} 60: type[89]={name="opls_235",nameB="opls_235"} 60: type[90]={name="opls_236",nameB="opls_236"} 60: type[91]={name="opls_238",nameB="opls_238"} 60: type[92]={name="opls_241",nameB="opls_241"} 60: type[93]={name="opls_224B",nameB="opls_224B"} 60: type[94]={name="opls_140",nameB="opls_140"} 60: type[95]={name="opls_206",nameB="opls_206"} 60: type[96]={name="opls_140",nameB="opls_140"} 60: type[97]={name="opls_140",nameB="opls_140"} 60: type[98]={name="opls_200",nameB="opls_200"} 60: type[99]={name="opls_204",nameB="opls_204"} 60: type[100]={name="opls_235",nameB="opls_235"} 60: type[101]={name="opls_236",nameB="opls_236"} 60: type[102]={name="opls_238",nameB="opls_238"} 60: type[103]={name="opls_241",nameB="opls_241"} 60: type[104]={name="opls_224B",nameB="opls_224B"} 60: type[105]={name="opls_140",nameB="opls_140"} 60: type[106]={name="opls_136",nameB="opls_136"} 60: type[107]={name="opls_140",nameB="opls_140"} 60: type[108]={name="opls_140",nameB="opls_140"} 60: type[109]={name="opls_274",nameB="opls_274"} 60: type[110]={name="opls_140",nameB="opls_140"} 60: type[111]={name="opls_140",nameB="opls_140"} 60: type[112]={name="opls_271",nameB="opls_271"} 60: type[113]={name="opls_272",nameB="opls_272"} 60: type[114]={name="opls_272",nameB="opls_272"} 60: type[115]={name="opls_235",nameB="opls_235"} 60: type[116]={name="opls_236",nameB="opls_236"} 60: type[117]={name="opls_238",nameB="opls_238"} 60: type[118]={name="opls_241",nameB="opls_241"} 60: type[119]={name="opls_224B",nameB="opls_224B"} 60: type[120]={name="opls_140",nameB="opls_140"} 60: type[121]={name="opls_136",nameB="opls_136"} 60: type[122]={name="opls_140",nameB="opls_140"} 60: type[123]={name="opls_140",nameB="opls_140"} 60: type[124]={name="opls_137",nameB="opls_137"} 60: type[125]={name="opls_140",nameB="opls_140"} 60: type[126]={name="opls_135",nameB="opls_135"} 60: type[127]={name="opls_140",nameB="opls_140"} 60: type[128]={name="opls_140",nameB="opls_140"} 60: type[129]={name="opls_140",nameB="opls_140"} 60: type[130]={name="opls_135",nameB="opls_135"} 60: type[131]={name="opls_140",nameB="opls_140"} 60: type[132]={name="opls_140",nameB="opls_140"} 60: type[133]={name="opls_140",nameB="opls_140"} 60: type[134]={name="opls_235",nameB="opls_235"} 60: type[135]={name="opls_236",nameB="opls_236"} 60: type[136]={name="opls_238",nameB="opls_238"} 60: type[137]={name="opls_241",nameB="opls_241"} 60: type[138]={name="opls_224B",nameB="opls_224B"} 60: type[139]={name="opls_140",nameB="opls_140"} 60: type[140]={name="opls_135",nameB="opls_135"} 60: type[141]={name="opls_140",nameB="opls_140"} 60: type[142]={name="opls_140",nameB="opls_140"} 60: type[143]={name="opls_140",nameB="opls_140"} 60: type[144]={name="opls_235",nameB="opls_235"} 60: type[145]={name="opls_236",nameB="opls_236"} 60: type[146]={name="opls_238",nameB="opls_238"} 60: type[147]={name="opls_241",nameB="opls_241"} 60: type[148]={name="opls_224B",nameB="opls_224B"} 60: type[149]={name="opls_140",nameB="opls_140"} 60: type[150]={name="opls_135",nameB="opls_135"} 60: type[151]={name="opls_140",nameB="opls_140"} 60: type[152]={name="opls_140",nameB="opls_140"} 60: type[153]={name="opls_140",nameB="opls_140"} 60: type[154]={name="opls_235",nameB="opls_235"} 60: type[155]={name="opls_236",nameB="opls_236"} 60: residue (10): 60: residue[0]={name="LYS", nr=1, ic=' '} 60: residue[1]={name="VAL", nr=2, ic=' '} 60: residue[2]={name="PHE", nr=3, ic=' '} 60: residue[3]={name="GLY", nr=4, ic=' '} 60: residue[4]={name="ARG", nr=5, ic=' '} 60: residue[5]={name="CYS", nr=6, ic=' '} 60: residue[6]={name="GLU", nr=7, ic=' '} 60: residue[7]={name="LEU", nr=8, ic=' '} 60: residue[8]={name="ALA", nr=9, ic=' '} 60: residue[9]={name="ALA", nr=10, ic=' '} 60: excls: 60: numLists=156 60: numElements=1828 60: excls[0][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} 60: excls[1][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 60: excls[2][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 60: excls[3][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 60: excls[4][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 60: 23, 24, 25, 26} 60: excls[5][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} 60: excls[6][num=19]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 60: 14, 15, 22, 23, 24} 60: excls[7][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} 60: excls[8][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} 60: excls[9][num=17]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 60: 16, 17, 18, 22} 60: excls[10][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} 60: excls[11][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} 60: excls[12][num=17]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 60: 17, 18, 19, 20, 21} 60: excls[13][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} 60: excls[14][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} 60: excls[15][num=14]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 60: 20, 21} 60: excls[16][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 60: excls[17][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 60: excls[18][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 60: excls[19][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 60: excls[20][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 60: excls[21][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 60: excls[22][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 60: 26, 27, 28, 38} 60: excls[23][num=9]={0, 4, 5, 6, 22, 23, 24, 25, 26} 60: excls[24][num=17]={0, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 60: 30, 34, 38, 39, 40} 60: excls[25][num=9]={4, 22, 23, 24, 25, 26, 27, 28, 38} 60: excls[26][num=22]={4, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 60: 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42} 60: excls[27][num=12]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, 60: 40} 60: excls[28][num=18]={22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 60: 34, 35, 36, 37, 38, 39, 40} 60: excls[29][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 60: 36, 37, 38} 60: excls[30][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 60: 36, 37, 38} 60: excls[31][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 60: excls[32][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 60: excls[33][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 60: excls[34][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 60: 36, 37, 38} 60: excls[35][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 60: excls[36][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 60: excls[37][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 60: excls[38][num=17]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, 60: 40, 41, 42, 43, 44, 58} 60: excls[39][num=9]={24, 26, 27, 28, 38, 39, 40, 41, 42} 60: excls[40][num=17]={24, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 60: 45, 46, 47, 58, 59, 60} 60: excls[41][num=9]={26, 38, 39, 40, 41, 42, 43, 44, 58} 60: excls[42][num=18]={26, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 60: 48, 50, 58, 59, 60, 61, 62} 60: excls[43][num=12]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 60: 60} 60: excls[44][num=18]={38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 60: 50, 51, 52, 54, 58, 59, 60} 60: excls[45][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} 60: excls[46][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} 60: excls[47][num=17]={40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 60: 52, 53, 54, 55, 56, 58} 60: excls[48][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 60: 54, 56, 57} 60: excls[49][num=8]={44, 47, 48, 49, 50, 52, 53, 56} 60: excls[50][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 60: 55, 56, 57} 60: excls[51][num=8]={44, 47, 48, 50, 51, 54, 55, 56} 60: excls[52][num=11]={44, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57} 60: excls[53][num=8]={47, 48, 49, 52, 53, 54, 56, 57} 60: excls[54][num=11]={44, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57} 60: excls[55][num=8]={47, 50, 51, 52, 54, 55, 56, 57} 60: excls[56][num=11]={47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57} 60: excls[57][num=8]={48, 50, 52, 53, 54, 55, 56, 57} 60: excls[58][num=17]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 60: 60, 61, 62, 63, 64, 65} 60: excls[59][num=9]={40, 42, 43, 44, 58, 59, 60, 61, 62} 60: excls[60][num=14]={40, 42, 43, 44, 58, 59, 60, 61, 62, 63, 64, 60: 65, 66, 67} 60: excls[61][num=9]={42, 58, 59, 60, 61, 62, 63, 64, 65} 60: excls[62][num=13]={42, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 60: 68, 69} 60: excls[63][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67} 60: excls[64][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67} 60: excls[65][num=14]={58, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 60: 70, 71, 89} 60: excls[66][num=9]={60, 62, 63, 64, 65, 66, 67, 68, 69} 60: excls[67][num=17]={60, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 60: 72, 73, 74, 89, 90, 91} 60: excls[68][num=9]={62, 65, 66, 67, 68, 69, 70, 71, 89} 60: excls[69][num=19]={62, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 60: 75, 76, 77, 89, 90, 91, 92, 93} 60: excls[70][num=12]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, 60: 91} 60: excls[71][num=18]={65, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 60: 77, 78, 79, 80, 89, 90, 91} 60: excls[72][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} 60: excls[73][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} 60: excls[74][num=16]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 60: 79, 80, 81, 82, 89} 60: excls[75][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} 60: excls[76][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} 60: excls[77][num=15]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 60: 81, 82, 83, 86} 60: excls[78][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} 60: excls[79][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} 60: excls[80][num=16]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 60: 84, 85, 86, 87, 88} 60: excls[81][num=9]={74, 77, 78, 79, 80, 81, 82, 83, 86} 60: excls[82][num=13]={74, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 60: 87, 88} 60: excls[83][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} 60: excls[84][num=6]={80, 82, 83, 84, 85, 86} 60: excls[85][num=6]={80, 82, 83, 84, 85, 86} 60: excls[86][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} 60: excls[87][num=6]={80, 82, 83, 86, 87, 88} 60: excls[88][num=6]={80, 82, 83, 86, 87, 88} 60: excls[89][num=17]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, 60: 91, 92, 93, 94, 95, 100} 60: excls[90][num=9]={67, 69, 70, 71, 89, 90, 91, 92, 93} 60: excls[91][num=17]={67, 69, 70, 71, 89, 90, 91, 92, 93, 94, 95, 60: 96, 97, 98, 100, 101, 102} 60: excls[92][num=9]={69, 89, 90, 91, 92, 93, 94, 95, 100} 60: excls[93][num=17]={69, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 60: 99, 100, 101, 102, 103, 104} 60: excls[94][num=12]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101, 60: 102} 60: excls[95][num=13]={89, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 60: 101, 102} 60: excls[96][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 60: excls[97][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 60: excls[98][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 60: excls[99][num=6]={93, 95, 96, 97, 98, 99} 60: excls[100][num=17]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101, 60: 102, 103, 104, 105, 106, 115} 60: excls[101][num=9]={91, 93, 94, 95, 100, 101, 102, 103, 104} 60: excls[102][num=17]={91, 93, 94, 95, 100, 101, 102, 103, 104, 105, 60: 106, 107, 108, 109, 115, 116, 117} 60: excls[103][num=9]={93, 100, 101, 102, 103, 104, 105, 106, 115} 60: excls[104][num=19]={93, 100, 101, 102, 103, 104, 105, 106, 107, 60: 108, 109, 110, 111, 112, 115, 116, 117, 118, 119} 60: excls[105][num=12]={100, 102, 103, 104, 105, 106, 107, 108, 109, 60: 115, 116, 117} 60: excls[106][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109, 60: 110, 111, 112, 113, 114, 115, 116, 117} 60: excls[107][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111, 60: 112, 115} 60: excls[108][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111, 60: 112, 115} 60: excls[109][num=13]={102, 104, 105, 106, 107, 108, 109, 110, 111, 60: 112, 113, 114, 115} 60: excls[110][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 60: 114} 60: excls[111][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 60: 114} 60: excls[112][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 60: 114} 60: excls[113][num=7]={106, 109, 110, 111, 112, 113, 114} 60: excls[114][num=7]={106, 109, 110, 111, 112, 113, 114} 60: excls[115][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109, 60: 115, 116, 117, 118, 119, 120, 121, 134} 60: excls[116][num=9]={102, 104, 105, 106, 115, 116, 117, 118, 119} 60: excls[117][num=17]={102, 104, 105, 106, 115, 116, 117, 118, 119, 60: 120, 121, 122, 123, 124, 134, 135, 136} 60: excls[118][num=9]={104, 115, 116, 117, 118, 119, 120, 121, 134} 60: excls[119][num=19]={104, 115, 116, 117, 118, 119, 120, 121, 122, 60: 123, 124, 125, 126, 130, 134, 135, 136, 137, 138} 60: excls[120][num=12]={115, 117, 118, 119, 120, 121, 122, 123, 124, 60: 134, 135, 136} 60: excls[121][num=21]={115, 117, 118, 119, 120, 121, 122, 123, 124, 60: 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136} 60: excls[122][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126, 60: 130, 134} 60: excls[123][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126, 60: 130, 134} 60: excls[124][num=17]={117, 119, 120, 121, 122, 123, 124, 125, 126, 60: 127, 128, 129, 130, 131, 132, 133, 134} 60: excls[125][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 60: 129, 130, 131, 132, 133} 60: excls[126][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 60: 129, 130, 131, 132, 133} 60: excls[127][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 60: excls[128][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 60: excls[129][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 60: excls[130][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 60: 129, 130, 131, 132, 133} 60: excls[131][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 60: excls[132][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 60: excls[133][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 60: excls[134][num=17]={115, 117, 118, 119, 120, 121, 122, 123, 124, 60: 134, 135, 136, 137, 138, 139, 140, 144} 60: excls[135][num=9]={117, 119, 120, 121, 134, 135, 136, 137, 138} 60: excls[136][num=17]={117, 119, 120, 121, 134, 135, 136, 137, 138, 60: 139, 140, 141, 142, 143, 144, 145, 146} 60: excls[137][num=9]={119, 134, 135, 136, 137, 138, 139, 140, 144} 60: excls[138][num=16]={119, 134, 135, 136, 137, 138, 139, 140, 141, 60: 142, 143, 144, 145, 146, 147, 148} 60: excls[139][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143, 60: 144, 145, 146} 60: excls[140][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143, 60: 144, 145, 146} 60: excls[141][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 60: excls[142][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 60: excls[143][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 60: excls[144][num=17]={134, 136, 137, 138, 139, 140, 141, 142, 143, 60: 144, 145, 146, 147, 148, 149, 150, 154} 60: excls[145][num=9]={136, 138, 139, 140, 144, 145, 146, 147, 148} 60: excls[146][num=16]={136, 138, 139, 140, 144, 145, 146, 147, 148, 60: 149, 150, 151, 152, 153, 154, 155} 60: excls[147][num=9]={138, 144, 145, 146, 147, 148, 149, 150, 154} 60: excls[148][num=13]={138, 144, 145, 146, 147, 148, 149, 150, 151, 60: 152, 153, 154, 155} 60: excls[149][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 60: 154, 155} 60: excls[150][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 60: 154, 155} 60: excls[151][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 60: excls[152][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 60: excls[153][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 60: excls[154][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 60: 154, 155} 60: excls[155][num=6]={146, 148, 149, 150, 154, 155} 60: Bond: 60: nr: 468 60: iatoms: 60: 0 type=100 (BONDS) 0 1 60: 1 type=100 (BONDS) 0 2 60: 2 type=100 (BONDS) 0 3 60: 3 type=101 (BONDS) 0 4 60: 4 type=102 (BONDS) 4 5 60: 5 type=103 (BONDS) 4 6 60: 6 type=104 (BONDS) 4 22 60: 7 type=102 (BONDS) 6 7 60: 8 type=102 (BONDS) 6 8 60: 9 type=103 (BONDS) 6 9 60: 10 type=102 (BONDS) 9 10 60: 11 type=102 (BONDS) 9 11 60: 12 type=103 (BONDS) 9 12 60: 13 type=102 (BONDS) 12 13 60: 14 type=102 (BONDS) 12 14 60: 15 type=103 (BONDS) 12 15 60: 16 type=102 (BONDS) 15 16 60: 17 type=102 (BONDS) 15 17 60: 18 type=101 (BONDS) 15 18 60: 19 type=100 (BONDS) 18 19 60: 20 type=100 (BONDS) 18 20 60: 21 type=100 (BONDS) 18 21 60: 22 type=105 (BONDS) 22 23 60: 23 type=106 (BONDS) 22 24 60: 24 type=100 (BONDS) 24 25 60: 25 type=107 (BONDS) 24 26 60: 26 type=102 (BONDS) 26 27 60: 27 type=103 (BONDS) 26 28 60: 28 type=104 (BONDS) 26 38 60: 29 type=102 (BONDS) 28 29 60: 30 type=103 (BONDS) 28 30 60: 31 type=103 (BONDS) 28 34 60: 32 type=102 (BONDS) 30 31 60: 33 type=102 (BONDS) 30 32 60: 34 type=102 (BONDS) 30 33 60: 35 type=102 (BONDS) 34 35 60: 36 type=102 (BONDS) 34 36 60: 37 type=102 (BONDS) 34 37 60: 38 type=105 (BONDS) 38 39 60: 39 type=106 (BONDS) 38 40 60: 40 type=100 (BONDS) 40 41 60: 41 type=107 (BONDS) 40 42 60: 42 type=102 (BONDS) 42 43 60: 43 type=103 (BONDS) 42 44 60: 44 type=104 (BONDS) 42 58 60: 45 type=102 (BONDS) 44 45 60: 46 type=102 (BONDS) 44 46 60: 47 type=108 (BONDS) 44 47 60: 48 type=109 (BONDS) 47 48 60: 49 type=109 (BONDS) 47 50 60: 50 type=110 (BONDS) 48 49 60: 51 type=109 (BONDS) 48 52 60: 52 type=110 (BONDS) 50 51 60: 53 type=109 (BONDS) 50 54 60: 54 type=110 (BONDS) 52 53 60: 55 type=109 (BONDS) 52 56 60: 56 type=110 (BONDS) 54 55 60: 57 type=109 (BONDS) 54 56 60: 58 type=110 (BONDS) 56 57 60: 59 type=105 (BONDS) 58 59 60: 60 type=106 (BONDS) 58 60 60: 61 type=100 (BONDS) 60 61 60: 62 type=107 (BONDS) 60 62 60: 63 type=102 (BONDS) 62 63 60: 64 type=102 (BONDS) 62 64 60: 65 type=104 (BONDS) 62 65 60: 66 type=105 (BONDS) 65 66 60: 67 type=106 (BONDS) 65 67 60: 68 type=100 (BONDS) 67 68 60: 69 type=107 (BONDS) 67 69 60: 70 type=102 (BONDS) 69 70 60: 71 type=103 (BONDS) 69 71 60: 72 type=104 (BONDS) 69 89 60: 73 type=102 (BONDS) 71 72 60: 74 type=102 (BONDS) 71 73 60: 75 type=103 (BONDS) 71 74 60: 76 type=102 (BONDS) 74 75 60: 77 type=102 (BONDS) 74 76 60: 78 type=103 (BONDS) 74 77 60: 79 type=102 (BONDS) 77 78 60: 80 type=102 (BONDS) 77 79 60: 81 type=111 (BONDS) 77 80 60: 82 type=100 (BONDS) 80 81 60: 83 type=112 (BONDS) 80 82 60: 84 type=112 (BONDS) 82 83 60: 85 type=112 (BONDS) 82 86 60: 86 type=100 (BONDS) 83 84 60: 87 type=100 (BONDS) 83 85 60: 88 type=100 (BONDS) 86 87 60: 89 type=100 (BONDS) 86 88 60: 90 type=105 (BONDS) 89 90 60: 91 type=106 (BONDS) 89 91 60: 92 type=100 (BONDS) 91 92 60: 93 type=107 (BONDS) 91 93 60: 94 type=102 (BONDS) 93 94 60: 95 type=103 (BONDS) 93 95 60: 96 type=104 (BONDS) 93 100 60: 97 type=102 (BONDS) 95 96 60: 98 type=102 (BONDS) 95 97 60: 99 type=113 (BONDS) 95 98 60: 100 type=114 (BONDS) 98 99 60: 101 type=105 (BONDS) 100 101 60: 102 type=106 (BONDS) 100 102 60: 103 type=100 (BONDS) 102 103 60: 104 type=107 (BONDS) 102 104 60: 105 type=102 (BONDS) 104 105 60: 106 type=103 (BONDS) 104 106 60: 107 type=104 (BONDS) 104 115 60: 108 type=102 (BONDS) 106 107 60: 109 type=102 (BONDS) 106 108 60: 110 type=103 (BONDS) 106 109 60: 111 type=102 (BONDS) 109 110 60: 112 type=102 (BONDS) 109 111 60: 113 type=104 (BONDS) 109 112 60: 114 type=115 (BONDS) 112 113 60: 115 type=115 (BONDS) 112 114 60: 116 type=105 (BONDS) 115 116 60: 117 type=106 (BONDS) 115 117 60: 118 type=100 (BONDS) 117 118 60: 119 type=107 (BONDS) 117 119 60: 120 type=102 (BONDS) 119 120 60: 121 type=103 (BONDS) 119 121 60: 122 type=104 (BONDS) 119 134 60: 123 type=102 (BONDS) 121 122 60: 124 type=102 (BONDS) 121 123 60: 125 type=103 (BONDS) 121 124 60: 126 type=102 (BONDS) 124 125 60: 127 type=103 (BONDS) 124 126 60: 128 type=103 (BONDS) 124 130 60: 129 type=102 (BONDS) 126 127 60: 130 type=102 (BONDS) 126 128 60: 131 type=102 (BONDS) 126 129 60: 132 type=102 (BONDS) 130 131 60: 133 type=102 (BONDS) 130 132 60: 134 type=102 (BONDS) 130 133 60: 135 type=105 (BONDS) 134 135 60: 136 type=106 (BONDS) 134 136 60: 137 type=100 (BONDS) 136 137 60: 138 type=107 (BONDS) 136 138 60: 139 type=102 (BONDS) 138 139 60: 140 type=103 (BONDS) 138 140 60: 141 type=104 (BONDS) 138 144 60: 142 type=102 (BONDS) 140 141 60: 143 type=102 (BONDS) 140 142 60: 144 type=102 (BONDS) 140 143 60: 145 type=105 (BONDS) 144 145 60: 146 type=106 (BONDS) 144 146 60: 147 type=100 (BONDS) 146 147 60: 148 type=107 (BONDS) 146 148 60: 149 type=102 (BONDS) 148 149 60: 150 type=103 (BONDS) 148 150 60: 151 type=104 (BONDS) 148 154 60: 152 type=102 (BONDS) 150 151 60: 153 type=102 (BONDS) 150 152 60: 154 type=102 (BONDS) 150 153 60: 155 type=105 (BONDS) 154 155 60: G96Bond: 60: nr: 0 60: Morse: 60: nr: 0 60: Cubic Bonds: 60: nr: 0 60: Connect Bonds: 60: nr: 0 60: Harmonic Pot.: 60: nr: 0 60: FENE Bonds: 60: nr: 0 60: Tab. Bonds: 60: nr: 0 60: Tab. Bonds NC: 60: nr: 0 60: Restraint Pot.: 60: nr: 0 60: Angle: 60: nr: 1124 60: iatoms: 60: 0 type=116 (ANGLES) 1 0 2 60: 1 type=116 (ANGLES) 1 0 3 60: 2 type=116 (ANGLES) 1 0 4 60: 3 type=116 (ANGLES) 2 0 3 60: 4 type=116 (ANGLES) 2 0 4 60: 5 type=116 (ANGLES) 3 0 4 60: 6 type=116 (ANGLES) 0 4 5 60: 7 type=117 (ANGLES) 0 4 6 60: 8 type=117 (ANGLES) 0 4 22 60: 9 type=118 (ANGLES) 5 4 6 60: 10 type=116 (ANGLES) 5 4 22 60: 11 type=119 (ANGLES) 6 4 22 60: 12 type=118 (ANGLES) 4 6 7 60: 13 type=118 (ANGLES) 4 6 8 60: 14 type=120 (ANGLES) 4 6 9 60: 15 type=121 (ANGLES) 7 6 8 60: 16 type=118 (ANGLES) 7 6 9 60: 17 type=118 (ANGLES) 8 6 9 60: 18 type=118 (ANGLES) 6 9 10 60: 19 type=118 (ANGLES) 6 9 11 60: 20 type=120 (ANGLES) 6 9 12 60: 21 type=121 (ANGLES) 10 9 11 60: 22 type=118 (ANGLES) 10 9 12 60: 23 type=118 (ANGLES) 11 9 12 60: 24 type=118 (ANGLES) 9 12 13 60: 25 type=118 (ANGLES) 9 12 14 60: 26 type=120 (ANGLES) 9 12 15 60: 27 type=121 (ANGLES) 13 12 14 60: 28 type=118 (ANGLES) 13 12 15 60: 29 type=118 (ANGLES) 14 12 15 60: 30 type=118 (ANGLES) 12 15 16 60: 31 type=118 (ANGLES) 12 15 17 60: 32 type=117 (ANGLES) 12 15 18 60: 33 type=121 (ANGLES) 16 15 17 60: 34 type=116 (ANGLES) 16 15 18 60: 35 type=116 (ANGLES) 17 15 18 60: 36 type=116 (ANGLES) 15 18 19 60: 37 type=116 (ANGLES) 15 18 20 60: 38 type=116 (ANGLES) 15 18 21 60: 39 type=116 (ANGLES) 19 18 20 60: 40 type=116 (ANGLES) 19 18 21 60: 41 type=116 (ANGLES) 20 18 21 60: 42 type=122 (ANGLES) 4 22 23 60: 43 type=123 (ANGLES) 4 22 24 60: 44 type=124 (ANGLES) 23 22 24 60: 45 type=125 (ANGLES) 22 24 25 60: 46 type=126 (ANGLES) 22 24 26 60: 47 type=127 (ANGLES) 25 24 26 60: 48 type=116 (ANGLES) 24 26 27 60: 49 type=128 (ANGLES) 24 26 28 60: 50 type=129 (ANGLES) 24 26 38 60: 51 type=118 (ANGLES) 27 26 28 60: 52 type=116 (ANGLES) 27 26 38 60: 53 type=119 (ANGLES) 28 26 38 60: 54 type=118 (ANGLES) 26 28 29 60: 55 type=120 (ANGLES) 26 28 30 60: 56 type=120 (ANGLES) 26 28 34 60: 57 type=118 (ANGLES) 29 28 30 60: 58 type=118 (ANGLES) 29 28 34 60: 59 type=120 (ANGLES) 30 28 34 60: 60 type=118 (ANGLES) 28 30 31 60: 61 type=118 (ANGLES) 28 30 32 60: 62 type=118 (ANGLES) 28 30 33 60: 63 type=121 (ANGLES) 31 30 32 60: 64 type=121 (ANGLES) 31 30 33 60: 65 type=121 (ANGLES) 32 30 33 60: 66 type=118 (ANGLES) 28 34 35 60: 67 type=118 (ANGLES) 28 34 36 60: 68 type=118 (ANGLES) 28 34 37 60: 69 type=121 (ANGLES) 35 34 36 60: 70 type=121 (ANGLES) 35 34 37 60: 71 type=121 (ANGLES) 36 34 37 60: 72 type=122 (ANGLES) 26 38 39 60: 73 type=123 (ANGLES) 26 38 40 60: 74 type=124 (ANGLES) 39 38 40 60: 75 type=125 (ANGLES) 38 40 41 60: 76 type=126 (ANGLES) 38 40 42 60: 77 type=127 (ANGLES) 41 40 42 60: 78 type=116 (ANGLES) 40 42 43 60: 79 type=128 (ANGLES) 40 42 44 60: 80 type=129 (ANGLES) 40 42 58 60: 81 type=118 (ANGLES) 43 42 44 60: 82 type=116 (ANGLES) 43 42 58 60: 83 type=119 (ANGLES) 44 42 58 60: 84 type=118 (ANGLES) 42 44 45 60: 85 type=118 (ANGLES) 42 44 46 60: 86 type=130 (ANGLES) 42 44 47 60: 87 type=121 (ANGLES) 45 44 46 60: 88 type=116 (ANGLES) 45 44 47 60: 89 type=116 (ANGLES) 46 44 47 60: 90 type=131 (ANGLES) 44 47 48 60: 91 type=131 (ANGLES) 44 47 50 60: 92 type=132 (ANGLES) 48 47 50 60: 93 type=133 (ANGLES) 47 48 49 60: 94 type=132 (ANGLES) 47 48 52 60: 95 type=133 (ANGLES) 49 48 52 60: 96 type=133 (ANGLES) 47 50 51 60: 97 type=132 (ANGLES) 47 50 54 60: 98 type=133 (ANGLES) 51 50 54 60: 99 type=133 (ANGLES) 48 52 53 60: 100 type=132 (ANGLES) 48 52 56 60: 101 type=133 (ANGLES) 53 52 56 60: 102 type=133 (ANGLES) 50 54 55 60: 103 type=132 (ANGLES) 50 54 56 60: 104 type=133 (ANGLES) 55 54 56 60: 105 type=132 (ANGLES) 52 56 54 60: 106 type=133 (ANGLES) 52 56 57 60: 107 type=133 (ANGLES) 54 56 57 60: 108 type=122 (ANGLES) 42 58 59 60: 109 type=123 (ANGLES) 42 58 60 60: 110 type=124 (ANGLES) 59 58 60 60: 111 type=125 (ANGLES) 58 60 61 60: 112 type=126 (ANGLES) 58 60 62 60: 113 type=127 (ANGLES) 61 60 62 60: 114 type=116 (ANGLES) 60 62 63 60: 115 type=116 (ANGLES) 60 62 64 60: 116 type=129 (ANGLES) 60 62 65 60: 117 type=121 (ANGLES) 63 62 64 60: 118 type=116 (ANGLES) 63 62 65 60: 119 type=116 (ANGLES) 64 62 65 60: 120 type=122 (ANGLES) 62 65 66 60: 121 type=123 (ANGLES) 62 65 67 60: 122 type=124 (ANGLES) 66 65 67 60: 123 type=125 (ANGLES) 65 67 68 60: 124 type=126 (ANGLES) 65 67 69 60: 125 type=127 (ANGLES) 68 67 69 60: 126 type=116 (ANGLES) 67 69 70 60: 127 type=128 (ANGLES) 67 69 71 60: 128 type=129 (ANGLES) 67 69 89 60: 129 type=118 (ANGLES) 70 69 71 60: 130 type=116 (ANGLES) 70 69 89 60: 131 type=119 (ANGLES) 71 69 89 60: 132 type=118 (ANGLES) 69 71 72 60: 133 type=118 (ANGLES) 69 71 73 60: 134 type=120 (ANGLES) 69 71 74 60: 135 type=121 (ANGLES) 72 71 73 60: 136 type=118 (ANGLES) 72 71 74 60: 137 type=118 (ANGLES) 73 71 74 60: 138 type=118 (ANGLES) 71 74 75 60: 139 type=118 (ANGLES) 71 74 76 60: 140 type=120 (ANGLES) 71 74 77 60: 141 type=121 (ANGLES) 75 74 76 60: 142 type=118 (ANGLES) 75 74 77 60: 143 type=118 (ANGLES) 76 74 77 60: 144 type=118 (ANGLES) 74 77 78 60: 145 type=118 (ANGLES) 74 77 79 60: 146 type=117 (ANGLES) 74 77 80 60: 147 type=121 (ANGLES) 78 77 79 60: 148 type=116 (ANGLES) 78 77 80 60: 149 type=116 (ANGLES) 79 77 80 60: 150 type=134 (ANGLES) 77 80 81 60: 151 type=135 (ANGLES) 77 80 82 60: 152 type=133 (ANGLES) 81 80 82 60: 153 type=131 (ANGLES) 80 82 83 60: 154 type=131 (ANGLES) 80 82 86 60: 155 type=131 (ANGLES) 83 82 86 60: 156 type=133 (ANGLES) 82 83 84 60: 157 type=133 (ANGLES) 82 83 85 60: 158 type=133 (ANGLES) 84 83 85 60: 159 type=133 (ANGLES) 82 86 87 60: 160 type=133 (ANGLES) 82 86 88 60: 161 type=133 (ANGLES) 87 86 88 60: 162 type=122 (ANGLES) 69 89 90 60: 163 type=123 (ANGLES) 69 89 91 60: 164 type=124 (ANGLES) 90 89 91 60: 165 type=125 (ANGLES) 89 91 92 60: 166 type=126 (ANGLES) 89 91 93 60: 167 type=127 (ANGLES) 92 91 93 60: 168 type=116 (ANGLES) 91 93 94 60: 169 type=128 (ANGLES) 91 93 95 60: 170 type=129 (ANGLES) 91 93 100 60: 171 type=118 (ANGLES) 94 93 95 60: 172 type=116 (ANGLES) 94 93 100 60: 173 type=119 (ANGLES) 95 93 100 60: 174 type=118 (ANGLES) 93 95 96 60: 175 type=118 (ANGLES) 93 95 97 60: 176 type=136 (ANGLES) 93 95 98 60: 177 type=121 (ANGLES) 96 95 97 60: 178 type=116 (ANGLES) 96 95 98 60: 179 type=116 (ANGLES) 97 95 98 60: 180 type=137 (ANGLES) 95 98 99 60: 181 type=122 (ANGLES) 93 100 101 60: 182 type=123 (ANGLES) 93 100 102 60: 183 type=124 (ANGLES) 101 100 102 60: 184 type=125 (ANGLES) 100 102 103 60: 185 type=126 (ANGLES) 100 102 104 60: 186 type=127 (ANGLES) 103 102 104 60: 187 type=116 (ANGLES) 102 104 105 60: 188 type=128 (ANGLES) 102 104 106 60: 189 type=129 (ANGLES) 102 104 115 60: 190 type=118 (ANGLES) 105 104 106 60: 191 type=116 (ANGLES) 105 104 115 60: 192 type=119 (ANGLES) 106 104 115 60: 193 type=118 (ANGLES) 104 106 107 60: 194 type=118 (ANGLES) 104 106 108 60: 195 type=120 (ANGLES) 104 106 109 60: 196 type=121 (ANGLES) 107 106 108 60: 197 type=118 (ANGLES) 107 106 109 60: 198 type=118 (ANGLES) 108 106 109 60: 199 type=118 (ANGLES) 106 109 110 60: 200 type=118 (ANGLES) 106 109 111 60: 201 type=119 (ANGLES) 106 109 112 60: 202 type=121 (ANGLES) 110 109 111 60: 203 type=116 (ANGLES) 110 109 112 60: 204 type=116 (ANGLES) 111 109 112 60: 205 type=138 (ANGLES) 109 112 113 60: 206 type=138 (ANGLES) 109 112 114 60: 207 type=139 (ANGLES) 113 112 114 60: 208 type=122 (ANGLES) 104 115 116 60: 209 type=123 (ANGLES) 104 115 117 60: 210 type=124 (ANGLES) 116 115 117 60: 211 type=125 (ANGLES) 115 117 118 60: 212 type=126 (ANGLES) 115 117 119 60: 213 type=127 (ANGLES) 118 117 119 60: 214 type=116 (ANGLES) 117 119 120 60: 215 type=128 (ANGLES) 117 119 121 60: 216 type=129 (ANGLES) 117 119 134 60: 217 type=118 (ANGLES) 120 119 121 60: 218 type=116 (ANGLES) 120 119 134 60: 219 type=119 (ANGLES) 121 119 134 60: 220 type=118 (ANGLES) 119 121 122 60: 221 type=118 (ANGLES) 119 121 123 60: 222 type=120 (ANGLES) 119 121 124 60: 223 type=121 (ANGLES) 122 121 123 60: 224 type=118 (ANGLES) 122 121 124 60: 225 type=118 (ANGLES) 123 121 124 60: 226 type=118 (ANGLES) 121 124 125 60: 227 type=120 (ANGLES) 121 124 126 60: 228 type=120 (ANGLES) 121 124 130 60: 229 type=118 (ANGLES) 125 124 126 60: 230 type=118 (ANGLES) 125 124 130 60: 231 type=120 (ANGLES) 126 124 130 60: 232 type=118 (ANGLES) 124 126 127 60: 233 type=118 (ANGLES) 124 126 128 60: 234 type=118 (ANGLES) 124 126 129 60: 235 type=121 (ANGLES) 127 126 128 60: 236 type=121 (ANGLES) 127 126 129 60: 237 type=121 (ANGLES) 128 126 129 60: 238 type=118 (ANGLES) 124 130 131 60: 239 type=118 (ANGLES) 124 130 132 60: 240 type=118 (ANGLES) 124 130 133 60: 241 type=121 (ANGLES) 131 130 132 60: 242 type=121 (ANGLES) 131 130 133 60: 243 type=121 (ANGLES) 132 130 133 60: 244 type=122 (ANGLES) 119 134 135 60: 245 type=123 (ANGLES) 119 134 136 60: 246 type=124 (ANGLES) 135 134 136 60: 247 type=125 (ANGLES) 134 136 137 60: 248 type=126 (ANGLES) 134 136 138 60: 249 type=127 (ANGLES) 137 136 138 60: 250 type=116 (ANGLES) 136 138 139 60: 251 type=128 (ANGLES) 136 138 140 60: 252 type=129 (ANGLES) 136 138 144 60: 253 type=118 (ANGLES) 139 138 140 60: 254 type=116 (ANGLES) 139 138 144 60: 255 type=119 (ANGLES) 140 138 144 60: 256 type=118 (ANGLES) 138 140 141 60: 257 type=118 (ANGLES) 138 140 142 60: 258 type=118 (ANGLES) 138 140 143 60: 259 type=121 (ANGLES) 141 140 142 60: 260 type=121 (ANGLES) 141 140 143 60: 261 type=121 (ANGLES) 142 140 143 60: 262 type=122 (ANGLES) 138 144 145 60: 263 type=123 (ANGLES) 138 144 146 60: 264 type=124 (ANGLES) 145 144 146 60: 265 type=125 (ANGLES) 144 146 147 60: 266 type=126 (ANGLES) 144 146 148 60: 267 type=127 (ANGLES) 147 146 148 60: 268 type=116 (ANGLES) 146 148 149 60: 269 type=128 (ANGLES) 146 148 150 60: 270 type=129 (ANGLES) 146 148 154 60: 271 type=118 (ANGLES) 149 148 150 60: 272 type=116 (ANGLES) 149 148 154 60: 273 type=119 (ANGLES) 150 148 154 60: 274 type=118 (ANGLES) 148 150 151 60: 275 type=118 (ANGLES) 148 150 152 60: 276 type=118 (ANGLES) 148 150 153 60: 277 type=121 (ANGLES) 151 150 152 60: 278 type=121 (ANGLES) 151 150 153 60: 279 type=121 (ANGLES) 152 150 153 60: 280 type=122 (ANGLES) 148 154 155 60: G96Angle: 60: nr: 0 60: Restr. Angles: 60: nr: 0 60: Lin. Angle: 60: nr: 0 60: Bond-Cross: 60: nr: 0 60: BA-Cross: 60: nr: 0 60: U-B: 60: nr: 0 60: Quartic Angles: 60: nr: 0 60: Tab. Angles: 60: nr: 0 60: Proper Dih.: 60: nr: 145 60: iatoms: 60: 0 type=140 (PDIHS) 4 24 22 23 60: 1 type=141 (PDIHS) 22 26 24 25 60: 2 type=140 (PDIHS) 26 40 38 39 60: 3 type=141 (PDIHS) 38 42 40 41 60: 4 type=140 (PDIHS) 42 60 58 59 60: 5 type=142 (PDIHS) 44 47 50 48 60: 6 type=142 (PDIHS) 47 52 48 49 60: 7 type=142 (PDIHS) 47 54 50 51 60: 8 type=142 (PDIHS) 48 56 52 53 60: 9 type=142 (PDIHS) 50 56 54 55 60: 10 type=142 (PDIHS) 52 54 56 57 60: 11 type=141 (PDIHS) 58 62 60 61 60: 12 type=140 (PDIHS) 62 67 65 66 60: 13 type=141 (PDIHS) 65 69 67 68 60: 14 type=140 (PDIHS) 69 91 89 90 60: 15 type=141 (PDIHS) 77 82 80 81 60: 16 type=140 (PDIHS) 80 83 82 86 60: 17 type=141 (PDIHS) 82 84 83 85 60: 18 type=141 (PDIHS) 82 87 86 88 60: 19 type=141 (PDIHS) 89 93 91 92 60: 20 type=140 (PDIHS) 93 102 100 101 60: 21 type=141 (PDIHS) 100 104 102 103 60: 22 type=140 (PDIHS) 104 117 115 116 60: 23 type=140 (PDIHS) 109 113 112 114 60: 24 type=141 (PDIHS) 115 119 117 118 60: 25 type=140 (PDIHS) 119 136 134 135 60: 26 type=141 (PDIHS) 134 138 136 137 60: 27 type=140 (PDIHS) 138 146 144 145 60: 28 type=141 (PDIHS) 144 148 146 147 60: Ryckaert-Bell.: 60: nr: 1565 60: iatoms: 60: 0 type=143 (RBDIHS) 1 0 4 5 60: 1 type=144 (RBDIHS) 1 0 4 6 60: 2 type=144 (RBDIHS) 1 0 4 22 60: 3 type=143 (RBDIHS) 2 0 4 5 60: 4 type=144 (RBDIHS) 2 0 4 6 60: 5 type=144 (RBDIHS) 2 0 4 22 60: 6 type=143 (RBDIHS) 3 0 4 5 60: 7 type=144 (RBDIHS) 3 0 4 6 60: 8 type=144 (RBDIHS) 3 0 4 22 60: 9 type=145 (RBDIHS) 0 4 6 9 60: 10 type=146 (RBDIHS) 22 4 6 9 60: 11 type=147 (RBDIHS) 0 4 6 7 60: 12 type=147 (RBDIHS) 0 4 6 8 60: 13 type=148 (RBDIHS) 5 4 6 7 60: 14 type=148 (RBDIHS) 5 4 6 8 60: 15 type=148 (RBDIHS) 5 4 6 9 60: 16 type=149 (RBDIHS) 22 4 6 7 60: 17 type=149 (RBDIHS) 22 4 6 8 60: 18 type=150 (RBDIHS) 0 4 22 24 60: 19 type=151 (RBDIHS) 6 4 22 24 60: 20 type=148 (RBDIHS) 4 6 9 10 60: 21 type=148 (RBDIHS) 4 6 9 11 60: 22 type=152 (RBDIHS) 4 6 9 12 60: 23 type=148 (RBDIHS) 7 6 9 10 60: 24 type=148 (RBDIHS) 7 6 9 11 60: 25 type=148 (RBDIHS) 7 6 9 12 60: 26 type=148 (RBDIHS) 8 6 9 10 60: 27 type=148 (RBDIHS) 8 6 9 11 60: 28 type=148 (RBDIHS) 8 6 9 12 60: 29 type=148 (RBDIHS) 6 9 12 13 60: 30 type=148 (RBDIHS) 6 9 12 14 60: 31 type=152 (RBDIHS) 6 9 12 15 60: 32 type=148 (RBDIHS) 10 9 12 13 60: 33 type=148 (RBDIHS) 10 9 12 14 60: 34 type=148 (RBDIHS) 10 9 12 15 60: 35 type=148 (RBDIHS) 11 9 12 13 60: 36 type=148 (RBDIHS) 11 9 12 14 60: 37 type=148 (RBDIHS) 11 9 12 15 60: 38 type=148 (RBDIHS) 9 12 15 16 60: 39 type=148 (RBDIHS) 9 12 15 17 60: 40 type=153 (RBDIHS) 9 12 15 18 60: 41 type=148 (RBDIHS) 13 12 15 16 60: 42 type=148 (RBDIHS) 13 12 15 17 60: 43 type=154 (RBDIHS) 13 12 15 18 60: 44 type=148 (RBDIHS) 14 12 15 16 60: 45 type=148 (RBDIHS) 14 12 15 17 60: 46 type=154 (RBDIHS) 14 12 15 18 60: 47 type=144 (RBDIHS) 12 15 18 19 60: 48 type=144 (RBDIHS) 12 15 18 20 60: 49 type=144 (RBDIHS) 12 15 18 21 60: 50 type=143 (RBDIHS) 16 15 18 19 60: 51 type=143 (RBDIHS) 16 15 18 20 60: 52 type=143 (RBDIHS) 16 15 18 21 60: 53 type=143 (RBDIHS) 17 15 18 19 60: 54 type=143 (RBDIHS) 17 15 18 20 60: 55 type=143 (RBDIHS) 17 15 18 21 60: 56 type=155 (RBDIHS) 4 22 24 25 60: 57 type=156 (RBDIHS) 4 22 24 26 60: 58 type=155 (RBDIHS) 23 22 24 25 60: 59 type=157 (RBDIHS) 23 22 24 26 60: 60 type=158 (RBDIHS) 22 24 26 28 60: 61 type=159 (RBDIHS) 22 24 26 38 60: 62 type=160 (RBDIHS) 24 26 28 30 60: 63 type=160 (RBDIHS) 24 26 28 34 60: 64 type=161 (RBDIHS) 38 26 28 30 60: 65 type=161 (RBDIHS) 38 26 28 34 60: 66 type=147 (RBDIHS) 24 26 28 29 60: 67 type=148 (RBDIHS) 27 26 28 29 60: 68 type=148 (RBDIHS) 27 26 28 30 60: 69 type=148 (RBDIHS) 27 26 28 34 60: 70 type=149 (RBDIHS) 38 26 28 29 60: 71 type=150 (RBDIHS) 24 26 38 40 60: 72 type=151 (RBDIHS) 28 26 38 40 60: 73 type=148 (RBDIHS) 26 28 30 31 60: 74 type=148 (RBDIHS) 26 28 30 32 60: 75 type=148 (RBDIHS) 26 28 30 33 60: 76 type=148 (RBDIHS) 29 28 30 31 60: 77 type=148 (RBDIHS) 29 28 30 32 60: 78 type=148 (RBDIHS) 29 28 30 33 60: 79 type=148 (RBDIHS) 34 28 30 31 60: 80 type=148 (RBDIHS) 34 28 30 32 60: 81 type=148 (RBDIHS) 34 28 30 33 60: 82 type=148 (RBDIHS) 26 28 34 35 60: 83 type=148 (RBDIHS) 26 28 34 36 60: 84 type=148 (RBDIHS) 26 28 34 37 60: 85 type=148 (RBDIHS) 29 28 34 35 60: 86 type=148 (RBDIHS) 29 28 34 36 60: 87 type=148 (RBDIHS) 29 28 34 37 60: 88 type=148 (RBDIHS) 30 28 34 35 60: 89 type=148 (RBDIHS) 30 28 34 36 60: 90 type=148 (RBDIHS) 30 28 34 37 60: 91 type=155 (RBDIHS) 26 38 40 41 60: 92 type=156 (RBDIHS) 26 38 40 42 60: 93 type=155 (RBDIHS) 39 38 40 41 60: 94 type=157 (RBDIHS) 39 38 40 42 60: 95 type=158 (RBDIHS) 38 40 42 44 60: 96 type=159 (RBDIHS) 38 40 42 58 60: 97 type=147 (RBDIHS) 40 42 44 45 60: 98 type=147 (RBDIHS) 40 42 44 46 60: 99 type=162 (RBDIHS) 40 42 44 47 60: 100 type=148 (RBDIHS) 43 42 44 45 60: 101 type=148 (RBDIHS) 43 42 44 46 60: 102 type=163 (RBDIHS) 43 42 44 47 60: 103 type=149 (RBDIHS) 58 42 44 45 60: 104 type=149 (RBDIHS) 58 42 44 46 60: 105 type=164 (RBDIHS) 58 42 44 47 60: 106 type=150 (RBDIHS) 40 42 58 60 60: 107 type=151 (RBDIHS) 44 42 58 60 60: 108 type=165 (RBDIHS) 44 47 48 49 60: 109 type=165 (RBDIHS) 44 47 48 52 60: 110 type=165 (RBDIHS) 50 47 48 49 60: 111 type=165 (RBDIHS) 50 47 48 52 60: 112 type=165 (RBDIHS) 44 47 50 51 60: 113 type=165 (RBDIHS) 44 47 50 54 60: 114 type=165 (RBDIHS) 48 47 50 51 60: 115 type=165 (RBDIHS) 48 47 50 54 60: 116 type=165 (RBDIHS) 47 48 52 53 60: 117 type=165 (RBDIHS) 47 48 52 56 60: 118 type=165 (RBDIHS) 49 48 52 53 60: 119 type=165 (RBDIHS) 49 48 52 56 60: 120 type=165 (RBDIHS) 47 50 54 55 60: 121 type=165 (RBDIHS) 47 50 54 56 60: 122 type=165 (RBDIHS) 51 50 54 55 60: 123 type=165 (RBDIHS) 51 50 54 56 60: 124 type=165 (RBDIHS) 48 52 56 54 60: 125 type=165 (RBDIHS) 48 52 56 57 60: 126 type=165 (RBDIHS) 53 52 56 54 60: 127 type=165 (RBDIHS) 53 52 56 57 60: 128 type=165 (RBDIHS) 50 54 56 52 60: 129 type=165 (RBDIHS) 50 54 56 57 60: 130 type=165 (RBDIHS) 55 54 56 52 60: 131 type=165 (RBDIHS) 55 54 56 57 60: 132 type=155 (RBDIHS) 42 58 60 61 60: 133 type=156 (RBDIHS) 42 58 60 62 60: 134 type=155 (RBDIHS) 59 58 60 61 60: 135 type=157 (RBDIHS) 59 58 60 62 60: 136 type=159 (RBDIHS) 58 60 62 65 60: 137 type=150 (RBDIHS) 60 62 65 67 60: 138 type=155 (RBDIHS) 62 65 67 68 60: 139 type=156 (RBDIHS) 62 65 67 69 60: 140 type=155 (RBDIHS) 66 65 67 68 60: 141 type=157 (RBDIHS) 66 65 67 69 60: 142 type=158 (RBDIHS) 65 67 69 71 60: 143 type=159 (RBDIHS) 65 67 69 89 60: 144 type=166 (RBDIHS) 67 69 71 74 60: 145 type=167 (RBDIHS) 89 69 71 74 60: 146 type=147 (RBDIHS) 67 69 71 72 60: 147 type=147 (RBDIHS) 67 69 71 73 60: 148 type=148 (RBDIHS) 70 69 71 72 60: 149 type=148 (RBDIHS) 70 69 71 73 60: 150 type=148 (RBDIHS) 70 69 71 74 60: 151 type=149 (RBDIHS) 89 69 71 72 60: 152 type=149 (RBDIHS) 89 69 71 73 60: 153 type=150 (RBDIHS) 67 69 89 91 60: 154 type=151 (RBDIHS) 71 69 89 91 60: 155 type=148 (RBDIHS) 69 71 74 75 60: 156 type=148 (RBDIHS) 69 71 74 76 60: 157 type=152 (RBDIHS) 69 71 74 77 60: 158 type=148 (RBDIHS) 72 71 74 75 60: 159 type=148 (RBDIHS) 72 71 74 76 60: 160 type=148 (RBDIHS) 72 71 74 77 60: 161 type=148 (RBDIHS) 73 71 74 75 60: 162 type=148 (RBDIHS) 73 71 74 76 60: 163 type=148 (RBDIHS) 73 71 74 77 60: 164 type=148 (RBDIHS) 71 74 77 78 60: 165 type=148 (RBDIHS) 71 74 77 79 60: 166 type=153 (RBDIHS) 71 74 77 80 60: 167 type=148 (RBDIHS) 75 74 77 78 60: 168 type=148 (RBDIHS) 75 74 77 79 60: 169 type=168 (RBDIHS) 75 74 77 80 60: 170 type=148 (RBDIHS) 76 74 77 78 60: 171 type=148 (RBDIHS) 76 74 77 79 60: 172 type=168 (RBDIHS) 76 74 77 80 60: 173 type=169 (RBDIHS) 74 77 80 81 60: 174 type=170 (RBDIHS) 74 77 80 82 60: 175 type=171 (RBDIHS) 78 77 80 82 60: 176 type=171 (RBDIHS) 79 77 80 82 60: 177 type=172 (RBDIHS) 77 80 82 83 60: 178 type=172 (RBDIHS) 77 80 82 86 60: 179 type=173 (RBDIHS) 81 80 82 83 60: 180 type=173 (RBDIHS) 81 80 82 86 60: 181 type=173 (RBDIHS) 80 82 83 84 60: 182 type=173 (RBDIHS) 80 82 83 85 60: 183 type=173 (RBDIHS) 86 82 83 84 60: 184 type=173 (RBDIHS) 86 82 83 85 60: 185 type=173 (RBDIHS) 80 82 86 87 60: 186 type=173 (RBDIHS) 80 82 86 88 60: 187 type=173 (RBDIHS) 83 82 86 87 60: 188 type=173 (RBDIHS) 83 82 86 88 60: 189 type=155 (RBDIHS) 69 89 91 92 60: 190 type=156 (RBDIHS) 69 89 91 93 60: 191 type=155 (RBDIHS) 90 89 91 92 60: 192 type=157 (RBDIHS) 90 89 91 93 60: 193 type=158 (RBDIHS) 89 91 93 95 60: 194 type=159 (RBDIHS) 89 91 93 100 60: 195 type=174 (RBDIHS) 91 93 95 98 60: 196 type=175 (RBDIHS) 100 93 95 98 60: 197 type=147 (RBDIHS) 91 93 95 96 60: 198 type=147 (RBDIHS) 91 93 95 97 60: 199 type=148 (RBDIHS) 94 93 95 96 60: 200 type=148 (RBDIHS) 94 93 95 97 60: 201 type=176 (RBDIHS) 94 93 95 98 60: 202 type=149 (RBDIHS) 100 93 95 96 60: 203 type=149 (RBDIHS) 100 93 95 97 60: 204 type=150 (RBDIHS) 91 93 100 102 60: 205 type=151 (RBDIHS) 95 93 100 102 60: 206 type=177 (RBDIHS) 93 95 98 99 60: 207 type=178 (RBDIHS) 96 95 98 99 60: 208 type=178 (RBDIHS) 97 95 98 99 60: 209 type=155 (RBDIHS) 93 100 102 103 60: 210 type=156 (RBDIHS) 93 100 102 104 60: 211 type=155 (RBDIHS) 101 100 102 103 60: 212 type=157 (RBDIHS) 101 100 102 104 60: 213 type=158 (RBDIHS) 100 102 104 106 60: 214 type=159 (RBDIHS) 100 102 104 115 60: 215 type=179 (RBDIHS) 102 104 106 109 60: 216 type=180 (RBDIHS) 115 104 106 109 60: 217 type=147 (RBDIHS) 102 104 106 107 60: 218 type=147 (RBDIHS) 102 104 106 108 60: 219 type=148 (RBDIHS) 105 104 106 107 60: 220 type=148 (RBDIHS) 105 104 106 108 60: 221 type=148 (RBDIHS) 105 104 106 109 60: 222 type=149 (RBDIHS) 115 104 106 107 60: 223 type=149 (RBDIHS) 115 104 106 108 60: 224 type=150 (RBDIHS) 102 104 115 117 60: 225 type=151 (RBDIHS) 106 104 115 117 60: 226 type=148 (RBDIHS) 104 106 109 110 60: 227 type=148 (RBDIHS) 104 106 109 111 60: 228 type=181 (RBDIHS) 104 106 109 112 60: 229 type=148 (RBDIHS) 107 106 109 110 60: 230 type=148 (RBDIHS) 107 106 109 111 60: 231 type=182 (RBDIHS) 107 106 109 112 60: 232 type=148 (RBDIHS) 108 106 109 110 60: 233 type=148 (RBDIHS) 108 106 109 111 60: 234 type=182 (RBDIHS) 108 106 109 112 60: 235 type=183 (RBDIHS) 106 109 112 113 60: 236 type=183 (RBDIHS) 106 109 112 114 60: 237 type=155 (RBDIHS) 104 115 117 118 60: 238 type=156 (RBDIHS) 104 115 117 119 60: 239 type=155 (RBDIHS) 116 115 117 118 60: 240 type=157 (RBDIHS) 116 115 117 119 60: 241 type=158 (RBDIHS) 115 117 119 121 60: 242 type=159 (RBDIHS) 115 117 119 134 60: 243 type=184 (RBDIHS) 117 119 121 124 60: 244 type=185 (RBDIHS) 134 119 121 124 60: 245 type=147 (RBDIHS) 117 119 121 122 60: 246 type=147 (RBDIHS) 117 119 121 123 60: 247 type=148 (RBDIHS) 120 119 121 122 60: 248 type=148 (RBDIHS) 120 119 121 123 60: 249 type=148 (RBDIHS) 120 119 121 124 60: 250 type=149 (RBDIHS) 134 119 121 122 60: 251 type=149 (RBDIHS) 134 119 121 123 60: 252 type=150 (RBDIHS) 117 119 134 136 60: 253 type=151 (RBDIHS) 121 119 134 136 60: 254 type=148 (RBDIHS) 119 121 124 125 60: 255 type=152 (RBDIHS) 119 121 124 126 60: 256 type=152 (RBDIHS) 119 121 124 130 60: 257 type=148 (RBDIHS) 122 121 124 125 60: 258 type=148 (RBDIHS) 122 121 124 126 60: 259 type=148 (RBDIHS) 122 121 124 130 60: 260 type=148 (RBDIHS) 123 121 124 125 60: 261 type=148 (RBDIHS) 123 121 124 126 60: 262 type=148 (RBDIHS) 123 121 124 130 60: 263 type=148 (RBDIHS) 121 124 126 127 60: 264 type=148 (RBDIHS) 121 124 126 128 60: 265 type=148 (RBDIHS) 121 124 126 129 60: 266 type=148 (RBDIHS) 125 124 126 127 60: 267 type=148 (RBDIHS) 125 124 126 128 60: 268 type=148 (RBDIHS) 125 124 126 129 60: 269 type=148 (RBDIHS) 130 124 126 127 60: 270 type=148 (RBDIHS) 130 124 126 128 60: 271 type=148 (RBDIHS) 130 124 126 129 60: 272 type=148 (RBDIHS) 121 124 130 131 60: 273 type=148 (RBDIHS) 121 124 130 132 60: 274 type=148 (RBDIHS) 121 124 130 133 60: 275 type=148 (RBDIHS) 125 124 130 131 60: 276 type=148 (RBDIHS) 125 124 130 132 60: 277 type=148 (RBDIHS) 125 124 130 133 60: 278 type=148 (RBDIHS) 126 124 130 131 60: 279 type=148 (RBDIHS) 126 124 130 132 60: 280 type=148 (RBDIHS) 126 124 130 133 60: 281 type=155 (RBDIHS) 119 134 136 137 60: 282 type=156 (RBDIHS) 119 134 136 138 60: 283 type=155 (RBDIHS) 135 134 136 137 60: 284 type=157 (RBDIHS) 135 134 136 138 60: 285 type=158 (RBDIHS) 134 136 138 140 60: 286 type=159 (RBDIHS) 134 136 138 144 60: 287 type=147 (RBDIHS) 136 138 140 141 60: 288 type=147 (RBDIHS) 136 138 140 142 60: 289 type=147 (RBDIHS) 136 138 140 143 60: 290 type=148 (RBDIHS) 139 138 140 141 60: 291 type=148 (RBDIHS) 139 138 140 142 60: 292 type=148 (RBDIHS) 139 138 140 143 60: 293 type=149 (RBDIHS) 144 138 140 141 60: 294 type=149 (RBDIHS) 144 138 140 142 60: 295 type=149 (RBDIHS) 144 138 140 143 60: 296 type=150 (RBDIHS) 136 138 144 146 60: 297 type=151 (RBDIHS) 140 138 144 146 60: 298 type=155 (RBDIHS) 138 144 146 147 60: 299 type=156 (RBDIHS) 138 144 146 148 60: 300 type=155 (RBDIHS) 145 144 146 147 60: 301 type=157 (RBDIHS) 145 144 146 148 60: 302 type=158 (RBDIHS) 144 146 148 150 60: 303 type=159 (RBDIHS) 144 146 148 154 60: 304 type=147 (RBDIHS) 146 148 150 151 60: 305 type=147 (RBDIHS) 146 148 150 152 60: 306 type=147 (RBDIHS) 146 148 150 153 60: 307 type=148 (RBDIHS) 149 148 150 151 60: 308 type=148 (RBDIHS) 149 148 150 152 60: 309 type=148 (RBDIHS) 149 148 150 153 60: 310 type=149 (RBDIHS) 154 148 150 151 60: 311 type=149 (RBDIHS) 154 148 150 152 60: 312 type=149 (RBDIHS) 154 148 150 153 60: Restr. Dih.: 60: nr: 0 60: CBT Dih.: 60: nr: 0 60: Fourier Dih.: 60: nr: 0 60: Improper Dih.: 60: nr: 0 60: Per. Imp. Dih.: 60: nr: 0 60: Tab. Dih.: 60: nr: 0 60: CMAP Dih.: 60: nr: 0 60: GB 1-2 Pol.: 60: nr: 0 60: GB 1-3 Pol.: 60: nr: 0 60: GB 1-4 Pol.: 60: nr: 0 60: GB Polariz.: 60: nr: 0 60: Nonpolar Sol.: 60: nr: 0 60: LJ-14: 60: nr: 1197 60: iatoms: 60: 0 type=186 (LJ14) 0 7 60: 1 type=186 (LJ14) 0 8 60: 2 type=187 (LJ14) 0 9 60: 3 type=188 (LJ14) 0 23 60: 4 type=189 (LJ14) 0 24 60: 5 type=190 (LJ14) 1 5 60: 6 type=190 (LJ14) 1 6 60: 7 type=190 (LJ14) 1 22 60: 8 type=190 (LJ14) 2 5 60: 9 type=190 (LJ14) 2 6 60: 10 type=190 (LJ14) 2 22 60: 11 type=190 (LJ14) 3 5 60: 12 type=190 (LJ14) 3 6 60: 13 type=190 (LJ14) 3 22 60: 14 type=191 (LJ14) 4 10 60: 15 type=191 (LJ14) 4 11 60: 16 type=192 (LJ14) 4 12 60: 17 type=190 (LJ14) 4 25 60: 18 type=192 (LJ14) 4 26 60: 19 type=193 (LJ14) 5 7 60: 20 type=193 (LJ14) 5 8 60: 21 type=191 (LJ14) 5 9 60: 22 type=194 (LJ14) 5 23 60: 23 type=186 (LJ14) 5 24 60: 24 type=191 (LJ14) 6 13 60: 25 type=191 (LJ14) 6 14 60: 26 type=192 (LJ14) 6 15 60: 27 type=195 (LJ14) 6 23 60: 28 type=187 (LJ14) 6 24 60: 29 type=193 (LJ14) 7 10 60: 30 type=193 (LJ14) 7 11 60: 31 type=191 (LJ14) 7 12 60: 32 type=196 (LJ14) 7 22 60: 33 type=193 (LJ14) 8 10 60: 34 type=193 (LJ14) 8 11 60: 35 type=191 (LJ14) 8 12 60: 36 type=196 (LJ14) 8 22 60: 37 type=191 (LJ14) 9 16 60: 38 type=191 (LJ14) 9 17 60: 39 type=187 (LJ14) 9 18 60: 40 type=197 (LJ14) 9 22 60: 41 type=193 (LJ14) 10 13 60: 42 type=193 (LJ14) 10 14 60: 43 type=191 (LJ14) 10 15 60: 44 type=193 (LJ14) 11 13 60: 45 type=193 (LJ14) 11 14 60: 46 type=191 (LJ14) 11 15 60: 47 type=190 (LJ14) 12 19 60: 48 type=190 (LJ14) 12 20 60: 49 type=190 (LJ14) 12 21 60: 50 type=193 (LJ14) 13 16 60: 51 type=193 (LJ14) 13 17 60: 52 type=186 (LJ14) 13 18 60: 53 type=193 (LJ14) 14 16 60: 54 type=193 (LJ14) 14 17 60: 55 type=186 (LJ14) 14 18 60: 56 type=190 (LJ14) 16 19 60: 57 type=190 (LJ14) 16 20 60: 58 type=190 (LJ14) 16 21 60: 59 type=190 (LJ14) 17 19 60: 60 type=190 (LJ14) 17 20 60: 61 type=190 (LJ14) 17 21 60: 62 type=196 (LJ14) 22 27 60: 63 type=197 (LJ14) 22 28 60: 64 type=198 (LJ14) 22 38 60: 65 type=190 (LJ14) 23 25 60: 66 type=195 (LJ14) 23 26 60: 67 type=186 (LJ14) 24 29 60: 68 type=187 (LJ14) 24 30 60: 69 type=187 (LJ14) 24 34 60: 70 type=188 (LJ14) 24 39 60: 71 type=189 (LJ14) 24 40 60: 72 type=190 (LJ14) 25 27 60: 73 type=190 (LJ14) 25 28 60: 74 type=190 (LJ14) 25 38 60: 75 type=191 (LJ14) 26 31 60: 76 type=191 (LJ14) 26 32 60: 77 type=191 (LJ14) 26 33 60: 78 type=191 (LJ14) 26 35 60: 79 type=191 (LJ14) 26 36 60: 80 type=191 (LJ14) 26 37 60: 81 type=190 (LJ14) 26 41 60: 82 type=192 (LJ14) 26 42 60: 83 type=193 (LJ14) 27 29 60: 84 type=191 (LJ14) 27 30 60: 85 type=191 (LJ14) 27 34 60: 86 type=194 (LJ14) 27 39 60: 87 type=186 (LJ14) 27 40 60: 88 type=195 (LJ14) 28 39 60: 89 type=187 (LJ14) 28 40 60: 90 type=193 (LJ14) 29 31 60: 91 type=193 (LJ14) 29 32 60: 92 type=193 (LJ14) 29 33 60: 93 type=193 (LJ14) 29 35 60: 94 type=193 (LJ14) 29 36 60: 95 type=193 (LJ14) 29 37 60: 96 type=196 (LJ14) 29 38 60: 97 type=191 (LJ14) 30 35 60: 98 type=191 (LJ14) 30 36 60: 99 type=191 (LJ14) 30 37 60: 100 type=197 (LJ14) 30 38 60: 101 type=191 (LJ14) 31 34 60: 102 type=191 (LJ14) 32 34 60: 103 type=191 (LJ14) 33 34 60: 104 type=197 (LJ14) 34 38 60: 105 type=196 (LJ14) 38 43 60: 106 type=197 (LJ14) 38 44 60: 107 type=198 (LJ14) 38 58 60: 108 type=190 (LJ14) 39 41 60: 109 type=195 (LJ14) 39 42 60: 110 type=186 (LJ14) 40 45 60: 111 type=186 (LJ14) 40 46 60: 112 type=199 (LJ14) 40 47 60: 113 type=188 (LJ14) 40 59 60: 114 type=189 (LJ14) 40 60 60: 115 type=190 (LJ14) 41 43 60: 116 type=190 (LJ14) 41 44 60: 117 type=190 (LJ14) 41 58 60: 118 type=200 (LJ14) 42 48 60: 119 type=200 (LJ14) 42 50 60: 120 type=190 (LJ14) 42 61 60: 121 type=192 (LJ14) 42 62 60: 122 type=193 (LJ14) 43 45 60: 123 type=193 (LJ14) 43 46 60: 124 type=201 (LJ14) 43 47 60: 125 type=194 (LJ14) 43 59 60: 126 type=186 (LJ14) 43 60 60: 127 type=202 (LJ14) 44 49 60: 128 type=202 (LJ14) 44 51 60: 129 type=200 (LJ14) 44 52 60: 130 type=200 (LJ14) 44 54 60: 131 type=195 (LJ14) 44 59 60: 132 type=187 (LJ14) 44 60 60: 133 type=201 (LJ14) 45 48 60: 134 type=201 (LJ14) 45 50 60: 135 type=196 (LJ14) 45 58 60: 136 type=201 (LJ14) 46 48 60: 137 type=201 (LJ14) 46 50 60: 138 type=196 (LJ14) 46 58 60: 139 type=203 (LJ14) 47 53 60: 140 type=203 (LJ14) 47 55 60: 141 type=204 (LJ14) 47 56 60: 142 type=205 (LJ14) 47 58 60: 143 type=203 (LJ14) 48 51 60: 144 type=204 (LJ14) 48 54 60: 145 type=203 (LJ14) 48 57 60: 146 type=203 (LJ14) 49 50 60: 147 type=206 (LJ14) 49 53 60: 148 type=203 (LJ14) 49 56 60: 149 type=204 (LJ14) 50 52 60: 150 type=203 (LJ14) 50 57 60: 151 type=206 (LJ14) 51 55 60: 152 type=203 (LJ14) 51 56 60: 153 type=203 (LJ14) 52 55 60: 154 type=203 (LJ14) 53 54 60: 155 type=206 (LJ14) 53 57 60: 156 type=206 (LJ14) 55 57 60: 157 type=196 (LJ14) 58 63 60: 158 type=196 (LJ14) 58 64 60: 159 type=198 (LJ14) 58 65 60: 160 type=190 (LJ14) 59 61 60: 161 type=195 (LJ14) 59 62 60: 162 type=188 (LJ14) 60 66 60: 163 type=189 (LJ14) 60 67 60: 164 type=190 (LJ14) 61 63 60: 165 type=190 (LJ14) 61 64 60: 166 type=190 (LJ14) 61 65 60: 167 type=190 (LJ14) 62 68 60: 168 type=192 (LJ14) 62 69 60: 169 type=194 (LJ14) 63 66 60: 170 type=186 (LJ14) 63 67 60: 171 type=194 (LJ14) 64 66 60: 172 type=186 (LJ14) 64 67 60: 173 type=196 (LJ14) 65 70 60: 174 type=197 (LJ14) 65 71 60: 175 type=198 (LJ14) 65 89 60: 176 type=190 (LJ14) 66 68 60: 177 type=195 (LJ14) 66 69 60: 178 type=186 (LJ14) 67 72 60: 179 type=186 (LJ14) 67 73 60: 180 type=187 (LJ14) 67 74 60: 181 type=188 (LJ14) 67 90 60: 182 type=189 (LJ14) 67 91 60: 183 type=190 (LJ14) 68 70 60: 184 type=190 (LJ14) 68 71 60: 185 type=190 (LJ14) 68 89 60: 186 type=191 (LJ14) 69 75 60: 187 type=191 (LJ14) 69 76 60: 188 type=192 (LJ14) 69 77 60: 189 type=190 (LJ14) 69 92 60: 190 type=192 (LJ14) 69 93 60: 191 type=193 (LJ14) 70 72 60: 192 type=193 (LJ14) 70 73 60: 193 type=191 (LJ14) 70 74 60: 194 type=194 (LJ14) 70 90 60: 195 type=186 (LJ14) 70 91 60: 196 type=191 (LJ14) 71 78 60: 197 type=191 (LJ14) 71 79 60: 198 type=187 (LJ14) 71 80 60: 199 type=195 (LJ14) 71 90 60: 200 type=187 (LJ14) 71 91 60: 201 type=193 (LJ14) 72 75 60: 202 type=193 (LJ14) 72 76 60: 203 type=191 (LJ14) 72 77 60: 204 type=196 (LJ14) 72 89 60: 205 type=193 (LJ14) 73 75 60: 206 type=193 (LJ14) 73 76 60: 207 type=191 (LJ14) 73 77 60: 208 type=196 (LJ14) 73 89 60: 209 type=190 (LJ14) 74 81 60: 210 type=207 (LJ14) 74 82 60: 211 type=197 (LJ14) 74 89 60: 212 type=193 (LJ14) 75 78 60: 213 type=193 (LJ14) 75 79 60: 214 type=186 (LJ14) 75 80 60: 215 type=193 (LJ14) 76 78 60: 216 type=193 (LJ14) 76 79 60: 217 type=186 (LJ14) 76 80 60: 218 type=187 (LJ14) 77 83 60: 219 type=187 (LJ14) 77 86 60: 220 type=190 (LJ14) 78 81 60: 221 type=208 (LJ14) 78 82 60: 222 type=190 (LJ14) 79 81 60: 223 type=208 (LJ14) 79 82 60: 224 type=190 (LJ14) 80 84 60: 225 type=190 (LJ14) 80 85 60: 226 type=190 (LJ14) 80 87 60: 227 type=190 (LJ14) 80 88 60: 228 type=190 (LJ14) 81 83 60: 229 type=190 (LJ14) 81 86 60: 230 type=190 (LJ14) 83 87 60: 231 type=190 (LJ14) 83 88 60: 232 type=190 (LJ14) 84 86 60: 233 type=190 (LJ14) 85 86 60: 234 type=196 (LJ14) 89 94 60: 235 type=197 (LJ14) 89 95 60: 236 type=198 (LJ14) 89 100 60: 237 type=190 (LJ14) 90 92 60: 238 type=195 (LJ14) 90 93 60: 239 type=186 (LJ14) 91 96 60: 240 type=186 (LJ14) 91 97 60: 241 type=209 (LJ14) 91 98 60: 242 type=188 (LJ14) 91 101 60: 243 type=189 (LJ14) 91 102 60: 244 type=190 (LJ14) 92 94 60: 245 type=190 (LJ14) 92 95 60: 246 type=190 (LJ14) 92 100 60: 247 type=190 (LJ14) 93 99 60: 248 type=190 (LJ14) 93 103 60: 249 type=192 (LJ14) 93 104 60: 250 type=193 (LJ14) 94 96 60: 251 type=193 (LJ14) 94 97 60: 252 type=210 (LJ14) 94 98 60: 253 type=194 (LJ14) 94 101 60: 254 type=186 (LJ14) 94 102 60: 255 type=195 (LJ14) 95 101 60: 256 type=187 (LJ14) 95 102 60: 257 type=190 (LJ14) 96 99 60: 258 type=196 (LJ14) 96 100 60: 259 type=190 (LJ14) 97 99 60: 260 type=196 (LJ14) 97 100 60: 261 type=211 (LJ14) 98 100 60: 262 type=196 (LJ14) 100 105 60: 263 type=197 (LJ14) 100 106 60: 264 type=198 (LJ14) 100 115 60: 265 type=190 (LJ14) 101 103 60: 266 type=195 (LJ14) 101 104 60: 267 type=186 (LJ14) 102 107 60: 268 type=186 (LJ14) 102 108 60: 269 type=187 (LJ14) 102 109 60: 270 type=188 (LJ14) 102 116 60: 271 type=189 (LJ14) 102 117 60: 272 type=190 (LJ14) 103 105 60: 273 type=190 (LJ14) 103 106 60: 274 type=190 (LJ14) 103 115 60: 275 type=191 (LJ14) 104 110 60: 276 type=191 (LJ14) 104 111 60: 277 type=197 (LJ14) 104 112 60: 278 type=190 (LJ14) 104 118 60: 279 type=192 (LJ14) 104 119 60: 280 type=193 (LJ14) 105 107 60: 281 type=193 (LJ14) 105 108 60: 282 type=191 (LJ14) 105 109 60: 283 type=194 (LJ14) 105 116 60: 284 type=186 (LJ14) 105 117 60: 285 type=195 (LJ14) 106 113 60: 286 type=195 (LJ14) 106 114 60: 287 type=195 (LJ14) 106 116 60: 288 type=187 (LJ14) 106 117 60: 289 type=193 (LJ14) 107 110 60: 290 type=193 (LJ14) 107 111 60: 291 type=196 (LJ14) 107 112 60: 292 type=196 (LJ14) 107 115 60: 293 type=193 (LJ14) 108 110 60: 294 type=193 (LJ14) 108 111 60: 295 type=196 (LJ14) 108 112 60: 296 type=196 (LJ14) 108 115 60: 297 type=197 (LJ14) 109 115 60: 298 type=194 (LJ14) 110 113 60: 299 type=194 (LJ14) 110 114 60: 300 type=194 (LJ14) 111 113 60: 301 type=194 (LJ14) 111 114 60: 302 type=196 (LJ14) 115 120 60: 303 type=197 (LJ14) 115 121 60: 304 type=198 (LJ14) 115 134 60: 305 type=190 (LJ14) 116 118 60: 306 type=195 (LJ14) 116 119 60: 307 type=186 (LJ14) 117 122 60: 308 type=186 (LJ14) 117 123 60: 309 type=187 (LJ14) 117 124 60: 310 type=188 (LJ14) 117 135 60: 311 type=189 (LJ14) 117 136 60: 312 type=190 (LJ14) 118 120 60: 313 type=190 (LJ14) 118 121 60: 314 type=190 (LJ14) 118 134 60: 315 type=191 (LJ14) 119 125 60: 316 type=192 (LJ14) 119 126 60: 317 type=192 (LJ14) 119 130 60: 318 type=190 (LJ14) 119 137 60: 319 type=192 (LJ14) 119 138 60: 320 type=193 (LJ14) 120 122 60: 321 type=193 (LJ14) 120 123 60: 322 type=191 (LJ14) 120 124 60: 323 type=194 (LJ14) 120 135 60: 324 type=186 (LJ14) 120 136 60: 325 type=191 (LJ14) 121 127 60: 326 type=191 (LJ14) 121 128 60: 327 type=191 (LJ14) 121 129 60: 328 type=191 (LJ14) 121 131 60: 329 type=191 (LJ14) 121 132 60: 330 type=191 (LJ14) 121 133 60: 331 type=195 (LJ14) 121 135 60: 332 type=187 (LJ14) 121 136 60: 333 type=193 (LJ14) 122 125 60: 334 type=191 (LJ14) 122 126 60: 335 type=191 (LJ14) 122 130 60: 336 type=196 (LJ14) 122 134 60: 337 type=193 (LJ14) 123 125 60: 338 type=191 (LJ14) 123 126 60: 339 type=191 (LJ14) 123 130 60: 340 type=196 (LJ14) 123 134 60: 341 type=197 (LJ14) 124 134 60: 342 type=193 (LJ14) 125 127 60: 343 type=193 (LJ14) 125 128 60: 344 type=193 (LJ14) 125 129 60: 345 type=193 (LJ14) 125 131 60: 346 type=193 (LJ14) 125 132 60: 347 type=193 (LJ14) 125 133 60: 348 type=191 (LJ14) 126 131 60: 349 type=191 (LJ14) 126 132 60: 350 type=191 (LJ14) 126 133 60: 351 type=191 (LJ14) 127 130 60: 352 type=191 (LJ14) 128 130 60: 353 type=191 (LJ14) 129 130 60: 354 type=196 (LJ14) 134 139 60: 355 type=197 (LJ14) 134 140 60: 356 type=198 (LJ14) 134 144 60: 357 type=190 (LJ14) 135 137 60: 358 type=195 (LJ14) 135 138 60: 359 type=186 (LJ14) 136 141 60: 360 type=186 (LJ14) 136 142 60: 361 type=186 (LJ14) 136 143 60: 362 type=188 (LJ14) 136 145 60: 363 type=189 (LJ14) 136 146 60: 364 type=190 (LJ14) 137 139 60: 365 type=190 (LJ14) 137 140 60: 366 type=190 (LJ14) 137 144 60: 367 type=190 (LJ14) 138 147 60: 368 type=192 (LJ14) 138 148 60: 369 type=193 (LJ14) 139 141 60: 370 type=193 (LJ14) 139 142 60: 371 type=193 (LJ14) 139 143 60: 372 type=194 (LJ14) 139 145 60: 373 type=186 (LJ14) 139 146 60: 374 type=195 (LJ14) 140 145 60: 375 type=187 (LJ14) 140 146 60: 376 type=196 (LJ14) 141 144 60: 377 type=196 (LJ14) 142 144 60: 378 type=196 (LJ14) 143 144 60: 379 type=196 (LJ14) 144 149 60: 380 type=197 (LJ14) 144 150 60: 381 type=198 (LJ14) 144 154 60: 382 type=190 (LJ14) 145 147 60: 383 type=195 (LJ14) 145 148 60: 384 type=186 (LJ14) 146 151 60: 385 type=186 (LJ14) 146 152 60: 386 type=186 (LJ14) 146 153 60: 387 type=188 (LJ14) 146 155 60: 388 type=190 (LJ14) 147 149 60: 389 type=190 (LJ14) 147 150 60: 390 type=190 (LJ14) 147 154 60: 391 type=193 (LJ14) 149 151 60: 392 type=193 (LJ14) 149 152 60: 393 type=193 (LJ14) 149 153 60: 394 type=194 (LJ14) 149 155 60: 395 type=195 (LJ14) 150 155 60: 396 type=196 (LJ14) 151 154 60: 397 type=196 (LJ14) 152 154 60: 398 type=196 (LJ14) 153 154 60: Coulomb-14: 60: nr: 0 60: LJC-14 q: 60: nr: 0 60: LJC Pairs NB: 60: nr: 0 60: LJ (SR): 60: nr: 0 60: Buck.ham (SR): 60: nr: 0 60: LJ: 60: nr: 0 60: B.ham: 60: nr: 0 60: Disper. corr.: 60: nr: 0 60: Coulomb (SR): 60: nr: 0 60: Coul: 60: nr: 0 60: RF excl.: 60: nr: 0 60: Coul. recip.: 60: nr: 0 60: LJ recip.: 60: nr: 0 60: DPD: 60: nr: 0 60: Polarization: 60: nr: 0 60: Water Pol.: 60: nr: 0 60: Thole Pol.: 60: nr: 0 60: Anharm. Pol.: 60: nr: 0 60: Position Rest.: 60: nr: 0 60: Flat-b. P-R.: 60: nr: 0 60: Dis. Rest.: 60: nr: 0 60: D.R.Viol. (nm): 60: nr: 0 60: Orient. Rest.: 60: nr: 0 60: Ori. R. RMSD: 60: nr: 0 60: Angle Rest.: 60: nr: 0 60: Angle Rest. Z: 60: nr: 0 60: Dih. Rest.: 60: nr: 0 60: Dih. Rest. Vi.: 60: nr: 0 60: Constraint: 60: nr: 0 60: Constr. No Co.: 60: nr: 0 60: Settle: 60: nr: 0 60: Virtual site 1: 60: nr: 0 60: Virtual site 2: 60: nr: 0 60: Virt. site 2fd: 60: nr: 0 60: Virtual site 3: 60: nr: 0 60: Virt. site 3fd: 60: nr: 0 60: Vir. site 3fad: 60: nr: 0 60: Vir. site 3out: 60: nr: 0 60: Virt. site 4fd: 60: nr: 0 60: Vir. site 4fdn: 60: nr: 0 60: Virtual site N: 60: nr: 0 60: COM Pull En.: 60: nr: 0 60: Dens. fitting: 60: nr: 0 60: Quantum En.: 60: nr: 0 60: NN Potential: 60: nr: 0 60: Potential: 60: nr: 0 60: Kinetic En.: 60: nr: 0 60: Total Energy: 60: nr: 0 60: Conserved En.: 60: nr: 0 60: Temperature: 60: nr: 0 60: Vir. Temp.: 60: nr: 0 60: Pres. DC: 60: nr: 0 60: Pressure: 60: nr: 0 60: dH/dl constr.: 60: nr: 0 60: dVremain/dl: 60: nr: 0 60: dEkin/dl: 60: nr: 0 60: dVcoul/dl: 60: nr: 0 60: dVvdw/dl: 60: nr: 0 60: dVbonded/dl: 60: nr: 0 60: dVrestraint/dl: 60: nr: 0 60: dVtemp/dl: 60: nr: 0 60: grp[T-Coupling ] nr=1, name=[ rest] 60: grp[Energy Mon. ] nr=1, name=[ rest] 60: grp[Acc. not used] nr=1, name=[ rest] 60: grp[Freeze ] nr=1, name=[ rest] 60: grp[User1 ] nr=1, name=[ rest] 60: grp[User2 ] nr=1, name=[ rest] 60: grp[VCM ] nr=1, name=[ rest] 60: grp[Compressed X] nr=1, name=[ rest] 60: grp[Or. Res. Fit] nr=1, name=[ rest] 60: grp[QMMM ] nr=1, name=[ rest] 60: grpname (11): 60: grpname[0]={name="System"} 60: grpname[1]={name="Protein"} 60: grpname[2]={name="Protein-H"} 60: grpname[3]={name="C-alpha"} 60: grpname[4]={name="Backbone"} 60: grpname[5]={name="MainChain"} 60: grpname[6]={name="MainChain+Cb"} 60: grpname[7]={name="MainChain+H"} 60: grpname[8]={name="SideChain"} 60: grpname[9]={name="SideChain-H"} 60: grpname[10]={name="rest"} 60: groups T-Cou Energ Acc. Freez User1 User2 VCM Compr Or. R QMMM 60: allocated 0 0 0 0 0 0 0 0 0 0 60: groupnr[ *] = 0 0 0 0 0 0 0 0 0 0 60: box (3x3): 60: box[ 0]={ 5.90620e+00, 0.00000e+00, 0.00000e+00} 60: box[ 1]={ 0.00000e+00, 6.84510e+00, 0.00000e+00} 60: box[ 2]={ 0.00000e+00, 0.00000e+00, 3.05170e+00} 60: box_rel (3x3): 60: box_rel[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: box_rel[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: box_rel[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: boxv (3x3): 60: boxv[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: boxv[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: boxv[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: pres_prev (3x3): 60: pres_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: pres_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: pres_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: svir_prev (3x3): 60: svir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: svir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: svir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: fvir_prev (3x3): 60: fvir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: fvir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: fvir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: nosehoover_xi: not available 60: x (156x3): 60: x[ 0]={ 3.53600e+00, 2.23400e+00, -1.19800e+00} 60: x[ 1]={ 3.61200e+00, 2.28800e+00, -1.23600e+00} 60: x[ 2]={ 3.47000e+00, 2.21400e+00, -1.27000e+00} 60: x[ 3]={ 3.49200e+00, 2.28600e+00, -1.12500e+00} 60: x[ 4]={ 3.58900e+00, 2.10700e+00, -1.14300e+00} 60: x[ 5]={ 3.63300e+00, 2.05500e+00, -1.21600e+00} 60: x[ 6]={ 3.68700e+00, 2.14400e+00, -1.03100e+00} 60: x[ 7]={ 3.76300e+00, 2.19500e+00, -1.07000e+00} 60: x[ 8]={ 3.63900e+00, 2.20100e+00, -9.64000e-01} 60: x[ 9]={ 3.74500e+00, 2.02500e+00, -9.56000e-01} 60: x[ 10]={ 3.67600e+00, 1.98900e+00, -8.94000e-01} 60: x[ 11]={ 3.77000e+00, 1.95400e+00, -1.02300e+00} 60: x[ 12]={ 3.86900e+00, 2.06500e+00, -8.77000e-01} 60: x[ 13]={ 3.94500e+00, 2.08300e+00, -9.40000e-01} 60: x[ 14]={ 3.84900e+00, 2.14700e+00, -8.24000e-01} 60: x[ 15]={ 3.90600e+00, 1.95100e+00, -7.84000e-01} 60: x[ 16]={ 3.84100e+00, 1.94600e+00, -7.08000e-01} 60: x[ 17]={ 3.90600e+00, 1.86400e+00, -8.33000e-01} 60: x[ 18]={ 4.04200e+00, 1.97700e+00, -7.30000e-01} 60: x[ 19]={ 4.06900e+00, 1.90300e+00, -6.68000e-01} 60: x[ 20]={ 4.10800e+00, 1.98200e+00, -8.06000e-01} 60: x[ 21]={ 4.04200e+00, 2.06400e+00, -6.80000e-01} 60: x[ 22]={ 3.47400e+00, 2.02600e+00, -1.08400e+00} 60: x[ 23]={ 3.39500e+00, 2.08100e+00, -1.00800e+00} 60: x[ 24]={ 3.47400e+00, 1.89600e+00, -1.10400e+00} 60: x[ 25]={ 3.53600e+00, 1.86000e+00, -1.17400e+00} 60: x[ 26]={ 3.39000e+00, 1.80000e+00, -1.03300e+00} 60: x[ 27]={ 3.31700e+00, 1.85200e+00, -9.90000e-01} 60: x[ 28]={ 3.31400e+00, 1.70300e+00, -1.12300e+00} 60: x[ 29]={ 3.38600e+00, 1.65200e+00, -1.17000e+00} 60: x[ 30]={ 3.22500e+00, 1.60800e+00, -1.04300e+00} 60: x[ 31]={ 3.17700e+00, 1.54700e+00, -1.10600e+00} 60: x[ 32]={ 3.28200e+00, 1.55500e+00, -9.81000e-01} 60: x[ 33]={ 3.15800e+00, 1.66100e+00, -9.91000e-01} 60: x[ 34]={ 3.22900e+00, 1.77100e+00, -1.22900e+00} 60: x[ 35]={ 3.18300e+00, 1.70200e+00, -1.28400e+00} 60: x[ 36]={ 3.16200e+00, 1.83000e+00, -1.18500e+00} 60: x[ 37]={ 3.28800e+00, 1.82700e+00, -1.28800e+00} 60: x[ 38]={ 3.48000e+00, 1.73100e+00, -9.29000e-01} 60: x[ 39]={ 3.57600e+00, 1.66100e+00, -9.66000e-01} 60: x[ 40]={ 3.44900e+00, 1.75500e+00, -8.04000e-01} 60: x[ 41]={ 3.37500e+00, 1.81900e+00, -7.84000e-01} 60: x[ 42]={ 3.51900e+00, 1.69000e+00, -6.92000e-01} 60: x[ 43]={ 3.61500e+00, 1.69700e+00, -7.17000e-01} 60: x[ 44]={ 3.49700e+00, 1.76300e+00, -5.59000e-01} 60: x[ 45]={ 3.40500e+00, 1.80200e+00, -5.58000e-01} 60: x[ 46]={ 3.50600e+00, 1.69800e+00, -4.84000e-01} 60: x[ 47]={ 3.59400e+00, 1.87400e+00, -5.38000e-01} 60: x[ 48]={ 3.56700e+00, 2.00500e+00, -5.80000e-01} 60: x[ 49]={ 3.48100e+00, 2.02500e+00, -6.27000e-01} 60: x[ 50]={ 3.70000e+00, 1.85600e+00, -4.47000e-01} 60: x[ 51]={ 3.71300e+00, 1.76600e+00, -4.05000e-01} 60: x[ 52]={ 3.65800e+00, 2.10800e+00, -5.57000e-01} 60: x[ 53]={ 3.64800e+00, 2.19500e+00, -6.04000e-01} 60: x[ 54]={ 3.78700e+00, 1.95900e+00, -4.16000e-01} 60: x[ 55]={ 3.86600e+00, 1.94200e+00, -3.57000e-01} 60: x[ 56]={ 3.76400e+00, 2.08700e+00, -4.67000e-01} 60: x[ 57]={ 3.82200e+00, 2.16400e+00, -4.39000e-01} 60: x[ 58]={ 3.47400e+00, 1.54400e+00, -6.77000e-01} 60: x[ 59]={ 3.35200e+00, 1.51600e+00, -6.86000e-01} 60: x[ 60]={ 3.57200e+00, 1.46400e+00, -6.33000e-01} 60: x[ 61]={ 3.66700e+00, 1.49500e+00, -6.32000e-01} 60: x[ 62]={ 3.53700e+00, 1.32800e+00, -5.87000e-01} 60: x[ 63]={ 3.46200e+00, 1.29200e+00, -6.43000e-01} 60: x[ 64]={ 3.61600e+00, 1.26800e+00, -5.94000e-01} 60: x[ 65]={ 3.49200e+00, 1.34200e+00, -4.42000e-01} 60: x[ 66]={ 3.53000e+00, 1.44000e+00, -3.78000e-01} 60: x[ 67]={ 3.40500e+00, 1.25400e+00, -3.97000e-01} 60: x[ 68]={ 3.37100e+00, 1.18400e+00, -4.60000e-01} 60: x[ 69]={ 3.35600e+00, 1.25400e+00, -2.59000e-01} 60: x[ 70]={ 3.29800e+00, 1.33400e+00, -2.52000e-01} 60: x[ 71]={ 3.27600e+00, 1.12600e+00, -2.33000e-01} 60: x[ 72]={ 3.20000e+00, 1.12200e+00, -2.97000e-01} 60: x[ 73]={ 3.33600e+00, 1.04700e+00, -2.47000e-01} 60: x[ 74]={ 3.22100e+00, 1.12000e+00, -9.20000e-02} 60: x[ 75]={ 3.29700e+00, 1.11700e+00, -2.70000e-02} 60: x[ 76]={ 3.16500e+00, 1.20100e+00, -7.50000e-02} 60: x[ 77]={ 3.13800e+00, 1.00000e+00, -7.20000e-02} 60: x[ 78]={ 3.10400e+00, 9.99000e-01, 2.20000e-02} 60: x[ 79]={ 3.06000e+00, 1.00500e+00, -1.35000e-01} 60: x[ 80]={ 3.20600e+00, 8.75000e-01, -9.60000e-02} 60: x[ 81]={ 3.20200e+00, 8.40000e-01, -1.89000e-01} 60: x[ 82]={ 3.27300e+00, 8.01000e-01, -1.00000e-02} 60: x[ 83]={ 3.28400e+00, 8.33000e-01, 1.19000e-01} 60: x[ 84]={ 3.23900e+00, 9.16000e-01, 1.53000e-01} 60: x[ 85]={ 3.33600e+00, 7.75000e-01, 1.81000e-01} 60: x[ 86]={ 3.32500e+00, 6.84000e-01, -5.30000e-02} 60: x[ 87]={ 3.31100e+00, 6.55000e-01, -1.47000e-01} 60: x[ 88]={ 3.37600e+00, 6.26000e-01, 1.00000e-02} 60: x[ 89]={ 3.46700e+00, 1.27300e+00, -1.56000e-01} 60: x[ 90]={ 3.46700e+00, 1.36500e+00, -7.00000e-02} 60: x[ 91]={ 3.56700e+00, 1.18500e+00, -1.61000e-01} 60: x[ 92]={ 3.56700e+00, 1.11600e+00, -2.33000e-01} 60: x[ 93]={ 3.67800e+00, 1.18700e+00, -6.50000e-02} 60: x[ 94]={ 3.63100e+00, 1.20200e+00, 2.20000e-02} 60: x[ 95]={ 3.74900e+00, 1.05300e+00, -6.20000e-02} 60: x[ 96]={ 3.77000e+00, 1.03400e+00, -1.58000e-01} 60: x[ 97]={ 3.83400e+00, 1.07200e+00, -1.30000e-02} 60: x[ 98]={ 3.65400e+00, 9.20000e-01, 1.40000e-02} 60: x[ 99]={ 3.70750e+00, 8.35500e-01, 1.20000e-02} 60: x[ 100]={ 3.77500e+00, 1.30500e+00, -7.80000e-02} 60: x[ 101]={ 3.81500e+00, 1.36100e+00, 2.60000e-02} 60: x[ 102]={ 3.78600e+00, 1.34800e+00, -2.02000e-01} 60: x[ 103]={ 3.74000e+00, 1.30000e+00, -2.76000e-01} 60: x[ 104]={ 3.86800e+00, 1.46900e+00, -2.31000e-01} 60: x[ 105]={ 3.96000e+00, 1.45500e+00, -1.93000e-01} 60: x[ 106]={ 3.87800e+00, 1.48500e+00, -3.82000e-01} 60: x[ 107]={ 3.92300e+00, 1.40200e+00, -4.17000e-01} 60: x[ 108]={ 3.78500e+00, 1.48900e+00, -4.17000e-01} 60: x[ 109]={ 3.95400e+00, 1.60500e+00, -4.38000e-01} 60: x[ 110]={ 3.91300e+00, 1.68700e+00, -3.99000e-01} 60: x[ 111]={ 4.04900e+00, 1.59800e+00, -4.07000e-01} 60: x[ 112]={ 3.95800e+00, 1.62400e+00, -5.87000e-01} 60: x[ 113]={ 3.86700e+00, 1.56400e+00, -6.49000e-01} 60: x[ 114]={ 4.04200e+00, 1.69500e+00, -6.38000e-01} 60: x[ 115]={ 3.80500e+00, 1.59300e+00, -1.66000e-01} 60: x[ 116]={ 3.87400e+00, 1.67300e+00, -1.01000e-01} 60: x[ 117]={ 3.67400e+00, 1.60500e+00, -1.82000e-01} 60: x[ 118]={ 3.62600e+00, 1.53500e+00, -2.35000e-01} 60: x[ 119]={ 3.59600e+00, 1.71600e+00, -1.25000e-01} 60: x[ 120]={ 3.64000e+00, 1.80100e+00, -1.56000e-01} 60: x[ 121]={ 3.45300e+00, 1.71700e+00, -1.81000e-01} 60: x[ 122]={ 3.45700e+00, 1.72200e+00, -2.81000e-01} 60: x[ 123]={ 3.40600e+00, 1.63300e+00, -1.53000e-01} 60: x[ 124]={ 3.37200e+00, 1.83500e+00, -1.31000e-01} 60: x[ 125]={ 3.37800e+00, 1.84200e+00, -3.10000e-02} 60: x[ 126]={ 3.43000e+00, 1.96600e+00, -1.84000e-01} 60: x[ 127]={ 3.37600e+00, 2.04300e+00, -1.50000e-01} 60: x[ 128]={ 3.52400e+00, 1.97500e+00, -1.53000e-01} 60: x[ 129]={ 3.42700e+00, 1.96500e+00, -2.84000e-01} 60: x[ 130]={ 3.22500e+00, 1.81400e+00, -1.60000e-01} 60: x[ 131]={ 3.17200e+00, 1.89300e+00, -1.26000e-01} 60: x[ 132]={ 3.21100e+00, 1.80500e+00, -2.58000e-01} 60: x[ 133]={ 3.19300e+00, 1.73100e+00, -1.14000e-01} 60: x[ 134]={ 3.60500e+00, 1.71300e+00, 2.70000e-02} 60: x[ 135]={ 3.61600e+00, 1.81700e+00, 9.20000e-02} 60: x[ 136]={ 3.57500e+00, 1.59800e+00, 8.30000e-02} 60: x[ 137]={ 3.54600e+00, 1.52200e+00, 2.40000e-02} 60: x[ 138]={ 3.58400e+00, 1.57600e+00, 2.28000e-01} 60: x[ 139]={ 3.50800e+00, 1.62600e+00, 2.69000e-01} 60: x[ 140]={ 3.56600e+00, 1.42900e+00, 2.62000e-01} 60: x[ 141]={ 3.57200e+00, 1.41600e+00, 3.61000e-01} 60: x[ 142]={ 3.47600e+00, 1.39800e+00, 2.30000e-01} 60: x[ 143]={ 3.63700e+00, 1.37500e+00, 2.18000e-01} 60: x[ 144]={ 3.71400e+00, 1.63100e+00, 2.84000e-01} 60: x[ 145]={ 3.71500e+00, 1.69800e+00, 3.90000e-01} 60: x[ 146]={ 3.82700e+00, 1.59800e+00, 2.20000e-01} 60: x[ 147]={ 3.82000e+00, 1.53900e+00, 1.40000e-01} 60: x[ 148]={ 3.96100e+00, 1.64300e+00, 2.62000e-01} 60: x[ 149]={ 3.96900e+00, 1.61900e+00, 3.58000e-01} 60: x[ 150]={ 4.07100e+00, 1.57100e+00, 1.84000e-01} 60: x[ 151]={ 4.16000e+00, 1.60300e+00, 2.15000e-01} 60: x[ 152]={ 4.06400e+00, 1.47200e+00, 2.01000e-01} 60: x[ 153]={ 4.06000e+00, 1.58900e+00, 8.60000e-02} 60: x[ 154]={ 3.97400e+00, 1.79400e+00, 2.46000e-01} 60: x[ 155]={ 4.01900e+00, 1.85000e+00, 3.47000e-01} 60: v (156x3): 60: v[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 3]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 4]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 5]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 6]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 7]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 8]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 9]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 10]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 11]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 12]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 13]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 14]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 15]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 16]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 17]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 18]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 19]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 20]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 21]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 22]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 23]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 24]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 25]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 26]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 27]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 28]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 29]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 30]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 31]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 32]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 33]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 34]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 35]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 36]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 37]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 38]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 39]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 40]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 41]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 42]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 43]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 44]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 45]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 46]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 47]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 48]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 49]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 50]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 51]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 52]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 53]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 54]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 55]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 56]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 57]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 58]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 59]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 60]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 61]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 62]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 63]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 64]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 65]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 66]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 67]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 68]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 69]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 70]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 71]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 72]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 73]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 74]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 75]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 76]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 77]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 78]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 79]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 80]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 81]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 82]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 83]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 84]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 85]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 86]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 87]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 88]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 89]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 90]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 91]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 92]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 93]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 94]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 95]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 96]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 97]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 98]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 99]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 100]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 101]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 102]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 103]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 104]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 105]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 106]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 107]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 108]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 109]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 110]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 111]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 112]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 113]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 114]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 115]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 116]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 117]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 118]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 119]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 120]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 121]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 122]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 123]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 124]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 125]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 126]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 127]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 128]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 129]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 130]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 131]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 132]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 133]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 134]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 135]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 136]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 137]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 138]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 139]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 140]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 141]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 142]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 143]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 144]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 145]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 146]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 147]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 148]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 149]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 150]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 151]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 152]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 153]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 154]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 155]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: Group statistics 60: T-Coupling : 156 (total 156 atoms) 60: Energy Mon. : 156 (total 156 atoms) 60: Acc. not used: 156 (total 156 atoms) 60: Freeze : 156 (total 156 atoms) 60: User1 : 156 (total 156 atoms) 60: User2 : 156 (total 156 atoms) 60: VCM : 156 (total 156 atoms) 60: Compressed X: 156 (total 156 atoms) 60: Or. Res. Fit: 156 (total 156 atoms) 60: QMMM : 156 (total 156 atoms) 60: [ OK ] DumpTest.WorksWithTpr (14 ms) 60: [ RUN ] DumpTest.WorksWithTprAndMdpWriting 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 60: [ OK ] DumpTest.WorksWithTprAndMdpWriting (1 ms) 60: [----------] 2 tests from DumpTest (15 ms total) 60: 60: [----------] 3 tests from HelpwritingTest 60: [ RUN ] HelpwritingTest.ConvertTprWritesHelp 60: [ OK ] HelpwritingTest.ConvertTprWritesHelp (0 ms) 60: [ RUN ] HelpwritingTest.DumpWritesHelp 60: [ OK ] HelpwritingTest.DumpWritesHelp (0 ms) 60: [ RUN ] HelpwritingTest.ReportMethodsWritesHelp 60: [ OK ] HelpwritingTest.ReportMethodsWritesHelp (0 ms) 60: [----------] 3 tests from HelpwritingTest (0 ms total) 60: 60: [----------] 7 tests from GmxMakeNdx 60: [ RUN ] GmxMakeNdx.WritesDefaultProteinIndexGroups 60: 60: Reading structure file 60: Going to read 0 old index file(s) 60: Analysing residue names: 60: There are: 16 Protein residues 60: Analysing Protein... 60: 60: 0 System : 256 atoms 60: 1 Protein : 256 atoms 60: 2 Protein-H : 139 atoms 60: 3 C-alpha : 16 atoms 60: 4 Backbone : 48 atoms 60: 5 MainChain : 63 atoms 60: 6 MainChain+Cb : 78 atoms 60: 7 MainChain+H : 81 atoms 60: 8 SideChain : 175 atoms 60: 9 SideChain-H : 76 atoms 60: 60: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 60: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 60: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 60: 'r': residue 'res' nr 'chain' char 60: "name": group 'case': case sensitive 'q': save and quit 60: 'ri': residue index 60: 60: > 60: [ OK ] GmxMakeNdx.WritesDefaultProteinIndexGroups (4 ms) 60: [ RUN ] GmxMakeNdx.HandlesNoStructureInput 60: Going to read 1 old index file(s) 60: Deducing 22 atoms in the system from indices in the index file 60: 60: 0 System : 22 atoms 60: 1 Protein : 22 atoms 60: 2 Protein-H : 10 atoms 60: 3 C-alpha : 1 atoms 60: 4 Backbone : 5 atoms 60: 5 MainChain : 7 atoms 60: 6 MainChain+Cb : 8 atoms 60: 7 MainChain+H : 9 atoms 60: 8 SideChain : 13 atoms 60: 9 SideChain-H : 3 atoms 60: 10 CA : 1 atoms 60: 11 C_&_r_1 : 1 atoms 60: 12 C_&_r_2 : 1 atoms 60: 13 N_&_r_2 : 1 atoms 60: 14 N_&_r_3 : 1 atoms 60: 60: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 60: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 60: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 60: 'r': residue 'res' nr 'chain' char 60: "name": group 'case': case sensitive 'q': save and quit 60: 'ri': residue index 60: 60: > 60: Copied index group 1 'Protein' 60: Copied index group 2 'Protein-H' 60: Merged two groups with OR: 22 10 -> 22 60: 60: > 60: [ OK ] GmxMakeNdx.HandlesNoStructureInput (1 ms) 60: [ RUN ] GmxMakeNdx.HandlesNotProtein 60: Going to read 1 old index file(s) 60: Deducing 6 atoms in the system from indices in the index file 60: 60: 0 System : 6 atoms 60: 60: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 60: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 60: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 60: 'r': residue 'res' nr 'chain' char 60: "name": group 'case': case sensitive 'q': save and quit 60: 'ri': residue index 60: 60: > 60: [ OK ] GmxMakeNdx.HandlesNotProtein (0 ms) 60: [ RUN ] GmxMakeNdx.HandlesEmptyIndexResult 60: Going to read 1 old index file(s) 60: Deducing 22 atoms in the system from indices in the index file 60: 60: 0 System : 22 atoms 60: 1 Protein : 22 atoms 60: 2 Protein-H : 10 atoms 60: 3 C-alpha : 1 atoms 60: 4 Backbone : 5 atoms 60: 5 MainChain : 7 atoms 60: 6 MainChain+Cb : 8 atoms 60: 7 MainChain+H : 9 atoms 60: 8 SideChain : 13 atoms 60: 9 SideChain-H : 3 atoms 60: 10 CA : 1 atoms 60: 11 C_&_r_1 : 1 atoms 60: 12 C_&_r_2 : 1 atoms 60: 13 N_&_r_2 : 1 atoms 60: 14 N_&_r_3 : 1 atoms 60: 60: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 60: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 60: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 60: 'r': residue 'res' nr 'chain' char 60: "name": group 'case': case sensitive 'q': save and quit 60: 'ri': residue index 60: 60: > 60: Copied index group 4 'Backbone' 60: Copied index group 8 'SideChain' 60: Merged two groups with AND: 5 13 -> 0 60: Group is empty 60: 60: > 60: [ OK ] GmxMakeNdx.HandlesEmptyIndexResult (0 ms) 60: [ RUN ] GmxMakeNdx.HandlesEmptyIndexFile 60: Going to read 1 old index file(s) 60: Deducing 6 atoms in the system from indices in the index file 60: 60: 0 System : 6 atoms 60: 60: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 60: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 60: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 60: 'r': residue 'res' nr 'chain' char 60: "name": group 'case': case sensitive 'q': save and quit 60: 'ri': residue index 60: 60: > 60: Removed group 0 'System' 60: 60: > 60: [ OK ] GmxMakeNdx.HandlesEmptyIndexFile (0 ms) 60: [ RUN ] GmxMakeNdx.Splitres 60: 60: Reading structure file 60: Going to read 0 old index file(s) 60: Analysing residue names: 60: There are: 2 Water residues 60: 60: 0 System : 6 atoms 60: 1 Water : 6 atoms 60: 2 SOL : 6 atoms 60: 60: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 60: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 60: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 60: 'r': residue 'res' nr 'chain' char 60: "name": group 'case': case sensitive 'q': save and quit 60: 'ri': residue index 60: 60: > 60: Splitting group 1 'Water' into residues 60: 60: > 60: [ OK ] GmxMakeNdx.Splitres (1 ms) 60: [ RUN ] GmxMakeNdx.Splitat 60: 60: Reading structure file 60: Going to read 0 old index file(s) 60: Analysing residue names: 60: There are: 2 Water residues 60: 60: 0 System : 6 atoms 60: 1 Water : 6 atoms 60: 2 SOL : 6 atoms 60: 60: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 60: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 60: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 60: 'r': residue 'res' nr 'chain' char 60: "name": group 'case': case sensitive 'q': save and quit 60: 'ri': residue index 60: 60: > 60: Splitting group 1 'Water' into atoms 60: 60: > 60: [ OK ] GmxMakeNdx.Splitat (1 ms) 60: [----------] 7 tests from GmxMakeNdx (10 ms total) 60: 60: [----------] 4 tests from ReportMethodsTest 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file lysozyme.top, line 1465]: 60: System has non-zero total charge: 2.000000 60: Total charge should normally be an integer. See 60: https://manual.gromacs.org/current/user-guide/floating-point.html 60: for discussion on how close it should be to an integer. 60: 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 465.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 60: NVE simulation with an initial temperature of zero: will use a Verlet 60: buffer of 10%. Check your energy drift! 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 NOTEs 60: Setting the LD random seed to 2146828239 60: 60: Generated 330891 of the 330891 non-bonded parameter combinations 60: 60: Generated 330891 of the 330891 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 60: Analysing residue names: 60: There are: 10 Protein residues 60: Analysing Protein... 60: 60: This run will generate roughly 0 Mb of data 60: [ RUN ] ReportMethodsTest.WritesCorrectHeadersFormated 60: [ OK ] ReportMethodsTest.WritesCorrectHeadersFormated (0 ms) 60: [ RUN ] ReportMethodsTest.WritesCorrectHeadersUnformatted 60: [ OK ] ReportMethodsTest.WritesCorrectHeadersUnformatted (0 ms) 60: [ RUN ] ReportMethodsTest.WritesCorrectInformation 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 60: [ OK ] ReportMethodsTest.WritesCorrectInformation (0 ms) 60: [ RUN ] ReportMethodsTest.ToolEndToEndTest 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 60: section: Methods 60: subsection: Simulation system 60: A system of 1 molecules (156 atoms) was simulated. 60: 60: subsection: Simulation settings 60: A total of 0 ns were simulated with a time step of 1 fs. 60: Neighbor searching was performed every 10 steps. 60: The Cut-off algorithm was used for electrostatic interactions. 60: with a cut-off of 1 nm. 60: A single cut-off of 1.1 nm was used for Van der Waals interactions. 60: [ OK ] ReportMethodsTest.ToolEndToEndTest (0 ms) 60: [----------] 4 tests from ReportMethodsTest (1 ms total) 60: 60: [----------] 4 tests from ConvertTprTest 60: [ RUN ] ConvertTprTest.ExtendRuntimeExtensionTest 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file lysozyme.top, line 1465]: 60: System has non-zero total charge: 2.000000 60: Total charge should normally be an integer. See 60: https://manual.gromacs.org/current/user-guide/floating-point.html 60: for discussion on how close it should be to an integer. 60: 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 465.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 60: NVE simulation with an initial temperature of zero: will use a Verlet 60: buffer of 10%. Check your energy drift! 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended_again.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 60: Setting the LD random seed to -75890945 60: 60: Generated 330891 of the 330891 non-bonded parameter combinations 60: 60: Generated 330891 of the 330891 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 60: Analysing residue names: 60: There are: 10 Protein residues 60: Analysing Protein... 60: 60: This run will generate roughly 0 Mb of data 60: Input file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 0 60: Runtime for the run 0 ps 60: Run end step 0 60: Run end time 0 ps 60: 60: Extending remaining runtime by 100 ps 60: 60: Output file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 100000 60: Runtime for the run 100 ps 60: Run end step 100000 60: Run end time 100 ps 60: 60: Input file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 100000 60: Runtime for the run 100 ps 60: Run end step 100000 60: Run end time 100 ps 60: 60: Extending remaining runtime by 100 ps 60: 60: Output file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 200000 60: Runtime for the run 200 ps 60: Run end step 200000 60: Run end time 200 ps 60: 60: [ OK ] ConvertTprTest.ExtendRuntimeExtensionTest (526 ms) 60: [ RUN ] ConvertTprTest.UntilRuntimeExtensionTest 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file lysozyme.top, line 1465]: 60: System has non-zero total charge: 2.000000 60: Total charge should normally be an integer. See 60: https://manual.gromacs.org/current/user-guide/floating-point.html 60: for discussion on how close it should be to an integer. 60: 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 465.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 60: NVE simulation with an initial temperature of zero: will use a Verlet 60: buffer of 10%. Check your energy drift! 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_extended.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 60: Setting the LD random seed to -3817218 60: 60: Generated 330891 of the 330891 non-bonded parameter combinations 60: 60: Generated 330891 of the 330891 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 60: Analysing residue names: 60: There are: 10 Protein residues 60: Analysing Protein... 60: 60: This run will generate roughly 0 Mb of data 60: Input file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 0 60: Runtime for the run 0 ps 60: Run end step 0 60: Run end time 0 ps 60: 60: Extending remaining runtime to 100 ps 60: 60: Output file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 100000 60: Runtime for the run 100 ps 60: Run end step 100000 60: Run end time 100 ps 60: 60: [ OK ] ConvertTprTest.UntilRuntimeExtensionTest (781 ms) 60: [ RUN ] ConvertTprTest.nstepRuntimeExtensionTest 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file lysozyme.top, line 1465]: 60: System has non-zero total charge: 2.000000 60: Total charge should normally be an integer. See 60: https://manual.gromacs.org/current/user-guide/floating-point.html 60: for discussion on how close it should be to an integer. 60: 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 465.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 60: NVE simulation with an initial temperature of zero: will use a Verlet 60: buffer of 10%. Check your energy drift! 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 60: Setting nsteps to 102 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_extended.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 60: Setting the LD random seed to -136577025 60: 60: Generated 330891 of the 330891 non-bonded parameter combinations 60: 60: Generated 330891 of the 330891 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 60: Analysing residue names: 60: There are: 10 Protein residues 60: Analysing Protein... 60: 60: This run will generate roughly 0 Mb of data 60: Input file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 0 60: Runtime for the run 0 ps 60: Run end step 0 60: Run end time 0 ps 60: 60: 60: Output file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 102 60: Runtime for the run 0.102 ps 60: Run end step 102 60: Run end time 0.102 ps 60: 60: [ OK ] ConvertTprTest.nstepRuntimeExtensionTest (496 ms) 60: [ RUN ] ConvertTprTest.generateVelocitiesTest 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file lysozyme.top, line 1465]: 60: System has non-zero total charge: 2.000000 60: Total charge should normally be an integer. See 60: https://manual.gromacs.org/current/user-guide/floating-point.html 60: for discussion on how close it should be to an integer. 60: 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 465.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 60: NVE simulation with an initial temperature of zero: will use a Verlet 60: buffer of 10%. Check your energy drift! 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_new_velocities.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 60: Setting the LD random seed to -4228615 60: 60: Generated 330891 of the 330891 non-bonded parameter combinations 60: 60: Generated 330891 of the 330891 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 60: Analysing residue names: 60: There are: 10 Protein residues 60: Analysing Protein... 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] ConvertTprTest.generateVelocitiesTest (650 ms) 60: [----------] 4 tests from ConvertTprTest (2454 ms total) 60: 60: [----------] 1 test from ConvertTprNoVelocityTest 60: [ RUN ] ConvertTprNoVelocityTest.refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest_lysozyme.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file lysozyme.top, line 1465]: 60: System has non-zero total charge: 2.000000 60: Total charge should normally be an integer. See 60: https://manual.gromacs.org/current/user-guide/floating-point.html 60: for discussion on how close it should be to an integer. 60: 60: 60: 60: 60: NOTE 3 [file lysozyme.top, line 1465]: 60: Zero-step energy minimization will alter the coordinates before 60: calculating the energy. If you just want the energy of a single point, 60: try zero-step MD (with unconstrained_start = yes). To do multiple 60: single-point energy evaluations of different configurations of the same 60: topology, use mdrun -rerun. 60: 60: Number of degrees of freedom in T-Coupling group rest is 465.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest_lysozyme.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 60: Setting the LD random seed to -4493313 60: 60: Generated 330891 of the 330891 non-bonded parameter combinations 60: 60: Generated 330891 of the 330891 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 60: Analysing residue names: 60: There are: 10 Protein residues 60: Analysing Protein... 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] ConvertTprNoVelocityTest.refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest (572 ms) 60: [----------] 1 test from ConvertTprNoVelocityTest (573 ms total) 60: 60: [----------] 12 tests from Works/TrjconvWithDifferentInputFormats 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_trr 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: trr version: GMX_trn_file (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_trr (2 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_tng 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 60: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_tng (1 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_xtc 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_xtc (0 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_gro 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 60: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_gro (0 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_pdb 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 60: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 60: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_pdb (0 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_g96 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_g96 (0 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_trr 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_trr (2 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_tng 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 60: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_tng (1 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_xtc 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_xtc (0 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_gro 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 60: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_gro (2 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_pdb 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 60: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 60: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_pdb (0 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_g96 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_g96 (1 ms) 60: [----------] 12 tests from Works/TrjconvWithDifferentInputFormats (17 ms total) 60: 60: [----------] 30 tests from Works/TrjconvDumpTest 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time__1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time__1_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_30 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_30 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_1_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_999999_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_999999_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time__1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 60: Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time__1_00 (1 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 60: Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_30 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 60: Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_30 (1 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 60: Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_1_00 (1 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_999999_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 60: Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_999999_00 (1 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time__1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time__1_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_30 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_30 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_1_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_999999_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_999999_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time__1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 60: Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time__1_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 60: Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_30 60: Will write trr: Trajectory in portable xdr format 60: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 60: Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_30 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 60: Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_1_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_999999_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 60: Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_999999_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time__1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 60: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 60: Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time__1_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 60: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 60: Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_30 60: Will write trr: Trajectory in portable xdr format 60: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 60: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 60: Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_30 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 60: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 60: Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_1_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_999999_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 60: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 60: Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_999999_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time__1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time__1_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_30 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_30 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_1_00 (1 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_999999_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_999999_00 (0 ms) 60: [----------] 30 tests from Works/TrjconvDumpTest (22 ms total) 60: 60: [----------] Global test environment tear-down 60: [==========] 63 tests from 8 test suites ran. (4179 ms total) 60: [ PASSED ] 63 tests. 60/90 Test #60: ToolUnitTests ............................. Passed 4.20 sec test 61 Start 61: ToolWithLeaksUnitTests 61: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/tool-test-with-leaks "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/ToolWithLeaksUnitTests.xml" 61: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests 61: Test timeout computed to be: 1920 61: [==========] Running 2 tests from 2 test suites. 61: [----------] Global test environment set-up. 61: [----------] 1 test from ConvertTprTest 61: [ RUN ] ConvertTprTest.selectIndexTest 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.mdp]: 61: For a correct single-point energy evaluation with nsteps = 0, use 61: continuation = yes to avoid constraining the input coordinates. 61: 61: Generating 1-4 interactions: fudge = 0.5 61: 61: NOTE 2 [file lysozyme.top, line 1465]: 61: System has non-zero total charge: 2.000000 61: Total charge should normally be an integer. See 61: https://manual.gromacs.org/current/user-guide/floating-point.html 61: for discussion on how close it should be to an integer. 61: 61: 61: 61: Number of degrees of freedom in T-Coupling group rest is 465.00 61: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 61: 61: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.mdp]: 61: NVE simulation with an initial temperature of zero: will use a Verlet 61: buffer of 10%. Check your energy drift! 61: 61: 61: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There were 4 NOTEs 61: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 61: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 61: Group 0 ( System) has 156 elements 61: Group 1 ( Protein) has 156 elements 61: Group 2 ( Protein-H) has 75 elements 61: Group 3 ( C-alpha) has 10 elements 61: Group 4 ( Backbone) has 30 elements 61: Group 5 ( MainChain) has 40 elements 61: Group 6 ( MainChain+Cb) has 49 elements 61: Group 7 ( MainChain+H) has 52 elements 61: Group 8 ( SideChain) has 104 elements 61: Group 9 ( SideChain-H) has 35 elements 61: Select a group: Will write subset Protein-H of original tpx containing 75 atoms 61: Reduced ilist BONDS from 156 to 75 entries 61: Reduced ilist ANGLES from 281 to 98 entries 61: Reduced ilist PDIHS from 29 to 12 entries 61: Reduced ilist RBDIHS from 313 to 89 entries 61: Reduced ilist LJ14 from 399 to 107 entries 61: Reduced block excls from 156 to 75 index-, 1828 to 635 a-entries 61: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_extended.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 61: Setting the LD random seed to -8421377 61: 61: Generated 330891 of the 330891 non-bonded parameter combinations 61: 61: Generated 330891 of the 330891 1-4 parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 61: 61: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 61: Analysing residue names: 61: There are: 10 Protein residues 61: Analysing Protein... 61: 61: This run will generate roughly 0 Mb of data 61: Selected 2: 'Protein-H' 61: [ OK ] ConvertTprTest.selectIndexTest (617 ms) 61: [----------] 1 test from ConvertTprTest (617 ms total) 61: 61: [----------] 1 test from ConvertTprNoVelocityTest 61: [ RUN ] ConvertTprNoVelocityTest.selectIndexTestWithoutVelocity 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.mdp]: 61: For a correct single-point energy evaluation with nsteps = 0, use 61: continuation = yes to avoid constraining the input coordinates. 61: 61: Generating 1-4 interactions: fudge = 0.5 61: 61: NOTE 2 [file lysozyme.top, line 1465]: 61: System has non-zero total charge: 2.000000 61: Total charge should normally be an integer. See 61: https://manual.gromacs.org/current/user-guide/floating-point.html 61: for discussion on how close it should be to an integer. 61: 61: 61: 61: 61: NOTE 3 [file lysozyme.top, line 1465]: 61: Zero-step energy minimization will alter the coordinates before 61: calculating the energy. If you just want the energy of a single point, 61: try zero-step MD (with unconstrained_start = yes). To do multiple 61: single-point energy evaluations of different configurations of the same 61: topology, use mdrun -rerun. 61: 61: Number of degrees of freedom in T-Coupling group rest is 465.00 61: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 61: 61: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There were 4 NOTEs 61: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 61: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 61: Group 0 ( System) has 156 elements 61: Group 1 ( Protein) has 156 elements 61: Group 2 ( Protein-H) has 75 elements 61: Group 3 ( C-alpha) has 10 elements 61: Group 4 ( Backbone) has 30 elements 61: Group 5 ( MainChain) has 40 elements 61: Group 6 ( MainChain+Cb) has 49 elements 61: Group 7 ( MainChain+H) has 52 elements 61: Group 8 ( SideChain) has 104 elements 61: Group 9 ( SideChain-H) has 35 elements 61: Select a group: Will write subset Protein-H of original tpx containing 75 atoms 61: Reduced ilist BONDS from 156 to 75 entries 61: Reduced ilist ANGLES from 281 to 98 entries 61: Reduced ilist PDIHS from 29 to 12 entries 61: Reduced ilist RBDIHS from 313 to 89 entries 61: Reduced ilist LJ14 from 399 to 107 entries 61: Reduced block excls from 156 to 75 index-, 1828 to 635 a-entries 61: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_extended.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 61: Setting the LD random seed to -672664162 61: 61: Generated 330891 of the 330891 non-bonded parameter combinations 61: 61: Generated 330891 of the 330891 1-4 parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 61: Analysing residue names: 61: There are: 10 Protein residues 61: Analysing Protein... 61: 61: This run will generate roughly 0 Mb of data 61: Selected 2: 'Protein-H' 61: [ OK ] ConvertTprNoVelocityTest.selectIndexTestWithoutVelocity (695 ms) 61: [----------] 1 test from ConvertTprNoVelocityTest (695 ms total) 61: 61: [----------] Global test environment tear-down 61: [==========] 2 tests from 2 test suites ran. (1312 ms total) 61: [ PASSED ] 2 tests. 61/90 Test #61: ToolWithLeaksUnitTests .................... Passed 1.35 sec test 62 Start 62: FileIOTests 62: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/fileio-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/FileIOTests.xml" 62: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/fileio/tests 62: Test timeout computed to be: 30 62: [==========] Running 421 tests from 17 test suites. 62: [----------] Global test environment set-up. 62: [----------] 4 tests from Checkpoint 62: [ RUN ] Checkpoint.ReadingThrowsWhenValueNotPresent 62: [ OK ] Checkpoint.ReadingThrowsWhenValueNotPresent (0 ms) 62: [ RUN ] Checkpoint.ReadingDoesNotThrowWhenValuePresent 62: [ OK ] Checkpoint.ReadingDoesNotThrowWhenValuePresent (0 ms) 62: [ RUN ] Checkpoint.KvtRoundTripInt64 62: [ OK ] Checkpoint.KvtRoundTripInt64 (0 ms) 62: [ RUN ] Checkpoint.KvtRoundTripReal 62: [ OK ] Checkpoint.KvtRoundTripReal (0 ms) 62: [----------] 4 tests from Checkpoint (0 ms total) 62: 62: [----------] 1 test from StructureIOTest 62: [ RUN ] StructureIOTest.ReadTpsConfRetainsChainids 62: [ OK ] StructureIOTest.ReadTpsConfRetainsChainids (0 ms) 62: [----------] 1 test from StructureIOTest (0 ms total) 62: 62: [----------] 2 tests from FileMD5Test 62: [ RUN ] FileMD5Test.CanComputeMD5 62: [ OK ] FileMD5Test.CanComputeMD5 (6 ms) 62: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong 62: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (1 ms) 62: [----------] 2 tests from FileMD5Test (8 ms total) 62: 62: [----------] 4 tests from FileTypeTest 62: [ RUN ] FileTypeTest.CorrectValueForEmptyString 62: [ OK ] FileTypeTest.CorrectValueForEmptyString (0 ms) 62: [ RUN ] FileTypeTest.CorrectValueForNoExtension 62: [ OK ] FileTypeTest.CorrectValueForNoExtension (0 ms) 62: [ RUN ] FileTypeTest.CorrectValueForEmptyExtension 62: [ OK ] FileTypeTest.CorrectValueForEmptyExtension (0 ms) 62: [ RUN ] FileTypeTest.CorrectValueForLongExtensionWithStrangeCharacters 62: [ OK ] FileTypeTest.CorrectValueForLongExtensionWithStrangeCharacters (0 ms) 62: [----------] 4 tests from FileTypeTest (0 ms total) 62: 62: [----------] 4 tests from ColorMapTest 62: [ RUN ] ColorMapTest.CanReadFromFile 62: [ OK ] ColorMapTest.CanReadFromFile (0 ms) 62: [ RUN ] ColorMapTest.CanWriteToFile 62: [ OK ] ColorMapTest.CanWriteToFile (0 ms) 62: [ RUN ] ColorMapTest.RoundTrip 62: [ OK ] ColorMapTest.RoundTrip (0 ms) 62: [ RUN ] ColorMapTest.SearchWorks 62: [ OK ] ColorMapTest.SearchWorks (0 ms) 62: [----------] 4 tests from ColorMapTest (2 ms total) 62: 62: [----------] 4 tests from MatioTest 62: [ RUN ] MatioTest.CanWriteToFile 62: 33% 66%100%[ OK ] MatioTest.CanWriteToFile (0 ms) 62: [ RUN ] MatioTest.CanConvertToExistingRealMatrix 62: Converted a 4x3 matrix with 4 levels to reals 62: [ OK ] MatioTest.CanConvertToExistingRealMatrix (0 ms) 62: [ RUN ] MatioTest.CanConvertToNewRealMatrix 62: Converted a 4x3 matrix with 4 levels to reals 62: [ OK ] MatioTest.CanConvertToNewRealMatrix (0 ms) 62: [ RUN ] MatioTest.CanReadSingleMatrixAfterWriting 62: 33% 66%100% 33% 66%100%[ OK ] MatioTest.CanReadSingleMatrixAfterWriting (4 ms) 62: [----------] 4 tests from MatioTest (4 ms total) 62: 62: [----------] 3 tests from MrcSerializer 62: [ RUN ] MrcSerializer.DefaultHeaderValuesAreSet 62: [ OK ] MrcSerializer.DefaultHeaderValuesAreSet (0 ms) 62: [ RUN ] MrcSerializer.DefaultHeaderHasRightSerialSize 62: [ OK ] MrcSerializer.DefaultHeaderHasRightSerialSize (0 ms) 62: [ RUN ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip 62: [ OK ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip (0 ms) 62: [----------] 3 tests from MrcSerializer (0 ms total) 62: 62: [----------] 4 tests from MrcDensityMap 62: [ RUN ] MrcDensityMap.RoundTripIsIdempotent 62: [ OK ] MrcDensityMap.RoundTripIsIdempotent (0 ms) 62: [ RUN ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent 62: [ OK ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent (0 ms) 62: [ RUN ] MrcDensityMap.ReadsCoordinateTransformationFromFile 62: [ OK ] MrcDensityMap.ReadsCoordinateTransformationFromFile (0 ms) 62: [ RUN ] MrcDensityMap.ReadsDensityDataFromFile 62: [ OK ] MrcDensityMap.ReadsDensityDataFromFile (1 ms) 62: [----------] 4 tests from MrcDensityMap (1 ms total) 62: 62: [----------] 8 tests from MrcDensityMapHeaderTest 62: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader 62: [ OK ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader (0 ms) 62: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsCorrect 62: [ OK ] MrcDensityMapHeaderTest.DataSizeIsCorrect (0 ms) 62: [ RUN ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid 62: [ OK ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid (0 ms) 62: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven 62: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven (0 ms) 62: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined 62: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined (0 ms) 62: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues 62: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues (0 ms) 62: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectExtents 62: [ OK ] MrcDensityMapHeaderTest.GetsCorrectExtents (0 ms) 62: [ RUN ] MrcDensityMapHeaderTest.IsSane 62: [ OK ] MrcDensityMapHeaderTest.IsSane (0 ms) 62: [----------] 8 tests from MrcDensityMapHeaderTest (0 ms total) 62: 62: [----------] 10 tests from ReadTest 62: [ RUN ] ReadTest.get_eint_ReadsInteger 62: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms) 62: [ RUN ] ReadTest.get_eint_WarnsAboutFloat 62: 62: ERROR 1 [file unknown]: 62: Right hand side '0.8' for parameter 'test' in parameter file is not an 62: integer value 62: 62: 62: [ OK ] ReadTest.get_eint_WarnsAboutFloat (0 ms) 62: [ RUN ] ReadTest.get_eint_WarnsAboutString 62: 62: ERROR 1 [file unknown]: 62: Right hand side 'hello' for parameter 'test' in parameter file is not an 62: integer value 62: 62: 62: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms) 62: [ RUN ] ReadTest.get_eint64_ReadsInteger 62: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms) 62: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat 62: 62: ERROR 1 [file unknown]: 62: Right hand side '0.8' for parameter 'test' in parameter file is not an 62: integer value 62: 62: 62: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (0 ms) 62: [ RUN ] ReadTest.get_eint64_WarnsAboutString 62: 62: ERROR 1 [file unknown]: 62: Right hand side 'hello' for parameter 'test' in parameter file is not an 62: integer value 62: 62: 62: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms) 62: [ RUN ] ReadTest.get_ereal_ReadsInteger 62: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms) 62: [ RUN ] ReadTest.get_ereal_ReadsFloat 62: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms) 62: [ RUN ] ReadTest.get_ereal_WarnsAboutString 62: 62: ERROR 1 [file unknown]: 62: Right hand side 'hello' for parameter 'test' in parameter file is not a 62: real value 62: 62: 62: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms) 62: [ RUN ] ReadTest.setStringEntry_ReturnsCorrectString 62: [ OK ] ReadTest.setStringEntry_ReturnsCorrectString (0 ms) 62: [----------] 10 tests from ReadTest (0 ms total) 62: 62: [----------] 3 tests from TimeControlTest 62: [ RUN ] TimeControlTest.UnSetHasNoValue 62: [ OK ] TimeControlTest.UnSetHasNoValue (0 ms) 62: [ RUN ] TimeControlTest.CanSetValue 62: [ OK ] TimeControlTest.CanSetValue (0 ms) 62: [ RUN ] TimeControlTest.CanUnsetValueAgain 62: [ OK ] TimeControlTest.CanUnsetValueAgain (0 ms) 62: [----------] 3 tests from TimeControlTest (0 ms total) 62: 62: [----------] 1 test from FileIOXdrSerializerTest 62: [ RUN ] FileIOXdrSerializerTest.SizeIsCorrect 62: [ OK ] FileIOXdrSerializerTest.SizeIsCorrect (0 ms) 62: [----------] 1 test from FileIOXdrSerializerTest (0 ms total) 62: 62: [----------] 1 test from TngTest 62: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal 62: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms) 62: [----------] 1 test from TngTest (0 ms total) 62: 62: [----------] 4 tests from XvgioTest 62: [ RUN ] XvgioTest.readXvgIntWorks 62: [ OK ] XvgioTest.readXvgIntWorks (0 ms) 62: [ RUN ] XvgioTest.readXvgRealWorks 62: [ OK ] XvgioTest.readXvgRealWorks (0 ms) 62: [ RUN ] XvgioTest.readXvgIgnoreCommentLineWorks 62: [ OK ] XvgioTest.readXvgIgnoreCommentLineWorks (0 ms) 62: [ RUN ] XvgioTest.readXvgDeprecatedWorks 62: [ OK ] XvgioTest.readXvgDeprecatedWorks (0 ms) 62: [----------] 4 tests from XvgioTest (0 ms total) 62: 62: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest 62: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 62: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (0 ms) 62: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 62: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (0 ms) 62: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 62: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (0 ms) 62: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 62: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (0 ms) 62: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (1 ms total) 62: 62: [----------] 360 tests from FileTypeMatch/FileTypeTest 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/0 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/0 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/1 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/1 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/2 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/2 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/3 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/3 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/4 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/4 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/5 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/5 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/6 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/6 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/7 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/7 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/8 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/8 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/9 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/9 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/10 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/10 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/11 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/11 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/12 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/12 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/13 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/13 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/14 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/14 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/15 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/15 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/16 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/16 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/17 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/17 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/18 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/18 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/19 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/19 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/20 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/20 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/21 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/21 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/22 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/22 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/23 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/23 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/24 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/24 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/25 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/25 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/26 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/26 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/27 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/27 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/28 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/28 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/29 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/29 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/30 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/30 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/31 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/31 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/32 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/32 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/33 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/33 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/34 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/34 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/35 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/35 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/36 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/36 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/37 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/37 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/38 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/38 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/39 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/39 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/40 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/40 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/41 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/41 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/42 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/42 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/43 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/43 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/44 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/44 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/45 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/45 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/46 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/46 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/47 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/47 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/48 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/48 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/49 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/49 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/50 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/50 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/51 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/51 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/52 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/52 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/53 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/53 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/54 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/54 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/55 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/55 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/56 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/56 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/57 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/57 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/58 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/58 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/59 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/59 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/60 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/60 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/61 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/61 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/62 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/62 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/63 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/63 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/64 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/64 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/65 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/65 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/66 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/66 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/67 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/67 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/68 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/68 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/69 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/69 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/70 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/70 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/71 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/71 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/72 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/72 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/73 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/73 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/74 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/74 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/75 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/75 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/76 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/76 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/77 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/77 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/78 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/78 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/79 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/79 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/80 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/80 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/81 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/81 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/82 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/82 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/83 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/83 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/84 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/84 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/85 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/85 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/86 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/86 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/87 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/87 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/88 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/88 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/89 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/89 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/90 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/90 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/91 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/91 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/92 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/92 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/93 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/93 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/94 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/94 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/95 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/95 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/96 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/96 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/97 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/97 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/98 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/98 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/99 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/99 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/100 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/100 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/101 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/101 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/102 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/102 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/103 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/103 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/104 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/104 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/105 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/105 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/106 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/106 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/107 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/107 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/108 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/108 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/109 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/109 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/110 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/110 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/111 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/111 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/112 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/112 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/113 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/113 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/114 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/114 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/115 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/115 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/116 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/116 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/117 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/117 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/118 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/118 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/119 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/119 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/120 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/120 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/121 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/121 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/122 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/122 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/123 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/123 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/124 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/124 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/125 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/125 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/126 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/126 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/127 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/127 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/128 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/128 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/129 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/129 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/130 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/130 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/131 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/131 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/132 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/132 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/133 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/133 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/134 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/134 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/135 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/135 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/136 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/136 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/137 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/137 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/138 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/138 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/139 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/139 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/140 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/140 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/141 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/141 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/142 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/142 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/143 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/143 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/144 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/144 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/145 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/145 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/146 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/146 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/147 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/147 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/148 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/148 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/149 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/149 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/150 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/150 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/151 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/151 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/152 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/152 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/153 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/153 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/154 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/154 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/155 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/155 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/156 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/156 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/157 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/157 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/158 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/158 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/159 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/159 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/160 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/160 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/161 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/161 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/162 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/162 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/163 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/163 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/164 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/164 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/165 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/165 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/166 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/166 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/167 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/167 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/168 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/168 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/169 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/169 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/170 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/170 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/171 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/171 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/172 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/172 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/173 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/173 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/174 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/174 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/175 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/175 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/176 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/176 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/177 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/177 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/178 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/178 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/179 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/179 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/0 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/0 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/1 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/1 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/2 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/2 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/3 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/3 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/4 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/4 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/5 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/5 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/6 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/6 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/7 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/7 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/8 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/8 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/9 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/9 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/10 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/10 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/11 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/11 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/12 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/12 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/13 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/13 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/14 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/14 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/15 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/15 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/16 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/16 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/17 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/17 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/18 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/18 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/19 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/19 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/20 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/20 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/21 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/21 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/22 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/22 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/23 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/23 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/24 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/24 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/25 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/25 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/26 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/26 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/27 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/27 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/28 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/28 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/29 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/29 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/30 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/30 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/31 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/31 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/32 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/32 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/33 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/33 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/34 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/34 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/35 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/35 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/36 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/36 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/37 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/37 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/38 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/38 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/39 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/39 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/40 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/40 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/41 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/41 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/42 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/42 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/43 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/43 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/44 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/44 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/45 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/45 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/46 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/46 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/47 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/47 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/48 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/48 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/49 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/49 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/50 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/50 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/51 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/51 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/52 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/52 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/53 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/53 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/54 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/54 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/55 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/55 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/56 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/56 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/57 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/57 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/58 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/58 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/59 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/59 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/60 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/60 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/61 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/61 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/62 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/62 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/63 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/63 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/64 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/64 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/65 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/65 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/66 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/66 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/67 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/67 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/68 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/68 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/69 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/69 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/70 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/70 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/71 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/71 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/72 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/72 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/73 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/73 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/74 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/74 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/75 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/75 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/76 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/76 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/77 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/77 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/78 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/78 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/79 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/79 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/80 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/80 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/81 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/81 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/82 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/82 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/83 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/83 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/84 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/84 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/85 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/85 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/86 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/86 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/87 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/87 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/88 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/88 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/89 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/89 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/90 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/90 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/91 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/91 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/92 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/92 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/93 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/93 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/94 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/94 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/95 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/95 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/96 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/96 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/97 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/97 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/98 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/98 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/99 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/99 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/100 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/100 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/101 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/101 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/102 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/102 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/103 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/103 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/104 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/104 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/105 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/105 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/106 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/106 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/107 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/107 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/108 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/108 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/109 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/109 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/110 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/110 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/111 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/111 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/112 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/112 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/113 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/113 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/114 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/114 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/115 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/115 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/116 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/116 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/117 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/117 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/118 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/118 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/119 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/119 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/120 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/120 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/121 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/121 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/122 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/122 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/123 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/123 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/124 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/124 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/125 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/125 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/126 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/126 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/127 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/127 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/128 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/128 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/129 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/129 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/130 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/130 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/131 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/131 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/132 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/132 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/133 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/133 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/134 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/134 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/135 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/135 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/136 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/136 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/137 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/137 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/138 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/138 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/139 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/139 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/140 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/140 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/141 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/141 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/142 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/142 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/143 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/143 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/144 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/144 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/145 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/145 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/146 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/146 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/147 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/147 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/148 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/148 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/149 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/149 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/150 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/150 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/151 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/151 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/152 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/152 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/153 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/153 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/154 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/154 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/155 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/155 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/156 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/156 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/157 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/157 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/158 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/158 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/159 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/159 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/160 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/160 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/161 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/161 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/162 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/162 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/163 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/163 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/164 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/164 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/165 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/165 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/166 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/166 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/167 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/167 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/168 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/168 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/169 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/169 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/170 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/170 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/171 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/171 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/172 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/172 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/173 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/173 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/174 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/174 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/175 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/175 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/176 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/176 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/177 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/177 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/178 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/178 (0 ms) 62: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/179 62: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/179 (0 ms) 62: [----------] 360 tests from FileTypeMatch/FileTypeTest (3 ms total) 62: 62: [----------] 4 tests from XvgReadTimeSeries/XvgioTest 62: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/0 62: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/0 (3 ms) 62: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/1 62: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/1 (0 ms) 62: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/2 62: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/2 (0 ms) 62: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/3 62: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/3 (0 ms) 62: [----------] 4 tests from XvgReadTimeSeries/XvgioTest (4 ms total) 62: 62: [----------] Global test environment tear-down 62: [==========] 421 tests from 17 test suites ran. (28 ms total) 62: [ PASSED ] 421 tests. 62/90 Test #62: FileIOTests ............................... Passed 0.08 sec test 63 Start 63: SelectionUnitTests 63: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/selection-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/SelectionUnitTests.xml" 63: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/selection/tests 63: Test timeout computed to be: 30 63: [==========] Running 201 tests from 11 test suites. 63: [----------] Global test environment set-up. 63: [----------] 1 test from IndexGroupTest 63: [ RUN ] IndexGroupTest.RemovesDuplicates 63: [ OK ] IndexGroupTest.RemovesDuplicates (0 ms) 63: [----------] 1 test from IndexGroupTest (0 ms total) 63: 63: [----------] 15 tests from IndexBlockTest 63: [ RUN ] IndexBlockTest.CreatesUnknownBlock 63: [ OK ] IndexBlockTest.CreatesUnknownBlock (0 ms) 63: [ RUN ] IndexBlockTest.CreatesAtomBlock 63: [ OK ] IndexBlockTest.CreatesAtomBlock (0 ms) 63: [ RUN ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology 63: [ OK ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology (0 ms) 63: [ RUN ] IndexBlockTest.CreatesResidueBlocksForComplexTopology 63: [ OK ] IndexBlockTest.CreatesResidueBlocksForComplexTopology (0 ms) 63: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology 63: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology (0 ms) 63: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology 63: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology (0 ms) 63: [ RUN ] IndexBlockTest.CreatesSingleBlock 63: [ OK ] IndexBlockTest.CreatesSingleBlock (0 ms) 63: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksPositive 63: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksPositive (0 ms) 63: [ RUN ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive 63: [ OK ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive (0 ms) 63: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksNegative 63: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksNegative (0 ms) 63: [ RUN ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial 63: [ OK ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial (0 ms) 63: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive 63: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive (0 ms) 63: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative 63: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative (0 ms) 63: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive 63: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive (0 ms) 63: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative 63: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative (0 ms) 63: [----------] 15 tests from IndexBlockTest (1 ms total) 63: 63: [----------] 11 tests from IndexMapTest 63: [ RUN ] IndexMapTest.InitializesAtomBlock 63: [ OK ] IndexMapTest.InitializesAtomBlock (0 ms) 63: [ RUN ] IndexMapTest.InitializesOrgIdGroupAtom 63: [ OK ] IndexMapTest.InitializesOrgIdGroupAtom (0 ms) 63: [ RUN ] IndexMapTest.InitializesOrgIdGroupSingle 63: [ OK ] IndexMapTest.InitializesOrgIdGroupSingle (0 ms) 63: [ RUN ] IndexMapTest.InitializesOrgIdGroupResidue 63: [ OK ] IndexMapTest.InitializesOrgIdGroupResidue (0 ms) 63: [ RUN ] IndexMapTest.InitializesOrgIdGroupMolecule 63: [ OK ] IndexMapTest.InitializesOrgIdGroupMolecule (0 ms) 63: [ RUN ] IndexMapTest.InitializesOrgIdGroupAll 63: [ OK ] IndexMapTest.InitializesOrgIdGroupAll (0 ms) 63: [ RUN ] IndexMapTest.InitializesMoleculeBlock 63: [ OK ] IndexMapTest.InitializesMoleculeBlock (0 ms) 63: [ RUN ] IndexMapTest.MapsSingleBlock 63: [ OK ] IndexMapTest.MapsSingleBlock (0 ms) 63: [ RUN ] IndexMapTest.MapsResidueBlocks 63: [ OK ] IndexMapTest.MapsResidueBlocks (0 ms) 63: [ RUN ] IndexMapTest.MapsResidueBlocksWithMask 63: [ OK ] IndexMapTest.MapsResidueBlocksWithMask (0 ms) 63: [ RUN ] IndexMapTest.HandlesMultipleRequests 63: [ OK ] IndexMapTest.HandlesMultipleRequests (0 ms) 63: [----------] 11 tests from IndexMapTest (2 ms total) 63: 63: [----------] 3 tests from IndexGroupsAndNamesTest 63: [ RUN ] IndexGroupsAndNamesTest.containsNames 63: [ OK ] IndexGroupsAndNamesTest.containsNames (0 ms) 63: [ RUN ] IndexGroupsAndNamesTest.throwsWhenNameMissing 63: [ OK ] IndexGroupsAndNamesTest.throwsWhenNameMissing (0 ms) 63: [ RUN ] IndexGroupsAndNamesTest.groupIndicesCorrect 63: [ OK ] IndexGroupsAndNamesTest.groupIndicesCorrect (0 ms) 63: [----------] 3 tests from IndexGroupsAndNamesTest (0 ms total) 63: 63: [----------] 15 tests from NeighborhoodSearchTest 63: [ RUN ] NeighborhoodSearchTest.SimpleSearch 63: [ OK ] NeighborhoodSearchTest.SimpleSearch (18 ms) 63: [ RUN ] NeighborhoodSearchTest.SimpleSearchXY 63: [ OK ] NeighborhoodSearchTest.SimpleSearchXY (24 ms) 63: [ RUN ] NeighborhoodSearchTest.GridSearchBox 63: [ OK ] NeighborhoodSearchTest.GridSearchBox (2 ms) 63: [ RUN ] NeighborhoodSearchTest.GridSearchTriclinic 63: [ OK ] NeighborhoodSearchTest.GridSearchTriclinic (10 ms) 63: [ RUN ] NeighborhoodSearchTest.GridSearch2DPBC 63: [ OK ] NeighborhoodSearchTest.GridSearch2DPBC (5 ms) 63: [ RUN ] NeighborhoodSearchTest.GridSearchNoPBC 63: [ OK ] NeighborhoodSearchTest.GridSearchNoPBC (1 ms) 63: [ RUN ] NeighborhoodSearchTest.GridSearchXYBox 63: [ OK ] NeighborhoodSearchTest.GridSearchXYBox (3 ms) 63: [ RUN ] NeighborhoodSearchTest.SimpleSelfPairsSearch 63: [ OK ] NeighborhoodSearchTest.SimpleSelfPairsSearch (0 ms) 63: [ RUN ] NeighborhoodSearchTest.GridSelfPairsSearch 63: [ OK ] NeighborhoodSearchTest.GridSelfPairsSearch (49 ms) 63: [ RUN ] NeighborhoodSearchTest.HandlesConcurrentSearches 63: [ OK ] NeighborhoodSearchTest.HandlesConcurrentSearches (0 ms) 63: [ RUN ] NeighborhoodSearchTest.HandlesNoPBC 63: [ OK ] NeighborhoodSearchTest.HandlesNoPBC (0 ms) 63: [ RUN ] NeighborhoodSearchTest.HandlesNullPBC 63: [ OK ] NeighborhoodSearchTest.HandlesNullPBC (0 ms) 63: [ RUN ] NeighborhoodSearchTest.HandlesSkippingPairs 63: [ OK ] NeighborhoodSearchTest.HandlesSkippingPairs (0 ms) 63: [ RUN ] NeighborhoodSearchTest.SimpleSearchExclusions 63: [ OK ] NeighborhoodSearchTest.SimpleSearchExclusions (4 ms) 63: [ RUN ] NeighborhoodSearchTest.GridSearchExclusions 63: [ OK ] NeighborhoodSearchTest.GridSearchExclusions (0 ms) 63: [----------] 15 tests from NeighborhoodSearchTest (122 ms total) 63: 63: [----------] 13 tests from PositionCalculationTest 63: [ RUN ] PositionCalculationTest.ComputesAtomPositions 63: [ OK ] PositionCalculationTest.ComputesAtomPositions (0 ms) 63: [ RUN ] PositionCalculationTest.ComputesAtomPositionsWithRepeatedIndex 63: [ OK ] PositionCalculationTest.ComputesAtomPositionsWithRepeatedIndex (0 ms) 63: [ RUN ] PositionCalculationTest.ComputesResidueCOGPositions 63: [ OK ] PositionCalculationTest.ComputesResidueCOGPositions (0 ms) 63: [ RUN ] PositionCalculationTest.ComputesResidueCOMPositions 63: [ OK ] PositionCalculationTest.ComputesResidueCOMPositions (0 ms) 63: [ RUN ] PositionCalculationTest.ComputesGroupCOGPositions 63: [ OK ] PositionCalculationTest.ComputesGroupCOGPositions (0 ms) 63: [ RUN ] PositionCalculationTest.ComputesGroupCOMPositions 63: [ OK ] PositionCalculationTest.ComputesGroupCOMPositions (0 ms) 63: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteWhole 63: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteWhole (0 ms) 63: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteMax 63: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteMax (0 ms) 63: [ RUN ] PositionCalculationTest.ComputesPositionMask 63: [ OK ] PositionCalculationTest.ComputesPositionMask (0 ms) 63: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms 63: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms (0 ms) 63: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms2 63: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms2 (0 ms) 63: [ RUN ] PositionCalculationTest.HandlesIdenticalStaticCalculations 63: [ OK ] PositionCalculationTest.HandlesIdenticalStaticCalculations (0 ms) 63: [ RUN ] PositionCalculationTest.HandlesOverlappingStaticCalculations 63: [ OK ] PositionCalculationTest.HandlesOverlappingStaticCalculations (0 ms) 63: [----------] 13 tests from PositionCalculationTest (3 ms total) 63: 63: [----------] 33 tests from SelectionCollectionTest 63: [ RUN ] SelectionCollectionTest.HandlesNoSelections 63: [ OK ] SelectionCollectionTest.HandlesNoSelections (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType 63: [ OK ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesVelocityAndForceRequests 63: [ OK ] SelectionCollectionTest.HandlesVelocityAndForceRequests (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry 63: [ OK ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry (0 ms) 63: [ RUN ] SelectionCollectionTest.ParsesSelectionsFromFile 63: [ OK ] SelectionCollectionTest.ParsesSelectionsFromFile (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesAtypicalWhitespace 63: [ OK ] SelectionCollectionTest.HandlesAtypicalWhitespace (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesInvalidRegularExpressions 63: [ OK ] SelectionCollectionTest.HandlesInvalidRegularExpressions (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue 63: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue2 63: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue2 (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue3 63: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue3 (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 63: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 63: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 63: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 63: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReference 63: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReference (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed 63: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup 63: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed 63: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 63: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 (0 ms) 63: [ RUN ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo 63: [ OK ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo (0 ms) 63: [ RUN ] SelectionCollectionTest.RecoversFromMissingAtomTypes 63: [ OK ] SelectionCollectionTest.RecoversFromMissingAtomTypes (0 ms) 63: [ RUN ] SelectionCollectionTest.RecoversFromMissingPDBInfo 63: [ OK ] SelectionCollectionTest.RecoversFromMissingPDBInfo (0 ms) 63: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation 63: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation (0 ms) 63: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation2 63: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation2 (0 ms) 63: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation3 63: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation3 (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets 63: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 63: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 63: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 (0 ms) 63: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 63: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 (0 ms) 63: [ RUN ] SelectionCollectionTest.RetrieveValidSelection 63: [ OK ] SelectionCollectionTest.RetrieveValidSelection (0 ms) 63: [ RUN ] SelectionCollectionTest.RetrieveInvalidSelection 63: [ OK ] SelectionCollectionTest.RetrieveInvalidSelection (0 ms) 63: [ RUN ] SelectionCollectionTest.CanCopyEmptyCollection 63: [ OK ] SelectionCollectionTest.CanCopyEmptyCollection (0 ms) 63: [ RUN ] SelectionCollectionTest.CopiedSelectionListsAreHandledSeparately 63: [ OK ] SelectionCollectionTest.CopiedSelectionListsAreHandledSeparately (0 ms) 63: [----------] 33 tests from SelectionCollectionTest (13 ms total) 63: 63: [----------] 14 tests from SelectionCollectionInteractiveTest 63: [ RUN ] SelectionCollectionInteractiveTest.HandlesBasicInput 63: [ OK ] SelectionCollectionInteractiveTest.HandlesBasicInput (0 ms) 63: [ RUN ] SelectionCollectionInteractiveTest.HandlesContinuation 63: [ OK ] SelectionCollectionInteractiveTest.HandlesContinuation (0 ms) 63: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput 63: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput (0 ms) 63: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput 63: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput (0 ms) 63: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups 63: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups (0 ms) 63: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections 63: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections (0 ms) 63: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus 63: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus (0 ms) 63: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus 63: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus (0 ms) 63: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus 63: [ OK ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus (0 ms) 63: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline 63: [ OK ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline (0 ms) 63: [ RUN ] SelectionCollectionInteractiveTest.HandlesEmptySelections 63: [ OK ] SelectionCollectionInteractiveTest.HandlesEmptySelections (0 ms) 63: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine 63: [ OK ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine (0 ms) 63: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput 63: [ OK ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput (0 ms) 63: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively 63: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively (0 ms) 63: [----------] 14 tests from SelectionCollectionInteractiveTest (6 ms total) 63: 63: [----------] 70 tests from SelectionCollectionDataTest 63: [ RUN ] SelectionCollectionDataTest.HandlesAllNone 63: [ OK ] SelectionCollectionDataTest.HandlesAllNone (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesAtomnr 63: [ OK ] SelectionCollectionDataTest.HandlesAtomnr (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesResnr 63: [ OK ] SelectionCollectionDataTest.HandlesResnr (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesResIndex 63: [ OK ] SelectionCollectionDataTest.HandlesResIndex (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesMolIndex 63: [ OK ] SelectionCollectionDataTest.HandlesMolIndex (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesAtomname 63: [ OK ] SelectionCollectionDataTest.HandlesAtomname (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesPdbAtomname 63: [ OK ] SelectionCollectionDataTest.HandlesPdbAtomname (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesAtomtype 63: [ OK ] SelectionCollectionDataTest.HandlesAtomtype (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesChain 63: [ OK ] SelectionCollectionDataTest.HandlesChain (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesMass 63: [ OK ] SelectionCollectionDataTest.HandlesMass (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesCharge 63: [ OK ] SelectionCollectionDataTest.HandlesCharge (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesAltLoc 63: [ OK ] SelectionCollectionDataTest.HandlesAltLoc (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesInsertCode 63: [ OK ] SelectionCollectionDataTest.HandlesInsertCode (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesOccupancy 63: [ OK ] SelectionCollectionDataTest.HandlesOccupancy (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesBeta 63: [ OK ] SelectionCollectionDataTest.HandlesBeta (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesResname 63: [ OK ] SelectionCollectionDataTest.HandlesResname (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesCoordinateKeywords 63: [ OK ] SelectionCollectionDataTest.HandlesCoordinateKeywords (1 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesSameResidue 63: [ OK ] SelectionCollectionDataTest.HandlesSameResidue (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesSameResidueName 63: [ OK ] SelectionCollectionDataTest.HandlesSameResidueName (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesPositionKeywords 63: [ OK ] SelectionCollectionDataTest.HandlesPositionKeywords (1 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesDistanceKeyword 63: [ OK ] SelectionCollectionDataTest.HandlesDistanceKeyword (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesMinDistanceKeyword 63: [ OK ] SelectionCollectionDataTest.HandlesMinDistanceKeyword (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesWithinKeyword 63: [ OK ] SelectionCollectionDataTest.HandlesWithinKeyword (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword 63: [ OK ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword (3 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesPermuteModifier 63: [ OK ] SelectionCollectionDataTest.HandlesPermuteModifier (1 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesPlusModifier 63: [ OK ] SelectionCollectionDataTest.HandlesPlusModifier (2 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesMergeModifier 63: [ OK ] SelectionCollectionDataTest.HandlesMergeModifier (2 ms) 63: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndCharges 63: [ OK ] SelectionCollectionDataTest.ComputesMassesAndCharges (1 ms) 63: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology 63: [ OK ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets 63: [ OK ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets (1 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesSelectionNames 63: [ OK ] SelectionCollectionDataTest.HandlesSelectionNames (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections 63: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed 63: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections 63: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections (1 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed 63: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed (1 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositions 63: [ OK ] SelectionCollectionDataTest.HandlesConstantPositions (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers 63: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesWithinConstantPositions 63: [ OK ] SelectionCollectionDataTest.HandlesWithinConstantPositions (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges 63: [ OK ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingRealRanges 63: [ OK ] SelectionCollectionDataTest.HandlesOverlappingRealRanges (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode 63: [ OK ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesWildcardMatching 63: [ OK ] SelectionCollectionDataTest.HandlesWildcardMatching (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesRegexMatching 63: [ OK ] SelectionCollectionDataTest.HandlesRegexMatching (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesBasicBoolean 63: [ OK ] SelectionCollectionDataTest.HandlesBasicBoolean (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters 63: [ OK ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters (1 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions 63: [ OK ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame 63: [ OK ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords 63: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods 63: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositions 63: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositions (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic 63: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesNumericComparisons 63: [ OK ] SelectionCollectionDataTest.HandlesNumericComparisons (1 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesArithmeticExpressions 63: [ OK ] SelectionCollectionDataTest.HandlesArithmeticExpressions (1 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesNumericVariables 63: [ OK ] SelectionCollectionDataTest.HandlesNumericVariables (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesComplexNumericVariables 63: [ OK ] SelectionCollectionDataTest.HandlesComplexNumericVariables (1 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariables 63: [ OK ] SelectionCollectionDataTest.HandlesPositionVariables (1 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariableInModifier 63: [ OK ] SelectionCollectionDataTest.HandlesPositionVariableInModifier (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionInVariable 63: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionInVariable (1 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables 63: [ OK ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis 63: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables 63: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables 63: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesUnusedVariables 63: [ OK ] SelectionCollectionDataTest.HandlesUnusedVariables (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups 63: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups 63: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups (0 ms) 63: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 63: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 (0 ms) 63: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWorksPreCompilation 63: [ OK ] SelectionCollectionDataTest.CopiedSelectionWorksPreCompilation (2 ms) 63: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation 63: [ OK ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation (2 ms) 63: [ RUN ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent 63: [ OK ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent (1 ms) 63: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation 63: [ OK ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation (1 ms) 63: [----------] 70 tests from SelectionCollectionDataTest (69 ms total) 63: 63: [----------] 17 tests from SelectionOptionTest 63: [ RUN ] SelectionOptionTest.ParsesSimpleSelection 63: [ OK ] SelectionOptionTest.ParsesSimpleSelection (0 ms) 63: [ RUN ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired 63: [ OK ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired (0 ms) 63: [ RUN ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired 63: [ OK ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired (0 ms) 63: [ RUN ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired 63: [ OK ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired (0 ms) 63: [ RUN ] SelectionOptionTest.ChecksEmptySelections 63: [ OK ] SelectionOptionTest.ChecksEmptySelections (0 ms) 63: [ RUN ] SelectionOptionTest.ChecksEmptyDelayedSelections 63: [ OK ] SelectionOptionTest.ChecksEmptyDelayedSelections (0 ms) 63: [ RUN ] SelectionOptionTest.HandlesTooManySelections 63: [ OK ] SelectionOptionTest.HandlesTooManySelections (0 ms) 63: [ RUN ] SelectionOptionTest.HandlesTooFewSelections 63: [ OK ] SelectionOptionTest.HandlesTooFewSelections (0 ms) 63: [ RUN ] SelectionOptionTest.HandlesDefaultSelectionText 63: [ OK ] SelectionOptionTest.HandlesDefaultSelectionText (0 ms) 63: [ RUN ] SelectionOptionTest.HandlesAdjuster 63: [ OK ] SelectionOptionTest.HandlesAdjuster (0 ms) 63: [ RUN ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster 63: [ OK ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster (0 ms) 63: [ RUN ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster 63: [ OK ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster (0 ms) 63: [ RUN ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster 63: [ OK ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster (0 ms) 63: [ RUN ] SelectionOptionTest.HandlesDelayedRequiredSelection 63: [ OK ] SelectionOptionTest.HandlesDelayedRequiredSelection (0 ms) 63: [ RUN ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections 63: [ OK ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections (0 ms) 63: [ RUN ] SelectionOptionTest.HandlesDelayedOptionalSelection 63: [ OK ] SelectionOptionTest.HandlesDelayedOptionalSelection (0 ms) 63: [ RUN ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster 63: [ OK ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster (0 ms) 63: [----------] 17 tests from SelectionOptionTest (5 ms total) 63: 63: [----------] 9 tests from SelectionFileOptionTest 63: [ RUN ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile 63: [ OK ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile (0 ms) 63: [ RUN ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions 63: [ OK ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions (0 ms) 63: [ RUN ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile 63: [ OK ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile (0 ms) 63: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFile 63: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFile (0 ms) 63: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet 63: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet (0 ms) 63: [ RUN ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile 63: [ OK ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile (0 ms) 63: [ RUN ] SelectionFileOptionTest.GivesErrorWithNoFile 63: [ OK ] SelectionFileOptionTest.GivesErrorWithNoFile (0 ms) 63: [ RUN ] SelectionFileOptionTest.GivesErrorWithNonExistentFile 63: [ OK ] SelectionFileOptionTest.GivesErrorWithNonExistentFile (0 ms) 63: [ RUN ] SelectionFileOptionTest.GivesErrorWithMultipleFiles 63: [ OK ] SelectionFileOptionTest.GivesErrorWithMultipleFiles (0 ms) 63: [----------] 9 tests from SelectionFileOptionTest (3 ms total) 63: 63: [----------] Global test environment tear-down 63: [==========] 201 tests from 11 test suites ran. (230 ms total) 63: [ PASSED ] 201 tests. 63/90 Test #63: SelectionUnitTests ........................ Passed 0.27 sec test 64 Start 64: MdrunOutputTests 64: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/mdrun-output-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/MdrunOutputTests.xml" 64: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests 64: Test timeout computed to be: 600 64: [==========] Running 12 tests from 5 test suites. 64: [----------] Global test environment set-up. 64: [----------] 1 test from MdrunTest 64: [ RUN ] MdrunTest.WritesHelp 64: [ OK ] MdrunTest.WritesHelp (154 ms) 64: [----------] 1 test from MdrunTest (154 ms total) 64: 64: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput 64: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group rest is 9.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 64: NVE simulation: will use the initial temperature of 2573.591 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 2 NOTEs 64: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc2' 64: 1 steps, 0.0 ps. 64: Setting the LD random seed to -182485137 64: 64: Generated 3 of the 3 non-bonded parameter combinations 64: 64: Generated 3 of the 3 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 64: 64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 64: 64: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.166 0.083 199.8 64: (ns/day) (hour/ns) 64: Performance: 2.075 11.568 64: Reading frame 0 time 0.000 64: # Atoms 6 64: Reading frame 1 time 0.001 Last frame 1 time 0.001 64: 64: 64: Item #frames Timestep (ps) 64: Step 2 0.001 64: Time 2 0.001 64: Lambda 0 64: Coords 2 0.001 64: Velocities 0 64: Forces 0 64: Box 2 0.001 64: Checking file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.xtc 64: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 (160 ms) 64: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group rest is 9.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 64: NVE simulation: will use the initial temperature of 2573.591 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 2 NOTEs 64: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc2' 64: 1 steps, 0.0 ps. 64: Setting the LD random seed to 1043300253 64: 64: Generated 3 of the 3 non-bonded parameter combinations 64: 64: Generated 3 of the 3 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 64: 64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 64: 64: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.039 0.019 199.1 64: (ns/day) (hour/ns) 64: Performance: 8.925 2.689 64: Reading frame 0 time 0.000 64: # Atoms 6 64: Reading frame 1 time 0.001 Last frame 1 time 0.001 64: 64: 64: Item #frames Timestep (ps) 64: Step 2 0.001 64: Time 2 0.001 64: Lambda 0 64: Coords 2 0.001 64: Velocities 0 64: Forces 0 64: Box 2 0.001 64: Checking file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.xtc 64: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 (48 ms) 64: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group rest is 9.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 64: NVE simulation: will use the initial temperature of 2573.591 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 2 NOTEs 64: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc2' 64: 1 steps, 0.0 ps. 64: Setting the LD random seed to 1744239358 64: 64: Generated 3 of the 3 non-bonded parameter combinations 64: 64: Generated 3 of the 3 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 64: 64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 64: 64: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.069 0.035 199.3 64: (ns/day) (hour/ns) 64: Performance: 5.005 4.795 64: Reading frame 0 time 0.000 64: # Atoms 3 64: Reading frame 1 time 0.001 Last frame 1 time 0.001 64: 64: 64: Item #frames Timestep (ps) 64: Step 2 0.001 64: Time 2 0.001 64: Lambda 0 64: Coords 2 0.001 64: Velocities 0 64: Forces 0 64: Box 2 0.001 64: Checking file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.xtc 64: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 (78 ms) 64: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput (288 ms total) 64: 64: [----------] 2 tests from Argon12/OutputFiles 64: [ RUN ] Argon12/OutputFiles.FilesArePresent/0 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Number of degrees of freedom in T-Coupling group System is 33.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 64: NVE simulation: will use the initial temperature of 68.810 K for 64: determining the Verlet buffer size 64: 64: 64: There were 3 NOTEs 64: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Argon' 64: 16 steps, 0.0 ps. 64: Generated 1 of the 1 non-bonded parameter combinations 64: 64: Excluding 1 bonded neighbours molecule type 'Argon' 64: 64: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.051 0.025 199.3 64: (ns/day) (hour/ns) 64: Performance: 57.838 0.415 64: [ OK ] Argon12/OutputFiles.FilesArePresent/0 (36 ms) 64: [ RUN ] Argon12/OutputFiles.FilesArePresent/1 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Number of degrees of freedom in T-Coupling group System is 33.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 64: NVE simulation: will use the initial temperature of 68.810 K for 64: determining the Verlet buffer size 64: 64: 64: There were 3 NOTEs 64: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Argon' 64: 16 steps, 0.0 ps. 64: Generated 1 of the 1 non-bonded parameter combinations 64: 64: Excluding 1 bonded neighbours molecule type 'Argon' 64: 64: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.075 0.038 199.5 64: (ns/day) (hour/ns) 64: Performance: 39.131 0.613 64: [ OK ] Argon12/OutputFiles.FilesArePresent/1 (66 ms) 64: [----------] 2 tests from Argon12/OutputFiles (103 ms total) 64: 64: [----------] 3 tests from MdrunCanWrite/Trajectories 64: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 64: Number of degrees of freedom in T-Coupling group System is 12.00 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There was 1 NOTE 64: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 64: Changing nstlist from 10 to 40, rlist from 1.034 to 1.183 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc-and-methanol' 64: 6 steps, 0.0 ps. 64: Setting the LD random seed to -537108513 64: 64: Generated 8 of the 10 non-bonded parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'Methanol' 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 64: 64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.209 0.105 199.7 64: (ns/day) (hour/ns) 64: Performance: 5.768 4.161 64: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 (123 ms) 64: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 64: Number of degrees of freedom in T-Coupling group System is 12.00 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There was 1 NOTE 64: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 64: Changing nstlist from 10 to 40, rlist from 1.034 to 1.183 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc-and-methanol' 64: 6 steps, 0.0 ps. 64: Setting the LD random seed to 1056686007 64: 64: Generated 8 of the 10 non-bonded parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'Methanol' 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 64: 64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.036 0.018 199.2 64: (ns/day) (hour/ns) 64: Performance: 33.477 0.717 64: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 (28 ms) 64: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 64: Number of degrees of freedom in T-Coupling group System is 12.00 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There was 1 NOTE 64: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 64: Changing nstlist from 10 to 40, rlist from 1.034 to 1.183 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc-and-methanol' 64: 6 steps, 0.0 ps. 64: Setting the LD random seed to -67651 64: 64: Generated 8 of the 10 non-bonded parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'Methanol' 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 64: 64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.042 0.021 199.3 64: (ns/day) (hour/ns) 64: Performance: 28.385 0.846 64: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 (32 ms) 64: [----------] 3 tests from MdrunCanWrite/Trajectories (184 ms total) 64: 64: [----------] 3 tests from MdrunCanWrite/NptTrajectories 64: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 64: Number of degrees of freedom in T-Coupling group System is 12.00 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There was 1 NOTE 64: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 64: Changing nstlist from 10 to 40, rlist from 1.034 to 1.183 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc-and-methanol' 64: 2 steps, 0.0 ps. 64: Setting the LD random seed to -28402852 64: 64: Generated 8 of the 10 non-bonded parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'Methanol' 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 64: 64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.119 0.060 199.7 64: (ns/day) (hour/ns) 64: Performance: 4.353 5.513 64: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 (73 ms) 64: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 64: 64: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: 64: The Berendsen barostat does not generate any strictly correct ensemble, 64: and should not be used for new production simulations (in our opinion). 64: We recommend using the C-rescale barostat instead. 64: 64: Number of degrees of freedom in T-Coupling group System is 12.00 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There was 1 NOTE 64: 64: There was 1 WARNING 64: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 64: Changing nstlist from 10 to 40, rlist from 1.034 to 1.183 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc-and-methanol' 64: 2 steps, 0.0 ps. 64: Setting the LD random seed to -576848412 64: 64: Generated 8 of the 10 non-bonded parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'Methanol' 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 64: 64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.116 0.058 199.5 64: (ns/day) (hour/ns) 64: Performance: 4.459 5.382 64: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 (73 ms) 64: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 64: Number of degrees of freedom in T-Coupling group System is 12.00 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There was 1 NOTE 64: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 64: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 64: Changing nstlist from 10 to 40, rlist from 1.034 to 1.183 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc-and-methanol' 64: 2 steps, 0.0 ps. 64: Setting the LD random seed to -1078075395 64: 64: Generated 8 of the 10 non-bonded parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'Methanol' 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 64: 64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.110 0.055 199.6 64: (ns/day) (hour/ns) 64: Performance: 4.711 5.094 64: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 (75 ms) 64: [----------] 3 tests from MdrunCanWrite/NptTrajectories (223 ms total) 64: 64: [----------] Global test environment tear-down 64: [==========] 12 tests from 5 test suites ran. (1507 ms total) 64: [ PASSED ] 12 tests. 64/90 Test #64: MdrunOutputTests .......................... Passed 1.54 sec test 65 Start 65: MdrunModulesTests 65: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/mdrun-modules-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/MdrunModulesTests.xml" 65: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests 65: Test timeout computed to be: 600 65: [==========] Running 15 tests from 3 test suites. 65: [----------] Global test environment set-up. 65: [----------] 9 tests from DensityFittingTest 65: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct 65: Number of degrees of freedom in T-Coupling group rest is 33.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 65: Using 1 MPI thread 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: 65: Steepest Descents: 65: Tolerance (Fmax) = 1.00000e+01 65: Number of steps = 2 65: 65: Energy minimization reached the maximum number of steps before the forces 65: reached the requested precision Fmax < 10. 65: 65: writing lowest energy coordinates. 65: 65: Steepest Descents did not converge to Fmax < 10 in 3 steps. 65: Potential Energy = -3.85652562592421e+03 65: Maximum force = 4.50998690851897e+03 on atom 3 65: Norm of force = 1.68168494163492e+03 65: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.edr as double precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to 1811742712 65: 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct (16 ms) 65: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation 65: Number of degrees of freedom in T-Coupling group rest is 33.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 65: Using 1 MPI thread 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: 65: Steepest Descents: 65: Tolerance (Fmax) = 1.00000e+01 65: Number of steps = 2 65: 65: Energy minimization reached the maximum number of steps before the forces 65: reached the requested precision Fmax < 10. 65: 65: writing lowest energy coordinates. 65: 65: Steepest Descents did not converge to Fmax < 10 in 3 steps. 65: Potential Energy = -9.82077921283928e+03 65: Maximum force = 7.39548334240075e+03 on atom 2 65: Norm of force = 2.78250777177324e+03 65: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.edr as double precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -1409291009 65: 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation (13 ms) 65: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff 65: 65: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1108:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/main/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. 65: [ OK ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff (14 ms) 65: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix 65: Number of degrees of freedom in T-Coupling group rest is 33.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 65: Overriding nsteps with value passed on the command line: 4 steps 65: 65: Using 1 MPI thread 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: 65: Steepest Descents: 65: Tolerance (Fmax) = 1.00000e+01 65: Number of steps = 4 65: 65: Energy minimization reached the maximum number of steps before the forces 65: reached the requested precision Fmax < 10. 65: 65: writing lowest energy coordinates. 65: 65: Steepest Descents did not converge to Fmax < 10 in 5 steps. 65: Potential Energy = -1.09549987768583e+04 65: Maximum force = 7.47247842297766e+03 on atom 2 65: Norm of force = 2.77579925913607e+03 65: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.edr as double precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Setting the LD random seed to -678021193 65: 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix (10 ms) 65: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff 65: 65: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1108:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/main/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. 65: [ OK ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff (14 ms) 65: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix 65: Number of degrees of freedom in T-Coupling group rest is 33.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 65: Using 1 MPI thread 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: 65: Steepest Descents: 65: Tolerance (Fmax) = 1.00000e+01 65: Number of steps = 2 65: 65: Energy minimization reached the maximum number of steps before the forces 65: reached the requested precision Fmax < 10. 65: 65: writing lowest energy coordinates. 65: 65: Steepest Descents did not converge to Fmax < 10 in 3 steps. 65: Potential Energy = -3.85652562592421e+03 65: Maximum force = 4.50998690851897e+03 on atom 3 65: Norm of force = 1.68168494163492e+03 65: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.edr as double precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -337660705 65: 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix (11 ms) 65: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy 65: Number of degrees of freedom in T-Coupling group rest is 33.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 65: Using 1 MPI thread 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: 65: Steepest Descents: 65: Tolerance (Fmax) = 1.00000e+01 65: Number of steps = 2 65: 65: Energy minimization reached the maximum number of steps before the forces 65: reached the requested precision Fmax < 10. 65: 65: writing lowest energy coordinates. 65: 65: Steepest Descents did not converge to Fmax < 10 in 3 steps. 65: Potential Energy = -2.71386626041483e+04 65: Maximum force = 6.78276504921089e+03 on atom 2 65: Norm of force = 1.96088640980697e+03 65: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.edr as double precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -489018401 65: 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy (9 ms) 65: [ RUN ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch 65: 65: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1108:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/main/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. 65: Setting the LD random seed to 2080357366 65: 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 65: [ OK ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch (13 ms) 65: [ RUN ] DensityFittingTest.CheckpointWorks 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (2) 65: 65: Number of degrees of freedom in T-Coupling group rest is 33.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: 65: NVE simulation: will use the initial temperature of 68.810 K for 65: determining the Verlet buffer size 65: 65: 65: There were 2 NOTEs 65: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI thread 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 2 steps, 0.0 ps. 65: Setting the LD random seed to -262186 65: 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 65: 65: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 68.8096 K 65: 65: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.469 0.235 199.9 65: (ns/day) (hour/ns) 65: Performance: 1.104 21.739 65: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 65: Overriding nsteps with value passed on the command line: 4 steps, 0.004 ps 65: Can not increase nstlist because an NVE ensemble is used 65: 65: Using 1 MPI thread 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 6 steps, 0.0 ps (continuing from step 2, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.036 0.018 199.2 65: (ns/day) (hour/ns) 65: Performance: 23.691 1.013 65: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.edr as double precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Last energy frame read 1 time 0.002 [ OK ] DensityFittingTest.CheckpointWorks (274 ms) 65: [----------] 9 tests from DensityFittingTest (378 ms total) 65: 65: [----------] 4 tests from MimicTest 65: [ RUN ] MimicTest.OneQuantumMol 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 65: For a correct single-point energy evaluation with nsteps = 0, use 65: continuation = yes to avoid constraining the input coordinates. 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group rest is 21.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 65: NVE simulation with an initial temperature of zero: will use a Verlet 65: buffer of 10%. Check your energy drift! 65: 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 3 NOTEs 65: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI thread 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro' 65: 65: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 65: Reading frame 0 time 0.000 Last frame 0 time 0.000 65: 65: NOTE: 31 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.001 0.000 188.3 65: (ns/day) (hour/ns) 65: Performance: 271.046 0.089 65: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as double precision energy file 65: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -1117401 65: 65: Generated 10 of the 10 non-bonded parameter combinations 65: 65: Generated 10 of the 10 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] MimicTest.OneQuantumMol (6 ms) 65: [ RUN ] MimicTest.AllQuantumMol 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 65: For a correct single-point energy evaluation with nsteps = 0, use 65: continuation = yes to avoid constraining the input coordinates. 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group rest is 21.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 65: NVE simulation with an initial temperature of zero: will use a Verlet 65: buffer of 10%. Check your energy drift! 65: 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 3 NOTEs 65: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI thread 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro' 65: 65: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 65: Reading frame 0 time 0.000 Last frame 0 time 0.000 65: 65: NOTE: 24 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.000 0.000 187.6 65: (ns/day) (hour/ns) 65: Performance: 356.330 0.067 65: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as double precision energy file 65: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -1765902346 65: 65: Generated 10 of the 10 non-bonded parameter combinations 65: 65: Generated 10 of the 10 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] MimicTest.AllQuantumMol (5 ms) 65: [ RUN ] MimicTest.TwoQuantumMol 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 65: For a correct single-point energy evaluation with nsteps = 0, use 65: continuation = yes to avoid constraining the input coordinates. 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group rest is 21.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 65: NVE simulation with an initial temperature of zero: will use a Verlet 65: buffer of 10%. Check your energy drift! 65: 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 3 NOTEs 65: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI thread 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro' 65: 65: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 65: Reading frame 0 time 0.000 Last frame 0 time 0.000 65: 65: NOTE: 25 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.001 0.000 186.5 65: (ns/day) (hour/ns) 65: Performance: 297.771 0.081 65: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as double precision energy file 65: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -344985619 65: 65: Generated 10 of the 10 non-bonded parameter combinations 65: 65: Generated 10 of the 10 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] MimicTest.TwoQuantumMol (7 ms) 65: [ RUN ] MimicTest.BondCuts 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 65: For a correct single-point energy evaluation with nsteps = 0, use 65: continuation = yes to avoid constraining the input coordinates. 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group rest is 66.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 65: NVE simulation: will use the initial temperature of 300.368 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 3 NOTEs 65: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI thread 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 65: 65: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 65: Reading frame 0 time 0.000 Last frame 0 time 0.000 65: 65: NOTE: 19 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.001 0.001 186.8 65: (ns/day) (hour/ns) 65: Performance: 118.042 0.203 65: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as double precision energy file 65: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -1497415938 65: 65: Generated 2211 of the 2211 non-bonded parameter combinations 65: 65: Generated 2211 of the 2211 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 65: 65: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 65: 65: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 65: 65: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] MimicTest.BondCuts (29 ms) 65: [----------] 4 tests from MimicTest (48 ms total) 65: 65: [----------] 2 tests from WithIntegrator/ImdTest 65: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/0 65: Generating 1-4 interactions: fudge = 1 65: 65: NOTE 1 [file glycine_vacuo.top, line 12]: 65: The bond in molecule-type Glycine between atoms 1 N and 2 H1 has an 65: estimated oscillational period of 1.0e-02 ps, which is less than 10 times 65: the time step of 2.0e-03 ps. 65: Maybe you forgot to change the constraints mdp option. 65: 65: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). 65: Number of degrees of freedom in T-Coupling group System is 27.00 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 2 NOTEs 65: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 65: Changing nstlist from 10 to 25, rlist from 1.077 to 1.248 65: 65: Using 1 MPI thread 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: 65: IMD: Enabled. This simulation will accept incoming IMD connections. 65: IMD: Pulling from IMD remote is enabled (-imdpull). 65: IMD: Setting port for connection requests to 0. 65: IMD: Setting up incoming socket. 65: IMD: Listening for IMD connection on port 54427. 65: IMD: -imdwait not set, starting simulation. 65: starting mdrun 'Glycine' 65: 2 steps, 0.0 ps. 65: Setting the LD random seed to -108220417 65: 65: Generated 20503 of the 20503 non-bonded parameter combinations 65: 65: Generated 17396 of the 20503 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Glycine' 65: 65: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/glycine_vacuo.gro', all velocities are zero 65: 65: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 65: 65: Calculated rlist for 1x1 atom pair-list as 1.093 nm, buffer size 0.093 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 1.071 nm, buffer size 0.071 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.059 0.030 199.5 65: (ns/day) (hour/ns) 65: Performance: 17.484 1.373 65: [ OK ] WithIntegrator/ImdTest.ImdCanRun/0 (157 ms) 65: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/1 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: 65: Setting tcoupl from 'V-rescale' to 'no'. Temperature coupling does not 65: apply to steep. 65: 65: Generating 1-4 interactions: fudge = 1 65: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). 65: Number of degrees of freedom in T-Coupling group System is 27.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 2 NOTEs 65: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 65: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 65: Using 1 MPI thread 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: 65: IMD: Enabled. This simulation will accept incoming IMD connections. 65: IMD: Pulling from IMD remote is enabled (-imdpull). 65: IMD: Setting port for connection requests to 0. 65: IMD: Setting up incoming socket. 65: IMD: Listening for IMD connection on port 60523. 65: IMD: -imdwait not set, starting simulation. 65: 65: Steepest Descents: 65: Tolerance (Fmax) = 1.00000e+01 65: Number of steps = 2 65: 65: Energy minimization reached the maximum number of steps before the forces 65: reached the requested precision Fmax < 10. 65: 65: writing lowest energy coordinates. 65: 65: Steepest Descents did not converge to Fmax < 10 in 3 steps. 65: Potential Energy = 1.19770464690297e+03 65: Maximum force = 1.77948604657896e+04 on atom 9 65: Norm of force = 7.87328617833980e+03 65: Setting the LD random seed to 1842983865 65: 65: Generated 20503 of the 20503 non-bonded parameter combinations 65: 65: Generated 17396 of the 20503 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Glycine' 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] WithIntegrator/ImdTest.ImdCanRun/1 (119 ms) 65: [----------] 2 tests from WithIntegrator/ImdTest (276 ms total) 65: 65: [----------] Global test environment tear-down 65: [==========] 15 tests from 3 test suites ran. (987 ms total) 65: [ PASSED ] 15 tests. 65/90 Test #65: MdrunModulesTests ......................... Passed 1.01 sec test 66 Start 66: MdrunIOTests 66: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/mdrun-io-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/MdrunIOTests.xml" 66: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests 66: Test timeout computed to be: 600 66: [==========] Running 76 tests from 13 test suites. 66: [----------] Global test environment set-up. 66: [----------] 9 tests from GromppTest 66: [ RUN ] GromppTest.EmptyMdpFileWorks 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 66: For a correct single-point energy evaluation with nsteps = 0, use 66: continuation = yes to avoid constraining the input coordinates. 66: 66: Number of degrees of freedom in T-Coupling group rest is 12.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 66: NVE simulation: will use the initial temperature of 1046.791 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: Setting the LD random seed to -1384748353 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: [ OK ] GromppTest.EmptyMdpFileWorks (5 ms) 66: [ RUN ] GromppTest.SimulatedAnnealingWorks 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 66: For a correct single-point energy evaluation with nsteps = 0, use 66: continuation = yes to avoid constraining the input coordinates. 66: 66: Simulated annealing for group rest: Periodic, 4 timepoints 66: Time (ps) Temperature (K) 66: 0.0 298.0 66: 2.0 320.0 66: 4.0 320.0 66: 6.0 298.0 66: Number of degrees of freedom in T-Coupling group rest is 12.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 66: NVE simulation: will use the initial temperature of 1046.791 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: Setting the LD random seed to -167790686 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: [ OK ] GromppTest.SimulatedAnnealingWorks (10 ms) 66: [ RUN ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 66: For a correct single-point energy evaluation with nsteps = 0, use 66: continuation = yes to avoid constraining the input coordinates. 66: 66: Simulated annealing for group Methanol: Single, 3 timepoints 66: Time (ps) Temperature (K) 66: 0.0 298.0 66: 3.0 280.0 66: 6.0- 270.0 66: Simulated annealing for group SOL: Periodic, 4 timepoints 66: Time (ps) Temperature (K) 66: 0.0 298.0 66: 2.0 320.0 66: 4.0 320.0 66: 6.0 298.0 66: Number of degrees of freedom in T-Coupling group Methanol is 7.20 66: Number of degrees of freedom in T-Coupling group SOL is 4.80 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 66: NVE simulation: will use the initial temperature of 1046.791 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: Setting the LD random seed to -71417213 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: [ OK ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups (8 ms) 66: [ RUN ] GromppTest.DeathTestHandlesNoMaxwarnError 66: Setting the LD random seed to 2141387604 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: [ OK ] GromppTest.DeathTestHandlesNoMaxwarnError (15 ms) 66: [ RUN ] GromppTest.HandlesMaxwarn 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 66: For a correct single-point energy evaluation with nsteps = 0, use 66: continuation = yes to avoid constraining the input coordinates. 66: 66: 66: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 66: The Berendsen thermostat does not generate the correct kinetic energy 66: distribution, and should not be used for new production simulations (in 66: our opinion). We would recommend the V-rescale thermostat. 66: 66: Number of degrees of freedom in T-Coupling group System is 12.00 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 2 NOTEs 66: 66: There was 1 WARNING 66: Setting the LD random seed to -1076068564 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: [ OK ] GromppTest.HandlesMaxwarn (4 ms) 66: [ RUN ] GromppTest.MaxwarnShouldBePositive 66: [ OK ] GromppTest.MaxwarnShouldBePositive (0 ms) 66: [ RUN ] GromppTest.ValidTransformationCoord 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 66: For a correct single-point energy evaluation with nsteps = 0, use 66: continuation = yes to avoid constraining the input coordinates. 66: 66: Pull group 1 'SOL' has 3 atoms 66: Pull group 2 'Methanol' has 3 atoms 66: Number of degrees of freedom in T-Coupling group rest is 12.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 66: NVE simulation: will use the initial temperature of 1046.791 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: Pull group natoms pbc atom distance at start reference at t=0 66: 1 3 5 66: 2 3 2 0.613 nm 0.000 nm 66: 1 3 5 66: 2 3 2 0.613 nm 0.000 nm 66: 66: There were 3 NOTEs 66: Setting the LD random seed to -799248386 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: [ OK ] GromppTest.ValidTransformationCoord (14 ms) 66: [ RUN ] GromppTest.InvalidTransformationCoord 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 66: For a correct single-point energy evaluation with nsteps = 0, use 66: continuation = yes to avoid constraining the input coordinates. 66: 66: Pull group 1 'SOL' has 3 atoms 66: Pull group 2 'Methanol' has 3 atoms 66: Number of degrees of freedom in T-Coupling group rest is 12.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 66: NVE simulation: will use the initial temperature of 1046.791 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: Pull group natoms pbc atom distance at start reference at t=0 66: 1 3 5 66: 2 3 2 0.613 nm 0.000 nm 66: 1 3 5 66: 2 3 2 Setting the LD random seed to 85415806 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: [ OK ] GromppTest.InvalidTransformationCoord (5 ms) 66: [ RUN ] GromppTest.RejectCRescaleAndAnisotropic 66: Setting the LD random seed to 2074046453 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: [ OK ] GromppTest.RejectCRescaleAndAnisotropic (14 ms) 66: [----------] 9 tests from GromppTest (80 ms total) 66: 66: [----------] 6 tests from MdrunTerminationTest 66: [ RUN ] MdrunTerminationTest.CheckpointRestartAppendsByDefault 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There was 1 NOTE 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 2 steps, 0.0 ps. 66: Setting the LD random seed to -1058945 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.020 0.010 198.7 66: (ns/day) (hour/ns) 66: Performance: 25.942 0.925 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Setting nsteps to 4 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 66: Input file: 66: Run start step 0 66: Run start time 0 ps 66: Step to be made during run 2 66: Runtime for the run 0.002 ps 66: Run end step 2 66: Run end time 0.002 ps 66: 66: 66: Output file: 66: Run start step 0 66: Run start time 0 ps 66: Step to be made during run 4 66: Runtime for the run 0.004 ps 66: Run end step 4 66: Run end time 0.004 ps 66: 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.013 0.007 198.0 66: (ns/day) (hour/ns) 66: Performance: 39.612 0.606 66: [ OK ] MdrunTerminationTest.CheckpointRestartAppendsByDefault (33 ms) 66: [ RUN ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There was 1 NOTE 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 10 to 1, rlist from 1.035 to 1 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 100 steps, 0.1 ps. 66: 66: Step 2: Run time exceeded 0.000 hours, will terminate the run within 200 steps 66: Setting the LD random seed to -1112670595 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.077 0.038 199.5 66: (ns/day) (hour/ns) 66: Performance: 226.946 0.106 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Setting nsteps to 102 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 102 steps, 0.1 ps (continuing from step 100, 0.1 ps). 66: Input file: 66: Run start step 0 66: Run start time 0 ps 66: Step to be made during run 100 66: Runtime for the run 0.1 ps 66: Run end step 100 66: Run end time 0.1 ps 66: 66: 66: Output file: 66: Run start step 0 66: Run start time 0 ps 66: Step to be made during run 102 66: Runtime for the run 0.102 ps 66: Run end step 102 66: Run end time 0.102 ps 66: 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.019 0.010 197.9 66: (ns/day) (hour/ns) 66: Performance: 26.726 0.898 66: [ OK ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (64 ms) 66: [ RUN ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There was 1 NOTE 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 2 steps, 0.0 ps. 66: Setting the LD random seed to 1599071767 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.027 0.014 198.9 66: (ns/day) (hour/ns) 66: Performance: 19.058 1.259 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Setting nsteps to 4 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 66: Input file: 66: Run start step 0 66: Run start time 0 ps 66: Step to be made during run 2 66: Runtime for the run 0.002 ps 66: Run end step 2 66: Run end time 0.002 ps 66: 66: 66: Output file: 66: Run start step 0 66: Run start time 0 ps 66: Step to be made during run 4 66: Runtime for the run 0.004 ps 66: Run end step 4 66: Run end time 0.004 ps 66: 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.052 0.026 199.6 66: (ns/day) (hour/ns) 66: Performance: 9.945 2.413 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Setting nsteps to 6 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 6 steps, 0.0 ps (continuing from step 4, 0.0 ps). 66: Input file: 66: Run start step 0 66: Run start time 0 ps 66: Step to be made during run 4 66: Runtime for the run 0.004 ps 66: Run end step 4 66: Run end time 0.004 ps 66: 66: 66: Output file: 66: Run start step 0 66: Run start time 0 ps 66: Step to be made during run 6 66: Runtime for the run 0.006 ps 66: Run end step 6 66: Run end time 0.006 ps 66: 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.047 0.024 199.5 66: (ns/day) (hour/ns) 66: Performance: 11.025 2.177 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Setting nsteps to 8 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 8 steps, 0.0 ps (continuing from step 6, 0.0 ps). 66: Input file: 66: Run start step 0 66: Run start time 0 ps 66: Step to be made during run 6 66: Runtime for the run 0.006 ps 66: Run end step 6 66: Run end time 0.006 ps 66: 66: 66: Output file: 66: Run start step 0 66: Run start time 0 ps 66: Step to be made during run 8 66: Runtime for the run 0.008 ps 66: Run end step 8 66: Run end time 0.008 ps 66: 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.028 0.014 198.9 66: (ns/day) (hour/ns) 66: Performance: 18.724 1.282 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 8 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: NOTE: 27 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.001 0.000 181.0 66: (ns/day) (hour/ns) 66: Performance: 223.145 0.108 66: [ OK ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend (126 ms) 66: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There was 1 NOTE 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 2 steps, 0.0 ps. 66: Setting the LD random seed to 1593724339 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.027 0.014 198.8 66: (ns/day) (hour/ns) 66: Performance: 18.954 1.266 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Setting nsteps to 4 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 4 steps, 0.0 ps. 66: Input file: 66: Run start step 0 66: Run start time 0 ps 66: Step to be made during run 2 66: Runtime for the run 0.002 ps 66: Run end step 2 66: Run end time 0.002 ps 66: 66: 66: Output file: 66: Run start step 0 66: Run start time 0 ps 66: Step to be made during run 4 66: Runtime for the run 0.004 ps 66: Run end step 4 66: Run end time 0.004 ps 66: 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.048 0.024 199.2 66: (ns/day) (hour/ns) 66: Performance: 17.770 1.351 66: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile (60 ms) 66: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There was 1 NOTE 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 2 steps, 0.0 ps. 66: Setting the LD random seed to -722764882 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.021 0.011 198.5 66: (ns/day) (hour/ns) 66: Performance: 24.536 0.978 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Setting nsteps to 4 66: Input file: 66: Run start step 0 66: Run start time 0 ps 66: Step to be made during run 2 66: Runtime for the run 0.002 ps 66: Run end step 2 66: Run end time 0.002 ps 66: 66: 66: Output file: 66: Run start step 0 66: Run start time 0 ps 66: Step to be made during run 4 66: Runtime for the run 0.004 ps 66: Run end step 4 66: Run end time 0.004 ps 66: 66: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile (30 ms) 66: [ RUN ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There was 1 NOTE 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 2 steps, 0.0 ps. 66: Setting the LD random seed to -646711994 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.023 0.012 198.7 66: (ns/day) (hour/ns) 66: Performance: 22.226 1.080 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Setting nsteps to 4 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 66: Input file: 66: Run start step 0 66: Run start time 0 ps 66: Step to be made during run 2 66: Runtime for the run 0.002 ps 66: Run end step 2 66: Run end time 0.002 ps 66: 66: 66: Output file: 66: Run start step 0 66: Run start time 0 ps 66: Step to be made during run 4 66: Runtime for the run 0.004 ps 66: Run end step 4 66: Run end time 0.004 ps 66: 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.026 0.013 199.2 66: (ns/day) (hour/ns) 66: Performance: 19.804 1.212 66: [ OK ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles (42 ms) 66: [----------] 6 tests from MdrunTerminationTest (358 ms total) 66: 66: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks 66: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps. 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.057 0.029 198.9 66: (ns/day) (hour/ns) 66: Performance: 51.506 0.466 66: trr version: GMX_trn_file (double precision) 66: 66: 66: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 (40 ms) 66: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps. 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.048 0.024 199.4 66: (ns/day) (hour/ns) 66: Performance: 61.468 0.390 66: 66: 66: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 (37 ms) 66: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks (77 ms total) 66: 66: [----------] 24 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: NVE simulation: will use the initial temperature of 68.810 K for 66: determining the Verlet buffer size 66: 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: NVE simulation: will use the initial temperature of 68.810 K for 66: determining the Verlet buffer size 66: 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.042 0.021 199.2 66: (ns/day) (hour/ns) 66: Performance: 70.029 0.343 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.055 0.027 199.5 66: (ns/day) (hour/ns) 66: Performance: 28.290 0.848 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.078 0.039 199.6 66: (ns/day) (hour/ns) 66: Performance: 19.947 1.203 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (116 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: NVE simulation: will use the initial temperature of 68.810 K for 66: determining the Verlet buffer size 66: 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: NVE simulation: will use the initial temperature of 68.810 K for 66: determining the Verlet buffer size 66: 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.076 0.038 199.6 66: (ns/day) (hour/ns) 66: Performance: 38.492 0.624 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.036 0.018 199.0 66: (ns/day) (hour/ns) 66: Performance: 43.299 0.554 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.154 0.077 199.8 66: (ns/day) (hour/ns) 66: Performance: 10.102 2.376 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (167 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: NVE simulation: will use the initial temperature of 68.810 K for 66: determining the Verlet buffer size 66: 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: NVE simulation: will use the initial temperature of 68.810 K for 66: determining the Verlet buffer size 66: 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.082 0.041 199.7 66: (ns/day) (hour/ns) 66: Performance: 35.787 0.671 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.051 0.025 199.2 66: (ns/day) (hour/ns) 66: Performance: 30.670 0.783 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.148 0.074 199.7 66: (ns/day) (hour/ns) 66: Performance: 10.524 2.280 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (180 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: NVE simulation: will use the initial temperature of 68.810 K for 66: determining the Verlet buffer size 66: 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: NVE simulation: will use the initial temperature of 68.810 K for 66: determining the Verlet buffer size 66: 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.124 0.062 199.8 66: (ns/day) (hour/ns) 66: Performance: 23.722 1.012 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.107 0.054 199.8 66: (ns/day) (hour/ns) 66: Performance: 14.506 1.654 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.082 0.041 199.5 66: (ns/day) (hour/ns) 66: Performance: 18.888 1.271 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (187 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.085 0.043 199.7 66: (ns/day) (hour/ns) 66: Performance: 34.536 0.695 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.063 0.032 199.6 66: (ns/day) (hour/ns) 66: Performance: 24.622 0.975 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.116 0.058 199.7 66: (ns/day) (hour/ns) 66: Performance: 13.404 1.791 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (158 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 100, rlist from 0.709 to 0.735 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.711 nm, buffer size 0.011 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.711 nm, buffer size 0.011 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.066 0.033 199.6 66: (ns/day) (hour/ns) 66: Performance: 44.659 0.537 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 100, rlist from 0.709 to 0.735 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.091 0.045 199.7 66: (ns/day) (hour/ns) 66: Performance: 17.136 1.401 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 100, rlist from 0.709 to 0.735 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.163 0.081 199.8 66: (ns/day) (hour/ns) 66: Performance: 9.543 2.515 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (188 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.046 0.023 199.4 66: (ns/day) (hour/ns) 66: Performance: 63.707 0.377 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.251 0.126 199.9 66: (ns/day) (hour/ns) 66: Performance: 6.184 3.881 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.179 0.090 199.8 66: (ns/day) (hour/ns) 66: Performance: 8.669 2.768 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (279 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.104 0.052 199.7 66: (ns/day) (hour/ns) 66: Performance: 28.326 0.847 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.083 0.041 199.6 66: (ns/day) (hour/ns) 66: Performance: 18.786 1.278 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.070 0.035 199.6 66: (ns/day) (hour/ns) 66: Performance: 22.103 1.086 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (162 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps. 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.156 0.078 199.8 66: (ns/day) (hour/ns) 66: Performance: 18.795 1.277 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.322 0.161 199.9 66: (ns/day) (hour/ns) 66: Performance: 4.826 4.973 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.404 0.202 199.9 66: (ns/day) (hour/ns) 66: Performance: 3.851 6.231 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (477 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps. 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.110 0.055 199.7 66: (ns/day) (hour/ns) 66: Performance: 26.632 0.901 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.203 0.102 199.8 66: (ns/day) (hour/ns) 66: Performance: 7.643 3.140 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.155 0.078 199.8 66: (ns/day) (hour/ns) 66: Performance: 10.022 2.395 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (266 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps. 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.211 0.106 199.9 66: (ns/day) (hour/ns) 66: Performance: 13.916 1.725 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.049 0.025 199.5 66: (ns/day) (hour/ns) 66: Performance: 31.620 0.759 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.031 0.015 198.8 66: (ns/day) (hour/ns) 66: Performance: 50.246 0.478 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_secondpart.part0002.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (183 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps. 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.051 0.025 199.5 66: (ns/day) (hour/ns) 66: Performance: 57.615 0.417 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.045 0.023 199.4 66: (ns/day) (hour/ns) 66: Performance: 34.530 0.695 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.039 0.020 199.2 66: (ns/day) (hour/ns) 66: Performance: 39.805 0.603 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_secondpart.part0002.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (90 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/12 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps. 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.037 0.019 199.2 66: (ns/day) (hour/ns) 66: Performance: 78.962 0.304 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.038 0.019 199.2 66: (ns/day) (hour/ns) 66: Performance: 40.314 0.595 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.037 0.019 198.9 66: (ns/day) (hour/ns) 66: Performance: 41.549 0.578 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_secondpart.part0002.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/12 (81 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/13 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 100, rlist from 0.73 to 0.814 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps. 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.045 0.023 199.2 66: (ns/day) (hour/ns) 66: Performance: 65.216 0.368 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 100, rlist from 0.73 to 0.814 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.024 0.012 198.8 66: (ns/day) (hour/ns) 66: Performance: 63.428 0.378 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 100, rlist from 0.73 to 0.814 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.067 0.034 199.6 66: (ns/day) (hour/ns) 66: Performance: 23.080 1.040 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_secondpart.part0002.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/13 (96 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/14 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps. 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.760 nm, buffer size 0.060 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.760 nm, buffer size 0.060 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.174 0.087 199.8 66: (ns/day) (hour/ns) 66: Performance: 16.854 1.424 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.141 0.071 199.8 66: (ns/day) (hour/ns) 66: Performance: 10.990 2.184 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.099 0.049 199.7 66: (ns/day) (hour/ns) 66: Performance: 15.725 1.526 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_secondpart.part0002.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/14 (232 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/15 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 25, rlist from 0.753 to 0.895 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps. 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.757 nm, buffer size 0.057 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.752 nm, buffer size 0.052 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.757 nm, buffer size 0.057 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.752 nm, buffer size 0.052 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.044 0.022 199.3 66: (ns/day) (hour/ns) 66: Performance: 65.903 0.364 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 25, rlist from 0.753 to 0.895 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.096 0.048 199.7 66: (ns/day) (hour/ns) 66: Performance: 16.202 1.481 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 25, rlist from 0.753 to 0.895 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.074 0.037 199.6 66: (ns/day) (hour/ns) 66: Performance: 20.875 1.150 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_secondpart.part0002.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/15 (133 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/16 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 66: NVE simulation: will use the initial temperature of 456.887 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 6 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 66: NVE simulation: will use the initial temperature of 456.887 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 6 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 16 steps, 0.0 ps. 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.082 0.041 199.5 66: (ns/day) (hour/ns) 66: Performance: 35.783 0.671 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.096 0.048 199.5 66: (ns/day) (hour/ns) 66: Performance: 16.093 1.491 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.153 0.077 199.7 66: (ns/day) (hour/ns) 66: Performance: 10.142 2.366 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_secondpart.part0002.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/16 (228 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/17 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 66: NVE simulation: will use the initial temperature of 456.887 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 6 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 66: NVE simulation: will use the initial temperature of 456.887 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 6 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 16 steps, 0.0 ps. 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.102 0.051 199.6 66: (ns/day) (hour/ns) 66: Performance: 28.856 0.832 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.138 0.069 199.7 66: (ns/day) (hour/ns) 66: Performance: 11.237 2.136 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.085 0.042 199.5 66: (ns/day) (hour/ns) 66: Performance: 18.320 1.310 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_secondpart.part0002.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/17 (228 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/18 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 66: NVE simulation: will use the initial temperature of 456.887 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 6 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 66: NVE simulation: will use the initial temperature of 456.887 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 6 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 16 steps, 0.0 ps. 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.077 0.038 199.5 66: (ns/day) (hour/ns) 66: Performance: 38.293 0.627 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.152 0.076 199.8 66: (ns/day) (hour/ns) 66: Performance: 10.235 2.345 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.055 0.028 199.3 66: (ns/day) (hour/ns) 66: Performance: 28.270 0.849 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_secondpart.part0002.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/18 (234 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/19 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 66: NVE simulation: will use the initial temperature of 456.887 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 6 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 66: NVE simulation: will use the initial temperature of 456.887 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 6 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 16 steps, 0.0 ps. 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.075 0.037 199.5 66: (ns/day) (hour/ns) 66: Performance: 39.176 0.613 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.075 0.037 199.5 66: (ns/day) (hour/ns) 66: Performance: 20.806 1.153 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.053 0.026 199.3 66: (ns/day) (hour/ns) 66: Performance: 29.414 0.816 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_secondpart.part0002.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/19 (174 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/20 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 5 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 5 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 16 steps, 0.0 ps. 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.147 0.074 199.8 66: (ns/day) (hour/ns) 66: Performance: 19.968 1.202 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.064 0.032 199.5 66: (ns/day) (hour/ns) 66: Performance: 24.236 0.990 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.135 0.067 199.8 66: (ns/day) (hour/ns) 66: Performance: 11.543 2.079 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_secondpart.part0002.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/20 (300 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/21 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 5 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 5 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 80, rlist from 0.743 to 0.847 66: 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 16 steps, 0.0 ps. 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.747 nm, buffer size 0.047 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.747 nm, buffer size 0.047 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.055 0.027 199.3 66: (ns/day) (hour/ns) 66: Performance: 53.652 0.447 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 80, rlist from 0.743 to 0.847 66: 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.033 0.017 199.1 66: (ns/day) (hour/ns) 66: Performance: 46.565 0.515 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 80, rlist from 0.743 to 0.846 66: 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.038 0.019 199.2 66: (ns/day) (hour/ns) 66: Performance: 40.324 0.595 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_secondpart.part0002.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/21 (341 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/22 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 5 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 5 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 16 steps, 0.0 ps. 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.037 0.019 199.2 66: (ns/day) (hour/ns) 66: Performance: 78.065 0.307 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.027 0.013 198.7 66: (ns/day) (hour/ns) 66: Performance: 58.228 0.412 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.029 0.015 198.4 66: (ns/day) (hour/ns) 66: Performance: 52.585 0.456 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_secondpart.part0002.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/22 (139 ms) 66: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/23 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 5 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 5 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 25, rlist from 0.725 to 0.797 66: 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 16 steps, 0.0 ps. 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.728 nm, buffer size 0.028 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.724 nm, buffer size 0.024 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.728 nm, buffer size 0.028 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.724 nm, buffer size 0.024 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.035 0.017 199.0 66: (ns/day) (hour/ns) 66: Performance: 84.050 0.286 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 25, rlist from 0.725 to 0.797 66: 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.037 0.019 198.7 66: (ns/day) (hour/ns) 66: Performance: 41.446 0.579 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 25, rlist from 0.725 to 0.797 66: 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.029 0.015 198.6 66: (ns/day) (hour/ns) 66: Performance: 53.068 0.452 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_secondpart.part0002.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/23 (188 ms) 66: [----------] 24 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact (4841 ms total) 66: 66: [----------] 8 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact 66: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: NVE simulation: will use the initial temperature of 294.908 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: NVE simulation: will use the initial temperature of 294.908 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps. 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.066 0.033 199.3 66: (ns/day) (hour/ns) 66: Performance: 44.045 0.545 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.153 0.077 199.6 66: (ns/day) (hour/ns) 66: Performance: 10.134 2.368 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.064 0.032 199.4 66: (ns/day) (hour/ns) 66: Performance: 24.358 0.985 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (208 ms) 66: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: NVE simulation: will use the initial temperature of 294.908 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: NVE simulation: will use the initial temperature of 294.908 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps. 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.047 0.024 199.1 66: (ns/day) (hour/ns) 66: Performance: 62.181 0.386 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.076 0.038 199.2 66: (ns/day) (hour/ns) 66: Performance: 20.397 1.177 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.042 0.021 198.9 66: (ns/day) (hour/ns) 66: Performance: 36.878 0.651 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (139 ms) 66: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: NVE simulation: will use the initial temperature of 294.908 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: NVE simulation: will use the initial temperature of 294.908 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps. 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.053 0.027 199.5 66: (ns/day) (hour/ns) 66: Performance: 55.060 0.436 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.048 0.024 199.4 66: (ns/day) (hour/ns) 66: Performance: 32.136 0.747 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.055 0.028 199.1 66: (ns/day) (hour/ns) 66: Performance: 27.893 0.860 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (135 ms) 66: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: NVE simulation: will use the initial temperature of 294.908 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: NVE simulation: will use the initial temperature of 294.908 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps. 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.089 0.045 199.6 66: (ns/day) (hour/ns) 66: Performance: 32.952 0.728 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.047 0.024 199.4 66: (ns/day) (hour/ns) 66: Performance: 32.729 0.733 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.044 0.022 198.8 66: (ns/day) (hour/ns) 66: Performance: 35.033 0.685 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (141 ms) 66: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/4 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps. 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.732 nm, buffer size 0.032 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.732 nm, buffer size 0.032 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.033 0.016 198.8 66: (ns/day) (hour/ns) 66: Performance: 89.640 0.268 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.039 0.021 188.1 66: (ns/day) (hour/ns) 66: Performance: 37.269 0.644 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.041 0.021 198.9 66: (ns/day) (hour/ns) 66: Performance: 37.285 0.644 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (145 ms) 66: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/5 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 100, rlist from 0.729 to 0.809 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps. 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.040 0.020 199.0 66: (ns/day) (hour/ns) 66: Performance: 72.281 0.332 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 100, rlist from 0.729 to 0.809 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.043 0.022 198.6 66: (ns/day) (hour/ns) 66: Performance: 35.724 0.672 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 100, rlist from 0.729 to 0.809 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.043 0.021 199.1 66: (ns/day) (hour/ns) 66: Performance: 36.189 0.663 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (345 ms) 66: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/6 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps. 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.051 0.026 199.2 66: (ns/day) (hour/ns) 66: Performance: 57.594 0.417 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.129 0.065 199.5 66: (ns/day) (hour/ns) 66: Performance: 12.050 1.992 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.035 0.019 185.6 66: (ns/day) (hour/ns) 66: Performance: 41.670 0.576 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (189 ms) 66: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/7 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 20, rlist from 0.751 to 0.848 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps. 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.043 0.022 199.1 66: (ns/day) (hour/ns) 66: Performance: 68.129 0.352 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 20, rlist from 0.751 to 0.848 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.085 0.043 199.4 66: (ns/day) (hour/ns) 66: Performance: 18.146 1.323 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 20, rlist from 0.751 to 0.848 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.064 0.032 199.4 66: (ns/day) (hour/ns) 66: Performance: 24.303 0.988 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (198 ms) 66: [----------] 8 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact (1505 ms total) 66: 66: [----------] 8 tests from NVT/MdrunNoAppendContinuationIsExact 66: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.023 0.012 198.6 66: (ns/day) (hour/ns) 66: Performance: 126.506 0.190 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.032 0.016 198.9 66: (ns/day) (hour/ns) 66: Performance: 48.066 0.499 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.025 0.013 198.8 66: (ns/day) (hour/ns) 66: Performance: 61.925 0.388 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (61 ms) 66: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.031 0.016 199.0 66: (ns/day) (hour/ns) 66: Performance: 93.372 0.257 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.035 0.018 199.1 66: (ns/day) (hour/ns) 66: Performance: 43.728 0.549 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.030 0.015 198.9 66: (ns/day) (hour/ns) 66: Performance: 51.843 0.463 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (70 ms) 66: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 66: 1 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 66: 1 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.043 0.022 199.3 66: (ns/day) (hour/ns) 66: Performance: 67.882 0.354 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.064 0.032 199.5 66: (ns/day) (hour/ns) 66: Performance: 24.328 0.987 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.027 0.014 198.9 66: (ns/day) (hour/ns) 66: Performance: 56.898 0.422 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (90 ms) 66: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 66: 1 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 66: 1 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.026 0.013 198.9 66: (ns/day) (hour/ns) 66: Performance: 114.140 0.210 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.028 0.014 198.8 66: (ns/day) (hour/ns) 66: Performance: 54.349 0.442 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.027 0.014 198.9 66: (ns/day) (hour/ns) 66: Performance: 56.609 0.424 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (70 ms) 66: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.060 0.030 199.5 66: (ns/day) (hour/ns) 66: Performance: 49.011 0.490 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.069 0.035 199.6 66: (ns/day) (hour/ns) 66: Performance: 22.464 1.068 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.044 0.022 199.1 66: (ns/day) (hour/ns) 66: Performance: 34.868 0.688 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (120 ms) 66: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.030 0.015 199.0 66: (ns/day) (hour/ns) 66: Performance: 99.023 0.242 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.041 0.020 199.4 66: (ns/day) (hour/ns) 66: Performance: 38.101 0.630 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.039 0.020 199.0 66: (ns/day) (hour/ns) 66: Performance: 39.832 0.603 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (80 ms) 66: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.034 0.017 199.3 66: (ns/day) (hour/ns) 66: Performance: 86.326 0.278 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.039 0.020 199.4 66: (ns/day) (hour/ns) 66: Performance: 39.488 0.608 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.054 0.027 199.2 66: (ns/day) (hour/ns) 66: Performance: 28.833 0.832 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (80 ms) 66: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.038 0.019 199.4 66: (ns/day) (hour/ns) 66: Performance: 77.505 0.310 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.069 0.035 199.6 66: (ns/day) (hour/ns) 66: Performance: 22.415 1.071 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.044 0.022 199.0 66: (ns/day) (hour/ns) 66: Performance: 35.070 0.684 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (94 ms) 66: [----------] 8 tests from NVT/MdrunNoAppendContinuationIsExact (669 ms total) 66: 66: [----------] 2 tests from NPH/MdrunNoAppendContinuationIsExact 66: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: NVE simulation: will use the initial temperature of 68.810 K for 66: determining the Verlet buffer size 66: 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: NVE simulation: will use the initial temperature of 68.810 K for 66: determining the Verlet buffer size 66: 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.049 0.024 199.4 66: (ns/day) (hour/ns) 66: Performance: 60.082 0.399 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.028 0.014 198.9 66: (ns/day) (hour/ns) 66: Performance: 54.344 0.442 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.044 0.022 199.1 66: (ns/day) (hour/ns) 66: Performance: 35.560 0.675 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (85 ms) 66: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: NVE simulation: will use the initial temperature of 68.810 K for 66: determining the Verlet buffer size 66: 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: NVE simulation: will use the initial temperature of 68.810 K for 66: determining the Verlet buffer size 66: 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.054 0.027 199.5 66: (ns/day) (hour/ns) 66: Performance: 54.450 0.441 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.038 0.019 199.3 66: (ns/day) (hour/ns) 66: Performance: 41.185 0.583 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.041 0.021 199.0 66: (ns/day) (hour/ns) 66: Performance: 37.670 0.637 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (91 ms) 66: [----------] 2 tests from NPH/MdrunNoAppendContinuationIsExact (177 ms total) 66: 66: [----------] 8 tests from NPT/MdrunNoAppendContinuationIsExact 66: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.036 0.018 199.1 66: (ns/day) (hour/ns) 66: Performance: 82.134 0.292 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.034 0.017 198.8 66: (ns/day) (hour/ns) 66: Performance: 46.065 0.521 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.030 0.015 198.8 66: (ns/day) (hour/ns) 66: Performance: 51.074 0.470 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (75 ms) 66: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.033 0.017 199.0 66: (ns/day) (hour/ns) 66: Performance: 88.739 0.270 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.121 0.061 199.7 66: (ns/day) (hour/ns) 66: Performance: 12.824 1.871 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.037 0.019 199.1 66: (ns/day) (hour/ns) 66: Performance: 41.381 0.580 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (126 ms) 66: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 66: 1 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 66: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 66: 1 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.032 0.016 199.0 66: (ns/day) (hour/ns) 66: Performance: 91.944 0.261 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.024 0.012 198.6 66: (ns/day) (hour/ns) 66: Performance: 64.943 0.370 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.084 0.042 199.6 66: (ns/day) (hour/ns) 66: Performance: 18.449 1.301 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (100 ms) 66: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 66: 1 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 66: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 66: 1 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.046 0.023 199.3 66: (ns/day) (hour/ns) 66: Performance: 63.502 0.378 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.023 0.011 198.6 66: (ns/day) (hour/ns) 66: Performance: 68.231 0.352 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.021 0.011 198.0 66: (ns/day) (hour/ns) 66: Performance: 72.513 0.331 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (67 ms) 66: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.035 0.017 199.2 66: (ns/day) (hour/ns) 66: Performance: 84.555 0.284 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.049 0.024 199.4 66: (ns/day) (hour/ns) 66: Performance: 31.834 0.754 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.035 0.017 198.6 66: (ns/day) (hour/ns) 66: Performance: 44.686 0.537 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (77 ms) 66: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.041 0.020 199.3 66: (ns/day) (hour/ns) 66: Performance: 72.126 0.333 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.036 0.018 199.3 66: (ns/day) (hour/ns) 66: Performance: 43.192 0.556 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.038 0.019 198.7 66: (ns/day) (hour/ns) 66: Performance: 41.092 0.584 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (92 ms) 66: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 66: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (0 ms) 66: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.038 0.019 199.2 66: (ns/day) (hour/ns) 66: Performance: 76.296 0.315 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.040 0.020 199.2 66: (ns/day) (hour/ns) 66: Performance: 38.357 0.626 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.038 0.019 198.8 66: (ns/day) (hour/ns) 66: Performance: 40.176 0.597 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (92 ms) 66: [----------] 8 tests from NPT/MdrunNoAppendContinuationIsExact (633 ms total) 66: 66: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact 66: [ RUN ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: MTTK coupling is deprecated and will soon be removed 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: MTTK coupling is deprecated and will soon be removed 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.048 0.024 199.2 66: (ns/day) (hour/ns) 66: Performance: 61.442 0.391 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.037 0.019 199.2 66: (ns/day) (hour/ns) 66: Performance: 41.935 0.572 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.037 0.019 197.9 66: (ns/day) (hour/ns) 66: Performance: 41.247 0.582 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (88 ms) 66: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact (88 ms total) 66: 66: [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact 66: [ RUN ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/0 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Pull group 1 'FirstWaterMolecule' has 3 atoms 66: Pull group 2 'SecondWaterMolecule' has 3 atoms 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: Pull group natoms pbc atom distance at start reference at t=0 66: 1 3 2 66: 2 3 5 1.112 nm 1.000 nm 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Pull group 1 'FirstWaterMolecule' has 3 atoms 66: Pull group 2 'SecondWaterMolecule' has 3 atoms 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: Pull group natoms pbc atom distance at start reference at t=0 66: 1 3 2 66: 2 3 5 1.112 nm 1.000 nm 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps. 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.045 0.023 199.1 66: (ns/day) (hour/ns) 66: Performance: 64.605 0.371 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.038 0.019 199.0 66: (ns/day) (hour/ns) 66: Performance: 40.494 0.593 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.066 0.033 199.3 66: (ns/day) (hour/ns) 66: Performance: 23.361 1.027 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (100 ms) 66: [ RUN ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/1 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Pull group 1 'FirstWaterMolecule' has 3 atoms 66: Pull group 2 'SecondWaterMolecule' has 3 atoms 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: Pull group natoms pbc atom distance at start reference at t=0 66: 1 3 2 66: 2 3 5 1.112 nm 1.000 nm 66: 66: There were 3 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Pull group 1 'FirstWaterMolecule' has 3 atoms 66: Pull group 2 'SecondWaterMolecule' has 3 atoms 66: Number of degrees of freedom in T-Coupling group System is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: Pull group natoms pbc atom distance at start reference at t=0 66: 1 3 2 66: 2 3 5 1.112 nm 1.000 nm 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps. 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.052 0.026 199.3 66: (ns/day) (hour/ns) 66: Performance: 55.935 0.429 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.040 0.020 199.1 66: (ns/day) (hour/ns) 66: Performance: 38.370 0.625 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.060 0.030 198.6 66: (ns/day) (hour/ns) 66: Performance: 25.765 0.932 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (111 ms) 66: [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact (211 ms total) 66: 66: [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact 66: [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 66: Setting the AWH bias MC random seed to -246981153 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Pull group 1 'C_&_r_1' has 1 atoms 66: Pull group 2 'N_&_r_2' has 1 atoms 66: Pull group 3 'CA' has 1 atoms 66: Pull group 4 'C_&_r_2' has 1 atoms 66: Pull group 5 'N_&_r_3' has 1 atoms 66: Number of degrees of freedom in T-Coupling group System is 51.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: Pull group natoms pbc atom distance at start reference at t=0 66: 1 1 0 66: 2 1 0 179.098 deg 0.000 deg 66: 2 1 0 66: 3 1 0 158.667 deg 0.000 deg 66: 66: There were 3 NOTEs 66: Setting the AWH bias MC random seed to -1365332225 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Pull group 1 'C_&_r_1' has 1 atoms 66: Pull group 2 'N_&_r_2' has 1 atoms 66: Pull group 3 'CA' has 1 atoms 66: Pull group 4 'C_&_r_2' has 1 atoms 66: Pull group 5 'N_&_r_3' has 1 atoms 66: Number of degrees of freedom in T-Coupling group System is 51.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: Pull group natoms pbc atom distance at start reference at t=0 66: 1 1 0 66: 2 1 0 179.098 deg 0.000 deg 66: 2 1 0 66: 3 1 0 158.667 deg 0.000 deg 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine-dipeptide' 66: 16 steps, 0.0 ps. 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.051 0.025 198.7 66: (ns/day) (hour/ns) 66: Performance: 57.785 0.415 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine-dipeptide' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.048 0.024 198.3 66: (ns/day) (hour/ns) 66: Performance: 32.073 0.748 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine-dipeptide' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.334 0.167 199.8 66: (ns/day) (hour/ns) 66: Performance: 4.657 5.154 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (370 ms) 66: [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 66: Setting the AWH bias MC random seed to 1072133610 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Pull group 1 'C_&_r_1' has 1 atoms 66: Pull group 2 'N_&_r_2' has 1 atoms 66: Pull group 3 'CA' has 1 atoms 66: Pull group 4 'C_&_r_2' has 1 atoms 66: Pull group 5 'N_&_r_3' has 1 atoms 66: Number of degrees of freedom in T-Coupling group System is 51.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: Pull group natoms pbc atom distance at start reference at t=0 66: 1 1 0 66: 2 1 0 179.098 deg 0.000 deg 66: 2 1 0 66: 3 1 0 158.667 deg 0.000 deg 66: 66: There were 3 NOTEs 66: Setting the AWH bias MC random seed to 830006724 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Pull group 1 'C_&_r_1' has 1 atoms 66: Pull group 2 'N_&_r_2' has 1 atoms 66: Pull group 3 'CA' has 1 atoms 66: Pull group 4 'C_&_r_2' has 1 atoms 66: Pull group 5 'N_&_r_3' has 1 atoms 66: Number of degrees of freedom in T-Coupling group System is 51.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: Pull group natoms pbc atom distance at start reference at t=0 66: 1 1 0 66: 2 1 0 179.098 deg 0.000 deg 66: 2 1 0 66: 3 1 0 158.667 deg 0.000 deg 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine-dipeptide' 66: 16 steps, 0.0 ps. 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.052 0.026 198.8 66: (ns/day) (hour/ns) 66: Performance: 55.724 0.431 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine-dipeptide' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.073 0.037 198.4 66: (ns/day) (hour/ns) 66: Performance: 21.189 1.133 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine-dipeptide' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.057 0.029 198.7 66: (ns/day) (hour/ns) 66: Performance: 27.017 0.888 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (189 ms) 66: [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact (559 ms total) 66: 66: [----------] 1 test from ExpandedEnsemble/MdrunNoAppendContinuationIsExact 66: [ RUN ] ExpandedEnsemble/MdrunNoAppendContinuationIsExact.WithinTolerances/0 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 2 NOTEs 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 79.00 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 2 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps. 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generated 2485 of the 2485 non-bonded parameter combinations 66: 66: Generated 2485 of the 2485 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'nonanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.051 0.026 199.4 66: (ns/day) (hour/ns) 66: Performance: 57.212 0.419 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.045 0.023 199.2 66: (ns/day) (hour/ns) 66: Performance: 34.322 0.699 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun '30 atom system in water' 66: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.049 0.025 198.4 66: (ns/day) (hour/ns) 66: Performance: 31.240 0.768 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] ExpandedEnsemble/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (161 ms) 66: [----------] 1 test from ExpandedEnsemble/MdrunNoAppendContinuationIsExact (161 ms total) 66: 66: [----------] 3 tests from Checking/InitialConstraintsTest 66: [ RUN ] Checking/InitialConstraintsTest.Works/0 66: Number of degrees of freedom in T-Coupling group rest is 11.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 66: NVE simulation: will use the initial temperature of 1141.954 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 2 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc-and-methanol' 66: 1 steps, 0.0 ps. 66: Setting the LD random seed to 2130311402 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.019 0.009 198.1 66: (ns/day) (hour/ns) 66: Performance: 18.274 1.313 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_spc-and-methanol.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/0 (19 ms) 66: [ RUN ] Checking/InitialConstraintsTest.Works/1 66: Number of degrees of freedom in T-Coupling group rest is 11.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 66: NVE simulation: will use the initial temperature of 1141.954 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 2 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc-and-methanol' 66: 1 steps, 0.0 ps. 66: Setting the LD random seed to 1988605951 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.041 0.021 199.3 66: (ns/day) (hour/ns) 66: Performance: 8.358 2.871 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_spc-and-methanol.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/1 (29 ms) 66: [ RUN ] Checking/InitialConstraintsTest.Works/2 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 66: Integrator method md-vv-avek is implemented primarily for validation 66: purposes; for molecular dynamics, you should probably be using md or 66: md-vv 66: 66: Number of degrees of freedom in T-Coupling group rest is 11.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 66: NVE simulation: will use the initial temperature of 1141.954 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc-and-methanol' 66: 1 steps, 0.0 ps. 66: Setting the LD random seed to -1086559305 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.015 0.008 198.1 66: (ns/day) (hour/ns) 66: Performance: 22.494 1.067 66: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_spc-and-methanol.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/2 (17 ms) 66: [----------] 3 tests from Checking/InitialConstraintsTest (66 ms total) 66: 66: [----------] Global test environment tear-down 66: [==========] 76 tests from 13 test suites ran. (10403 ms total) 66: [ PASSED ] 76 tests. 66/90 Test #66: MdrunIOTests .............................. Passed 10.44 sec test 67 Start 67: MdrunTestsOneRank 67: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/mdrun-test "-ntomp" "2" "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/MdrunTestsOneRank.xml" 67: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests 67: Test timeout computed to be: 600 67: [==========] Running 29 tests from 8 test suites. 67: [----------] Global test environment set-up. 67: [----------] 1 test from CompelTest 67: [ RUN ] CompelTest.SwapCanRun 67: Generating 1-4 interactions: fudge = 0.5 67: Split0 group 'Ch0' contains 83 atoms. 67: Split1 group 'Ch1' contains 83 atoms. 67: Solvent group 'SOL' contains 11931 atoms. 67: Swap group 'NA+' contains 19 atoms. 67: Swap group 'CL-' contains 19 atoms. 67: Number of degrees of freedom in T-Coupling group System is 27869.00 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 67: Removing center of mass motion in the presence of position restraints 67: might cause artifacts. When you are using position restraints to 67: equilibrate a macro-molecule, the artifacts are usually negligible. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 2 NOTEs 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 67: Update groups can not be used for this system because there are three or more consecutively coupled constraints 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: SWAP: Determining initial numbers of ions per compartment. 67: SWAP: Setting pointers for checkpoint writing 67: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 67: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 67: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 67: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 67: starting mdrun 'Channel_coco in octane membrane' 67: 2 steps, 0.0 ps. 67: Setting the LD random seed to 2146435071 67: 67: Generated 330891 of the 330891 non-bonded parameter combinations 67: 67: Generated 330891 of the 330891 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Protein' 67: 67: turning all bonds into constraints... 67: 67: Excluding 3 bonded neighbours molecule type 'OCT' 67: 67: turning all bonds into constraints... 67: 67: Excluding 1 bonded neighbours molecule type 'NA' 67: 67: turning all bonds into constraints... 67: 67: Excluding 1 bonded neighbours molecule type 'CL' 67: 67: turning all bonds into constraints... 67: 67: Excluding 3 bonded neighbours molecule type 'Protein' 67: 67: Excluding 3 bonded neighbours molecule type 'OCT' 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: turning all bonds into constraints... 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/OctaneSandwich.gro' 67: 67: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 67: 67: Calculated rlist for 1x1 atom pair-list as 1.316 nm, buffer size 0.316 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 1.262 nm, buffer size 0.262 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 1 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 2.796 1.398 200.0 67: (ns/day) (hour/ns) 67: Performance: 0.927 25.892 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 67: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps 67: 67: Update groups can not be used for this system because there are three or more consecutively coupled constraints 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: SWAP: Setting pointers for checkpoint writing 67: SWAP: Copying channel fluxes from checkpoint file data 67: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 67: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 67: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 67: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 67: starting mdrun 'Channel_coco in octane membrane' 67: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 67: 67: Writing final coordinates. 67: 67: NOTE: 22 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.395 0.198 199.8 67: (ns/day) (hour/ns) 67: Performance: 6.552 3.663 67: [ OK ] CompelTest.SwapCanRun (2426 ms) 67: [----------] 1 test from CompelTest (2426 ms total) 67: 67: [----------] 6 tests from BondedInteractionsTest 67: [ RUN ] BondedInteractionsTest.NormalBondWorks 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: 67: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: 67: In moleculetype 'butane' 2 atoms are not bound by a potential or 67: constraint to any other atom in the same moleculetype. Although 67: technically this might not cause issues in a simulation, this often means 67: that the user forgot to add a bond/potential/constraint or put multiple 67: molecules in the same moleculetype definition by mistake. Run with -v to 67: get information for each atom. 67: 67: Number of degrees of freedom in T-Coupling group rest is 9.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 67: NVE simulation with an initial temperature of zero: will use a Verlet 67: buffer of 10%. Check your energy drift! 67: 67: 67: There were 3 NOTEs 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 67: 67: Reading frames from gro file 'A single butane', 4 atoms. 67: Reading frame 0 time 0.000 Last frame 0 time 0.000 67: 67: NOTE: 25 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.001 0.000 188.8 67: (ns/day) (hour/ns) 67: Performance: 180.382 0.133 67: Setting the LD random seed to 1967053966 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'butane' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] BondedInteractionsTest.NormalBondWorks (9 ms) 67: [ RUN ] BondedInteractionsTest.TabulatedBondWorks 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: 67: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: 67: In moleculetype 'butane' 2 atoms are not bound by a potential or 67: constraint to any other atom in the same moleculetype. Although 67: technically this might not cause issues in a simulation, this often means 67: that the user forgot to add a bond/potential/constraint or put multiple 67: molecules in the same moleculetype definition by mistake. Run with -v to 67: get information for each atom. 67: 67: Number of degrees of freedom in T-Coupling group rest is 9.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 67: NVE simulation with an initial temperature of zero: will use a Verlet 67: buffer of 10%. Check your energy drift! 67: 67: 67: There were 3 NOTEs 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 67: 67: Reading frames from gro file 'A single butane', 4 atoms. 67: Reading frame 0 time 0.000 Last frame 0 time 0.000 67: 67: NOTE: 20 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.001 0.000 188.4 67: (ns/day) (hour/ns) 67: Performance: 208.389 0.115 67: Setting the LD random seed to -537188417 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'butane' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] BondedInteractionsTest.TabulatedBondWorks (9 ms) 67: [ RUN ] BondedInteractionsTest.NormalAngleWorks 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: 67: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: 67: In moleculetype 'butane' 4 atoms are not bound by a potential or 67: constraint to any other atom in the same moleculetype. Although 67: technically this might not cause issues in a simulation, this often means 67: that the user forgot to add a bond/potential/constraint or put multiple 67: molecules in the same moleculetype definition by mistake. Run with -v to 67: get information for each atom. 67: 67: Number of degrees of freedom in T-Coupling group rest is 9.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 67: NVE simulation with an initial temperature of zero: will use a Verlet 67: buffer of 10%. Check your energy drift! 67: 67: 67: There were 3 NOTEs 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 67: 67: Reading frames from gro file 'A single butane', 4 atoms. 67: Reading frame 0 time 0.000 Last frame 0 time 0.000 67: 67: NOTE: 21 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.001 0.000 188.8 67: (ns/day) (hour/ns) 67: Performance: 209.715 0.114 67: Setting the LD random seed to -605456403 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'butane' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] BondedInteractionsTest.NormalAngleWorks (10 ms) 67: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: 67: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: 67: In moleculetype 'butane' 4 atoms are not bound by a potential or 67: constraint to any other atom in the same moleculetype. Although 67: technically this might not cause issues in a simulation, this often means 67: that the user forgot to add a bond/potential/constraint or put multiple 67: molecules in the same moleculetype definition by mistake. Run with -v to 67: get information for each atom. 67: 67: Number of degrees of freedom in T-Coupling group rest is 9.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 67: NVE simulation with an initial temperature of zero: will use a Verlet 67: buffer of 10%. Check your energy drift! 67: 67: 67: There were 3 NOTEs 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 67: 67: Reading frames from gro file 'A single butane', 4 atoms. 67: Reading frame 0 time 0.000 Last frame 0 time 0.000 67: 67: NOTE: 22 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.001 0.001 170.1 67: (ns/day) (hour/ns) 67: Performance: 126.842 0.189 67: Setting the LD random seed to -539173707 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'butane' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (12 ms) 67: [ RUN ] BondedInteractionsTest.NormalDihedralWorks 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: 67: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]: 67: In moleculetype 'butane' 4 atoms are not bound by a potential or 67: constraint to any other atom in the same moleculetype. Although 67: technically this might not cause issues in a simulation, this often means 67: that the user forgot to add a bond/potential/constraint or put multiple 67: molecules in the same moleculetype definition by mistake. Run with -v to 67: get information for each atom. 67: 67: Number of degrees of freedom in T-Coupling group rest is 9.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 67: NVE simulation with an initial temperature of zero: will use a Verlet 67: buffer of 10%. Check your energy drift! 67: 67: 67: There were 3 NOTEs 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 67: 67: Reading frames from gro file 'A single butane', 4 atoms. 67: Reading frame 0 time 0.000 Last frame 0 time 0.000 67: 67: NOTE: 30 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.001 0.000 189.8 67: (ns/day) (hour/ns) 67: Performance: 216.480 0.111 67: Setting the LD random seed to 2147003774 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'butane' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] BondedInteractionsTest.NormalDihedralWorks (7 ms) 67: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: 67: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]: 67: In moleculetype 'butane' 4 atoms are not bound by a potential or 67: constraint to any other atom in the same moleculetype. Although 67: technically this might not cause issues in a simulation, this often means 67: that the user forgot to add a bond/potential/constraint or put multiple 67: molecules in the same moleculetype definition by mistake. Run with -v to 67: get information for each atom. 67: 67: Number of degrees of freedom in T-Coupling group rest is 9.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 67: NVE simulation with an initial temperature of zero: will use a Verlet 67: buffer of 10%. Check your energy drift! 67: 67: 67: There were 3 NOTEs 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 67: 67: Reading frames from gro file 'A single butane', 4 atoms. 67: Reading frame 0 time 0.000 Last frame 0 time 0.000 67: 67: NOTE: 29 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.001 0.000 190.0 67: (ns/day) (hour/ns) 67: Performance: 211.552 0.113 67: Setting the LD random seed to -1582746 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'butane' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (8 ms) 67: [----------] 6 tests from BondedInteractionsTest (58 ms total) 67: 67: [----------] 2 tests from BoxDeformationTest 67: [ RUN ] BoxDeformationTest.flowDoesNotAffectEkin 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (10) 67: 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: Number of degrees of freedom in T-Coupling group rest is 33.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: There were 3 NOTEs 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Argon' 67: 0 steps, 0.0 ps. 67: 67: NOTE: 30 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.001 0.000 167.2 67: (ns/day) (hour/ns) 67: Performance: 458.719 0.052 67: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.edr as double precision energy file 67: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -1082278979 67: 67: Generated 1 of the 1 non-bonded parameter combinations 67: 67: Excluding 1 bonded neighbours molecule type 'Argon' 67: 67: Setting gen_seed to -672436306 67: 67: Velocities were taken from a Maxwell distribution at 0 K 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] BoxDeformationTest.flowDoesNotAffectEkin (9 ms) 67: [ RUN ] BoxDeformationTest.EnergiesWithinTolerances 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (10) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Number of degrees of freedom in T-Coupling group rest is 1293.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: There were 2 NOTEs 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'spc2' 67: 20 steps, 0.0 ps. 67: Setting the LD random seed to -546308101 67: 67: Generated 330891 of the 330891 non-bonded parameter combinations 67: 67: Generated 330891 of the 330891 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc216.gro' 67: 67: The largest distance between excluded atoms is 0.152 nm between atom 41 and 42 67: Calculating fourier grid dimensions for X Y Z 67: Using a fourier grid of 16x16x16, spacing 0.116 0.116 0.116 67: 67: Estimate for the relative computational load of the PME mesh part: 0.15 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 1.147 0.574 199.9 67: (ns/day) (hour/ns) 67: Performance: 6.326 3.794 67: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.edr as double precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Reading energy frame 2 time 0.040 Last energy frame read 2 time 0.040 [ OK ] BoxDeformationTest.EnergiesWithinTolerances (1458 ms) 67: [----------] 2 tests from BoxDeformationTest (1468 ms total) 67: 67: [----------] 1 test from PositionRestraintCommTest 67: [ RUN ] PositionRestraintCommTest.PositionRestraintsTwoCOMs 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 67: You have set rlist larger than the interaction cut-off, but you also have 67: verlet-buffer-tolerance > 0. Will set rlist using 67: verlet-buffer-tolerance. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (10) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 67: 13489 atoms are not part of any of the VCM groups 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 67: 13489 atoms are not part of any center of mass motion removal group. 67: This may lead to artifacts. 67: In most cases one should use one group for the whole system. 67: 67: Number of degrees of freedom in T-Coupling group System is 29527.73 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 67: Removing center of mass motion in the presence of position restraints 67: might cause artifacts. When you are using position restraints to 67: equilibrate a macro-molecule, the artifacts are usually negligible. 67: 67: 67: There were 4 NOTEs 67: 67: There was 1 WARNING 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 67: Changing nstlist from 10 to 20, rlist from 0.971 to 1.08 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Channel_coco in octane membrane' 67: 10 steps, 0.0 ps. 67: Setting the LD random seed to -35726633 67: 67: Generated 330891 of the 330891 non-bonded parameter combinations 67: 67: Generated 330891 of the 330891 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Protein' 67: 67: Excluding 3 bonded neighbours molecule type 'OCT' 67: 67: Excluding 1 bonded neighbours molecule type 'NA' 67: 67: Excluding 1 bonded neighbours molecule type 'CL' 67: 67: Excluding 3 bonded neighbours molecule type 'Protein' 67: 67: Excluding 3 bonded neighbours molecule type 'OCT' 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/OctaneSandwich.gro' 67: 67: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.990 nm, buffer size 0.090 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.965 nm, buffer size 0.065 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: Chain0: 2.207 2.168 7.330 67: Chain1: 2.228 2.186 2.401 67: Chain0: 2.207 2.168 7.330 67: Chain1: 2.228 2.186 2.401 67: 67: This run will generate roughly 1 Mb of data 67: 67: Writing final coordinates. 67: 67: NOTE: 16 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.910 0.455 199.9 67: (ns/day) (hour/ns) 67: Performance: 4.174 5.750 67: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.edr as double precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Last energy frame read 1 time 0.020 [ OK ] PositionRestraintCommTest.PositionRestraintsTwoCOMs (1371 ms) 67: [----------] 1 test from PositionRestraintCommTest (1371 ms total) 67: 67: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest 67: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 2 [file ala.top, line 256]: 67: For energy conservation with LINCS, lincs_iter should be 2 or larger. 67: 67: 67: Number of degrees of freedom in T-Coupling group rest is 54.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 67: The optimal PME mesh load for parallel simulations is below 0.5 67: and for highly parallel simulations between 0.25 and 0.33, 67: for higher performance, increase the cut-off and the PME grid spacing. 67: 67: 67: 67: There were 3 NOTEs 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'UNNAMED in water' 67: 4 steps, 0.0 ps. 67: Setting the LD random seed to -1242581002 67: 67: Generated 2211 of the 2211 non-bonded parameter combinations 67: 67: Generated 2211 of the 2211 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 67: 67: turning H bonds into constraints... 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 67: 67: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 67: Calculating fourier grid dimensions for X Y Z 67: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 67: 67: Estimate for the relative computational load of the PME mesh part: 0.94 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.328 0.164 199.8 67: (ns/day) (hour/ns) 67: Performance: 2.629 9.130 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 2 [file ala.top, line 256]: 67: For energy conservation with LINCS, lincs_iter should be 2 or larger. 67: 67: 67: Number of degrees of freedom in T-Coupling group rest is 54.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 67: The optimal PME mesh load for parallel simulations is below 0.5 67: and for highly parallel simulations between 0.25 and 0.33, 67: for higher performance, increase the cut-off and the PME grid spacing. 67: 67: 67: 67: There were 3 NOTEs 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'UNNAMED in water' 67: 4 steps, 0.0 ps. 67: Setting the LD random seed to -591937 67: 67: Generated 2211 of the 2211 non-bonded parameter combinations 67: 67: Generated 2211 of the 2211 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 67: 67: turning H bonds into constraints... 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 67: 67: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 67: Calculating fourier grid dimensions for X Y Z 67: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 67: 67: Estimate for the relative computational load of the PME mesh part: 0.94 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: NOTE: 5 % of the run time was spent in domain decomposition, 67: 20 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.141 0.071 199.4 67: (ns/day) (hour/ns) 67: Performance: 6.117 3.924 67: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 67: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 trr version: GMX_trn_file (double precision) 67: 67: 67: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 67: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (822 ms) 67: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 2 [file ala.top, line 256]: 67: For energy conservation with LINCS, lincs_iter should be 2 or larger. 67: 67: 67: Number of degrees of freedom in T-Coupling group rest is 54.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 67: The optimal PME mesh load for parallel simulations is below 0.5 67: and for highly parallel simulations between 0.25 and 0.33, 67: for higher performance, increase the cut-off and the PME grid spacing. 67: 67: 67: 67: There were 3 NOTEs 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'UNNAMED in water' 67: 4 steps, 0.0 ps. 67: Setting the LD random seed to -25166294 67: 67: Generated 2211 of the 2211 non-bonded parameter combinations 67: 67: Generated 2211 of the 2211 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 67: 67: turning H bonds into constraints... 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 67: 67: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 67: Calculating fourier grid dimensions for X Y Z 67: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 67: 67: Estimate for the relative computational load of the PME mesh part: 0.94 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.090 0.045 199.1 67: (ns/day) (hour/ns) 67: Performance: 9.548 2.514 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 2 [file ala.top, line 256]: 67: For energy conservation with LINCS, lincs_iter should be 2 or larger. 67: 67: 67: Number of degrees of freedom in T-Coupling group rest is 54.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 67: The optimal PME mesh load for parallel simulations is below 0.5 67: and for highly parallel simulations between 0.25 and 0.33, 67: for higher performance, increase the cut-off and the PME grid spacing. 67: 67: 67: 67: There were 3 NOTEs 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 67: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 67: Can not increase nstlist because an NVE ensemble is used 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'UNNAMED in water' 67: 4 steps, 0.0 ps. 67: Setting the LD random seed to -2017559329 67: 67: Generated 2211 of the 2211 non-bonded parameter combinations 67: 67: Generated 2211 of the 2211 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 67: 67: turning H bonds into constraints... 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 67: 67: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 67: Calculating fourier grid dimensions for X Y Z 67: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 67: 67: Estimate for the relative computational load of the PME mesh part: 0.94 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.075 0.038 199.1 67: (ns/day) (hour/ns) 67: Performance: 11.421 2.101 67: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file 67: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 67: 67: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file 67: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (169 ms) 67: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (992 ms total) 67: 67: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest 67: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Pull group 1 'FirstWaterMolecule' has 3 atoms 67: Pull group 2 'SecondWaterMolecule' has 3 atoms 67: Number of degrees of freedom in T-Coupling group rest is 9.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: Pull group natoms pbc atom distance at start reference at t=0 67: 1 3 2 67: 2 3 5 1.112 nm 1.000 nm 67: 67: There was 1 NOTE 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'spc2' 67: 4 steps, 0.0 ps. 67: Setting the LD random seed to -671256657 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Generated 3 of the 3 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: turning H bonds into constraints... 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.156 0.078 199.7 67: (ns/day) (hour/ns) 67: Performance: 5.512 4.354 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Pull group 1 'FirstWaterMolecule' has 3 atoms 67: Pull group 2 'SecondWaterMolecule' has 3 atoms 67: Number of degrees of freedom in T-Coupling group rest is 9.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: Pull group natoms pbc atom distance at start reference at t=0 67: 1 3 2 67: 2 3 5 1.112 nm 1.000 nm 67: 67: There was 1 NOTE 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 67: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 67: Can not increase nstlist because an NVE ensemble is used 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'spc2' 67: 4 steps, 0.0 ps. 67: Setting the LD random seed to 2146697213 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Generated 3 of the 3 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: turning H bonds into constraints... 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.093 0.046 199.3 67: (ns/day) (hour/ns) 67: Performance: 9.295 2.582 67: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 67: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 67: 67: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 67: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (181 ms) 67: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (181 ms total) 67: 67: [----------] 12 tests from FreezeWorks/FreezeGroupTest 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 33.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 67: NVE simulation: will use the initial temperature of 246.451 K for 67: determining the Verlet buffer size 67: 67: 67: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 5 NOTEs 67: 67: There was 1 WARNING 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.093 0.047 199.6 67: (ns/day) (hour/ns) 67: Performance: 16.703 1.437 67: 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (97 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 33.00 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 67: NVE simulation: will use the initial temperature of 246.451 K for 67: determining the Verlet buffer size 67: 67: 67: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 5 NOTEs 67: 67: There was 1 WARNING 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.068 0.034 199.1 67: (ns/day) (hour/ns) 67: Performance: 22.874 1.049 67: 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (72 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 33.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 67: NVE simulation: will use the initial temperature of 246.451 K for 67: determining the Verlet buffer size 67: 67: 67: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 5 NOTEs 67: 67: There was 1 WARNING 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 1.374 0.687 200.0 67: (ns/day) (hour/ns) 67: Performance: 1.132 21.202 67: 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (722 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 33.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 67: NVE simulation: will use the initial temperature of 246.451 K for 67: determining the Verlet buffer size 67: 67: 67: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 5 NOTEs 67: 67: There was 1 WARNING 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.071 0.036 198.9 67: (ns/day) (hour/ns) 67: Performance: 21.794 1.101 67: 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 (76 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 33.00 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 67: NVE simulation: will use the initial temperature of 246.451 K for 67: determining the Verlet buffer size 67: 67: 67: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 5 NOTEs 67: 67: There was 1 WARNING 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.041 0.021 198.7 67: (ns/day) (hour/ns) 67: Performance: 37.880 0.634 67: 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (63 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 67: ./src/programs/mdrun/tests/freezegroups.cpp:209: Skipped 67: Parrinello-Rahman is not implemented in md-vv. 67: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (0 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 33.00 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 4 NOTEs 67: 67: There was 1 WARNING 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 67: Changing nstlist from 8 to 20, rlist from 0.756 to 0.861 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.441 0.222 198.7 67: (ns/day) (hour/ns) 67: Performance: 3.504 6.850 67: 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (261 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 33.00 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 4 NOTEs 67: 67: There was 1 WARNING 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 67: Changing nstlist from 8 to 20, rlist from 0.756 to 0.861 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.071 0.036 199.0 67: (ns/day) (hour/ns) 67: Performance: 21.670 1.107 67: 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (80 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 33.00 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 4 NOTEs 67: 67: There was 1 WARNING 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 67: Changing nstlist from 8 to 20, rlist from 0.756 to 0.861 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.083 0.042 199.3 67: (ns/day) (hour/ns) 67: Performance: 18.653 1.287 67: 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 (91 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 33.00 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 4 NOTEs 67: 67: There was 1 WARNING 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 67: Changing nstlist from 8 to 100, rlist from 0.735 to 0.832 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.072 0.036 199.1 67: (ns/day) (hour/ns) 67: Performance: 21.634 1.109 67: 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 (115 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 33.00 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 4 NOTEs 67: 67: There was 1 WARNING 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 67: Changing nstlist from 8 to 100, rlist from 0.735 to 0.832 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.079 0.040 199.2 67: (ns/day) (hour/ns) 67: Performance: 19.608 1.224 67: 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 (139 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 33.00 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 4 NOTEs 67: 67: There was 1 WARNING 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 67: Changing nstlist from 8 to 100, rlist from 0.735 to 0.832 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.099 0.050 199.2 67: (ns/day) (hour/ns) 67: Performance: 15.682 1.530 67: 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 (131 ms) 67: [----------] 12 tests from FreezeWorks/FreezeGroupTest (1853 ms total) 67: 67: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest 67: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 67: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: Net Acceleration in X direction, will not be corrected 67: Net Acceleration in Y direction, will not be corrected 67: Net Acceleration in Z direction, will not be corrected 67: 67: There were 3 NOTEs 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'spc2' 67: 8 steps, 0.0 ps. 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Generated 3 of the 3 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Setting gen_seed to 2138811839 67: 67: Velocities were taken from a Maxwell distribution at 0 K 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.080 0.040 199.4 67: (ns/day) (hour/ns) 67: Performance: 38.579 0.622 67: 67: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (61 ms) 67: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 67: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 67: Net Acceleration in X direction, will not be corrected 67: Net Acceleration in Y direction, will not be corrected 67: Net Acceleration in Z direction, will not be corrected 67: 67: There were 3 NOTEs 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 67: Can not increase nstlist because verlet-buffer-tolerance is not set or used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'spc2' 67: 8 steps, 0.0 ps. 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Generated 3 of the 3 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Setting gen_seed to -212453953 67: 67: Velocities were taken from a Maxwell distribution at 0 K 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.067 0.034 199.3 67: (ns/day) (hour/ns) 67: Performance: 46.068 0.521 67: 67: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (47 ms) 67: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 67: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: Net Acceleration in X direction, will not be corrected 67: Net Acceleration in Y direction, will not be corrected 67: Net Acceleration in Z direction, will not be corrected 67: 67: There were 3 NOTEs 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'spc2' 67: 8 steps, 0.0 ps. 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Generated 3 of the 3 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Setting gen_seed to -78217221 67: 67: Velocities were taken from a Maxwell distribution at 0 K 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.024 0.012 197.9 67: (ns/day) (hour/ns) 67: Performance: 126.270 0.190 67: 67: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 (28 ms) 67: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 67: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 67: Net Acceleration in X direction, will not be corrected 67: Net Acceleration in Y direction, will not be corrected 67: Net Acceleration in Z direction, will not be corrected 67: 67: There were 3 NOTEs 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 67: Can not increase nstlist because verlet-buffer-tolerance is not set or used 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'spc2' 67: 8 steps, 0.0 ps. 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Generated 3 of the 3 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Setting gen_seed to 520077308 67: 67: Velocities were taken from a Maxwell distribution at 0 K 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.039 0.020 198.6 67: (ns/day) (hour/ns) 67: Performance: 79.588 0.302 67: 67: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (35 ms) 67: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (173 ms total) 67: 67: [----------] Global test environment tear-down 67: [==========] 29 tests from 8 test suites ran. (9580 ms total) 67: [ PASSED ] 28 tests. 67: [ SKIPPED ] 1 test, listed below: 67: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 67/90 Test #67: MdrunTestsOneRank ......................... Passed 9.62 sec test 68 Start 68: MdrunTestsTwoRanks 68: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/mdrun-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/MdrunTestsTwoRanks.xml" 68: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests 68: Test timeout computed to be: 600 68: [==========] Running 29 tests from 8 test suites. 68: [----------] Global test environment set-up. 68: [----------] 1 test from CompelTest 68: [ RUN ] CompelTest.SwapCanRun 68: Generating 1-4 interactions: fudge = 0.5 68: Split0 group 'Ch0' contains 83 atoms. 68: Split1 group 'Ch1' contains 83 atoms. 68: Solvent group 'SOL' contains 11931 atoms. 68: Swap group 'NA+' contains 19 atoms. 68: Swap group 'CL-' contains 19 atoms. 68: Number of degrees of freedom in T-Coupling group System is 27869.00 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 68: Removing center of mass motion in the presence of position restraints 68: might cause artifacts. When you are using position restraints to 68: equilibrate a macro-molecule, the artifacts are usually negligible. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 2 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 68: Update groups can not be used for this system because there are three or more consecutively coupled constraints 68: 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: SWAP: Determining initial numbers of ions per compartment. 68: SWAP: Setting pointers for checkpoint writing 68: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 68: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 68: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 68: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 68: starting mdrun 'Channel_coco in octane membrane' 68: 2 steps, 0.0 ps. 68: Setting the LD random seed to 1862116351 68: 68: Generated 330891 of the 330891 non-bonded parameter combinations 68: 68: Generated 330891 of the 330891 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Protein' 68: 68: turning all bonds into constraints... 68: 68: Excluding 3 bonded neighbours molecule type 'OCT' 68: 68: turning all bonds into constraints... 68: 68: Excluding 1 bonded neighbours molecule type 'NA' 68: 68: turning all bonds into constraints... 68: 68: Excluding 1 bonded neighbours molecule type 'CL' 68: 68: turning all bonds into constraints... 68: 68: Excluding 3 bonded neighbours molecule type 'Protein' 68: 68: Excluding 3 bonded neighbours molecule type 'OCT' 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/OctaneSandwich.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.316 nm, buffer size 0.316 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.262 nm, buffer size 0.262 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 1 Mb of data 68: 68: Writing final coordinates. 68: 68: 68: Dynamic load balancing report: 68: DLB was off during the run due to low measured imbalance. 68: Average load imbalance: 24.9%. 68: The balanceable part of the MD step is 24%, load imbalance is computed from this. 68: Part of the total run time spent waiting due to load imbalance: 5.9%. 68: 68: NOTE: 5.9 % of the available CPU time was lost due to load imbalance 68: in the domain decomposition. 68: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 68: You can also consider manually changing the decomposition (option -dd); 68: e.g. by using fewer domains along the box dimension in which there is 68: considerable inhomogeneity in the simulated system. 68: 68: NOTE: 14 % of the run time was spent in domain decomposition, 68: 23 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 2.461 0.618 398.1 68: (ns/day) (hour/ns) 68: Performance: 2.096 11.448 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 68: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps 68: 68: Update groups can not be used for this system because there are three or more consecutively coupled constraints 68: 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: SWAP: Setting pointers for checkpoint writing 68: SWAP: Copying channel fluxes from checkpoint file data 68: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 68: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 68: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 68: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 68: starting mdrun 'Channel_coco in octane membrane' 68: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: NOTE: 18 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 1.224 0.306 399.6 68: (ns/day) (hour/ns) 68: Performance: 4.230 5.673 68: [ OK ] CompelTest.SwapCanRun (2665 ms) 68: [----------] 1 test from CompelTest (2665 ms total) 68: 68: [----------] 6 tests from BondedInteractionsTest 68: [ RUN ] BondedInteractionsTest.NormalBondWorks 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 68: For a correct single-point energy evaluation with nsteps = 0, use 68: continuation = yes to avoid constraining the input coordinates. 68: 68: 68: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: 68: In moleculetype 'butane' 2 atoms are not bound by a potential or 68: constraint to any other atom in the same moleculetype. Although 68: technically this might not cause issues in a simulation, this often means 68: that the user forgot to add a bond/potential/constraint or put multiple 68: molecules in the same moleculetype definition by mistake. Run with -v to 68: get information for each atom. 68: 68: Number of degrees of freedom in T-Coupling group rest is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 68: NVE simulation with an initial temperature of zero: will use a Verlet 68: buffer of 10%. Check your energy drift! 68: 68: 68: There were 3 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 68: 68: Reading frames from gro file 'A single butane', 4 atoms. 68: Reading frame 0 time 0.000 Last frame 0 time 0.000 68: 68: NOTE: 72 % of the run time was spent in domain decomposition, 68: 1 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.063 0.016 398.9 68: (ns/day) (hour/ns) 68: Performance: 5.480 4.380 68: Setting the LD random seed to -2097158 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'butane' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] BondedInteractionsTest.NormalBondWorks (132 ms) 68: [ RUN ] BondedInteractionsTest.TabulatedBondWorks 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 68: For a correct single-point energy evaluation with nsteps = 0, use 68: continuation = yes to avoid constraining the input coordinates. 68: 68: 68: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: 68: In moleculetype 'butane' 2 atoms are not bound by a potential or 68: constraint to any other atom in the same moleculetype. Although 68: technically this might not cause issues in a simulation, this often means 68: that the user forgot to add a bond/potential/constraint or put multiple 68: molecules in the same moleculetype definition by mistake. Run with -v to 68: get information for each atom. 68: 68: Number of degrees of freedom in T-Coupling group rest is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 68: NVE simulation with an initial temperature of zero: will use a Verlet 68: buffer of 10%. Check your energy drift! 68: 68: 68: There were 3 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 68: 68: Reading frames from gro file 'A single butane', 4 atoms. 68: Reading frame 0 time 0.000 Last frame 0 time 0.000 68: 68: NOTE: 19 % of the run time was spent in domain decomposition, 68: 14 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: NOTE: 5 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.004 0.001 383.0 68: (ns/day) (hour/ns) 68: Performance: 74.765 0.321 68: Setting the LD random seed to 1838148349 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'butane' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] BondedInteractionsTest.TabulatedBondWorks (71 ms) 68: [ RUN ] BondedInteractionsTest.NormalAngleWorks 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 68: For a correct single-point energy evaluation with nsteps = 0, use 68: continuation = yes to avoid constraining the input coordinates. 68: 68: 68: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: 68: In moleculetype 'butane' 4 atoms are not bound by a potential or 68: constraint to any other atom in the same moleculetype. Although 68: technically this might not cause issues in a simulation, this often means 68: that the user forgot to add a bond/potential/constraint or put multiple 68: molecules in the same moleculetype definition by mistake. Run with -v to 68: get information for each atom. 68: 68: Number of degrees of freedom in T-Coupling group rest is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 68: NVE simulation with an initial temperature of zero: will use a Verlet 68: buffer of 10%. Check your energy drift! 68: 68: 68: There were 3 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 68: 68: Reading frames from gro file 'A single butane', 4 atoms. 68: Reading frame 0 time 0.000 Last frame 0 time 0.000 68: 68: NOTE: 18 % of the run time was spent in domain decomposition, 68: 12 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.003 0.001 383.8 68: (ns/day) (hour/ns) 68: Performance: 95.908 0.250 68: Setting the LD random seed to 1795162044 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'butane' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] BondedInteractionsTest.NormalAngleWorks (51 ms) 68: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 68: For a correct single-point energy evaluation with nsteps = 0, use 68: continuation = yes to avoid constraining the input coordinates. 68: 68: 68: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: 68: In moleculetype 'butane' 4 atoms are not bound by a potential or 68: constraint to any other atom in the same moleculetype. Although 68: technically this might not cause issues in a simulation, this often means 68: that the user forgot to add a bond/potential/constraint or put multiple 68: molecules in the same moleculetype definition by mistake. Run with -v to 68: get information for each atom. 68: 68: Number of degrees of freedom in T-Coupling group rest is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 68: NVE simulation with an initial temperature of zero: will use a Verlet 68: buffer of 10%. Check your energy drift! 68: 68: 68: There were 3 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 68: 68: Reading frames from gro file 'A single butane', 4 atoms. 68: Reading frame 0 time 0.000 Last frame 0 time 0.000 68: 68: NOTE: 58 % of the run time was spent in domain decomposition, 68: 0 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: NOTE: 16 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.252 0.063 399.7 68: (ns/day) (hour/ns) 68: Performance: 1.372 17.491 68: Setting the LD random seed to -1051786 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'butane' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (155 ms) 68: [ RUN ] BondedInteractionsTest.NormalDihedralWorks 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 68: For a correct single-point energy evaluation with nsteps = 0, use 68: continuation = yes to avoid constraining the input coordinates. 68: 68: 68: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]: 68: In moleculetype 'butane' 4 atoms are not bound by a potential or 68: constraint to any other atom in the same moleculetype. Although 68: technically this might not cause issues in a simulation, this often means 68: that the user forgot to add a bond/potential/constraint or put multiple 68: molecules in the same moleculetype definition by mistake. Run with -v to 68: get information for each atom. 68: 68: Number of degrees of freedom in T-Coupling group rest is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 68: NVE simulation with an initial temperature of zero: will use a Verlet 68: buffer of 10%. Check your energy drift! 68: 68: 68: There were 3 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 68: 68: Reading frames from gro file 'A single butane', 4 atoms. 68: Reading frame 0 time 0.000 Last frame 0 time 0.000 68: 68: NOTE: 17 % of the run time was spent in domain decomposition, 68: 14 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.003 0.001 380.3 68: (ns/day) (hour/ns) 68: Performance: 107.629 0.223 68: Setting the LD random seed to -585707797 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'butane' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] BondedInteractionsTest.NormalDihedralWorks (80 ms) 68: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 68: For a correct single-point energy evaluation with nsteps = 0, use 68: continuation = yes to avoid constraining the input coordinates. 68: 68: 68: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]: 68: In moleculetype 'butane' 4 atoms are not bound by a potential or 68: constraint to any other atom in the same moleculetype. Although 68: technically this might not cause issues in a simulation, this often means 68: that the user forgot to add a bond/potential/constraint or put multiple 68: molecules in the same moleculetype definition by mistake. Run with -v to 68: get information for each atom. 68: 68: Number of degrees of freedom in T-Coupling group rest is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 68: NVE simulation with an initial temperature of zero: will use a Verlet 68: buffer of 10%. Check your energy drift! 68: 68: 68: There were 3 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 68: 68: Reading frames from gro file 'A single butane', 4 atoms. 68: Reading frame 0 time 0.000 Last frame 0 time 0.000 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.007 0.002 392.0 68: (ns/day) (hour/ns) 68: Performance: 47.238 0.508 68: Setting the LD random seed to -156279897 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'butane' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (99 ms) 68: [----------] 6 tests from BondedInteractionsTest (592 ms total) 68: 68: [----------] 2 tests from BoxDeformationTest 68: [ RUN ] BoxDeformationTest.flowDoesNotAffectEkin 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 68: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 68: < 0 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (10) 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 68: For a correct single-point energy evaluation with nsteps = 0, use 68: continuation = yes to avoid constraining the input coordinates. 68: 68: Number of degrees of freedom in T-Coupling group rest is 33.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: There were 3 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 0 steps, 0.0 ps. 68: 68: NOTE: 18 % of the run time was spent in domain decomposition, 68: 26 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: NOTE: 5 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.002 0.001 332.6 68: (ns/day) (hour/ns) 68: Performance: 261.416 0.092 68: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -1613571 68: 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Setting gen_seed to 2011605787 68: 68: Velocities were taken from a Maxwell distribution at 0 K 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] BoxDeformationTest.flowDoesNotAffectEkin (48 ms) 68: [ RUN ] BoxDeformationTest.EnergiesWithinTolerances 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 68: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 68: < 0 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (10) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group rest is 1293.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: There were 2 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 20 steps, 0.0 ps. 68: Setting the LD random seed to -1363190915 68: 68: Generated 330891 of the 330891 non-bonded parameter combinations 68: 68: Generated 330891 of the 330891 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc216.gro' 68: 68: The largest distance between excluded atoms is 0.152 nm between atom 41 and 42 68: Calculating fourier grid dimensions for X Y Z 68: Using a fourier grid of 16x16x16, spacing 0.116 0.116 0.116 68: 68: Estimate for the relative computational load of the PME mesh part: 0.15 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: 68: Dynamic load balancing report: 68: DLB got disabled because it was unsuitable to use. 68: Average load imbalance: 47.2%. 68: The balanceable part of the MD step is 9%, load imbalance is computed from this. 68: Part of the total run time spent waiting due to load imbalance: 4.4%. 68: 68: 68: Core t (s) Wall t (s) (%) 68: Time: 4.404 1.101 399.9 68: (ns/day) (hour/ns) 68: Performance: 3.295 7.283 68: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Reading energy frame 2 time 0.040 Last energy frame read 2 time 0.040 [ OK ] BoxDeformationTest.EnergiesWithinTolerances (2928 ms) 68: [----------] 2 tests from BoxDeformationTest (2977 ms total) 68: 68: [----------] 1 test from PositionRestraintCommTest 68: [ RUN ] PositionRestraintCommTest.PositionRestraintsTwoCOMs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 68: You have set rlist larger than the interaction cut-off, but you also have 68: verlet-buffer-tolerance > 0. Will set rlist using 68: verlet-buffer-tolerance. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (10) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 68: 13489 atoms are not part of any of the VCM groups 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 68: 13489 atoms are not part of any center of mass motion removal group. 68: This may lead to artifacts. 68: In most cases one should use one group for the whole system. 68: 68: Number of degrees of freedom in T-Coupling group System is 29527.73 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 68: Removing center of mass motion in the presence of position restraints 68: might cause artifacts. When you are using position restraints to 68: equilibrate a macro-molecule, the artifacts are usually negligible. 68: 68: 68: There were 4 NOTEs 68: 68: There was 1 WARNING 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 68: Changing nstlist from 10 to 20, rlist from 0.971 to 1.08 68: 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Channel_coco in octane membrane' 68: 10 steps, 0.0 ps. 68: Setting the LD random seed to -35675171 68: 68: Generated 330891 of the 330891 non-bonded parameter combinations 68: 68: Generated 330891 of the 330891 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Protein' 68: 68: Excluding 3 bonded neighbours molecule type 'OCT' 68: 68: Excluding 1 bonded neighbours molecule type 'NA' 68: 68: Excluding 1 bonded neighbours molecule type 'CL' 68: 68: Excluding 3 bonded neighbours molecule type 'Protein' 68: 68: Excluding 3 bonded neighbours molecule type 'OCT' 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/OctaneSandwich.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.990 nm, buffer size 0.090 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.965 nm, buffer size 0.065 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: Chain0: 2.207 2.168 7.330 68: Chain1: 2.228 2.186 2.401 68: Chain0: 2.207 2.168 7.330 68: Chain1: 2.228 2.186 2.401 68: 68: This run will generate roughly 1 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 22 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 5.268 1.317 399.9 68: (ns/day) (hour/ns) 68: Performance: 1.443 16.632 68: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Last energy frame read 1 time 0.020 [ OK ] PositionRestraintCommTest.PositionRestraintsTwoCOMs (2988 ms) 68: [----------] 1 test from PositionRestraintCommTest (2988 ms total) 68: 68: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest 68: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 68: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 68: < 0 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 2 [file ala.top, line 256]: 68: For energy conservation with LINCS, lincs_iter should be 2 or larger. 68: 68: 68: Number of degrees of freedom in T-Coupling group rest is 54.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 68: The optimal PME mesh load for parallel simulations is below 0.5 68: and for highly parallel simulations between 0.25 and 0.33, 68: for higher performance, increase the cut-off and the PME grid spacing. 68: 68: 68: 68: There were 3 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'UNNAMED in water' 68: 4 steps, 0.0 ps. 68: Setting the LD random seed to -570425353 68: 68: Generated 2211 of the 2211 non-bonded parameter combinations 68: 68: Generated 2211 of the 2211 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 68: 68: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 68: Calculating fourier grid dimensions for X Y Z 68: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 68: 68: Estimate for the relative computational load of the PME mesh part: 0.94 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 8 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 1.631 0.408 399.8 68: (ns/day) (hour/ns) 68: Performance: 1.059 22.665 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 68: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 68: < 0 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 2 [file ala.top, line 256]: 68: For energy conservation with LINCS, lincs_iter should be 2 or larger. 68: 68: 68: Number of degrees of freedom in T-Coupling group rest is 54.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 68: The optimal PME mesh load for parallel simulations is below 0.5 68: and for highly parallel simulations between 0.25 and 0.33, 68: for higher performance, increase the cut-off and the PME grid spacing. 68: 68: 68: 68: There were 3 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'UNNAMED in water' 68: 4 steps, 0.0 ps. 68: Setting the LD random seed to -1141243963 68: 68: Generated 2211 of the 2211 non-bonded parameter combinations 68: 68: Generated 2211 of the 2211 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 68: 68: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 68: Calculating fourier grid dimensions for X Y Z 68: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 68: 68: Estimate for the relative computational load of the PME mesh part: 0.94 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 29 % of the run time was spent in domain decomposition, 68: 0 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: NOTE: 25 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.404 0.101 399.0 68: (ns/day) (hour/ns) 68: Performance: 4.272 5.618 68: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 trr version: GMX_trn_file (double precision) 68: 68: 68: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (1665 ms) 68: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 68: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 68: < 0 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 2 [file ala.top, line 256]: 68: For energy conservation with LINCS, lincs_iter should be 2 or larger. 68: 68: 68: Number of degrees of freedom in T-Coupling group rest is 54.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 68: The optimal PME mesh load for parallel simulations is below 0.5 68: and for highly parallel simulations between 0.25 and 0.33, 68: for higher performance, increase the cut-off and the PME grid spacing. 68: 68: 68: 68: There were 3 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'UNNAMED in water' 68: 4 steps, 0.0 ps. 68: Setting the LD random seed to -17310018 68: 68: Generated 2211 of the 2211 non-bonded parameter combinations 68: 68: Generated 2211 of the 2211 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 68: 68: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 68: Calculating fourier grid dimensions for X Y Z 68: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 68: 68: Estimate for the relative computational load of the PME mesh part: 0.94 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 67 % of the run time was spent in domain decomposition, 68: 0 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: NOTE: 7 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 1.136 0.284 399.7 68: (ns/day) (hour/ns) 68: Performance: 1.519 15.795 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 68: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 68: < 0 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 2 [file ala.top, line 256]: 68: For energy conservation with LINCS, lincs_iter should be 2 or larger. 68: 68: 68: Number of degrees of freedom in T-Coupling group rest is 54.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 68: The optimal PME mesh load for parallel simulations is below 0.5 68: and for highly parallel simulations between 0.25 and 0.33, 68: for higher performance, increase the cut-off and the PME grid spacing. 68: 68: 68: 68: There were 3 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 68: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 68: Can not increase nstlist because an NVE ensemble is used 68: 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'UNNAMED in water' 68: 4 steps, 0.0 ps. 68: Setting the LD random seed to 2142943186 68: 68: Generated 2211 of the 2211 non-bonded parameter combinations 68: 68: Generated 2211 of the 2211 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 68: 68: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 68: Calculating fourier grid dimensions for X Y Z 68: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 68: 68: Estimate for the relative computational load of the PME mesh part: 0.94 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 11 % of the run time was spent in domain decomposition, 68: 5 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 7.245 1.812 399.9 68: (ns/day) (hour/ns) 68: Performance: 0.238 100.648 68: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 68: 68: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (3396 ms) 68: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (5061 ms total) 68: 68: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest 68: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 68: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 68: < 0 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Pull group 1 'FirstWaterMolecule' has 3 atoms 68: Pull group 2 'SecondWaterMolecule' has 3 atoms 68: Number of degrees of freedom in T-Coupling group rest is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 3 2 68: 2 3 5 1.112 nm 1.000 nm 68: 68: There was 1 NOTE 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 4 steps, 0.0 ps. 68: Setting the LD random seed to -10555937 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 11 % of the run time was spent in domain decomposition, 68: 0 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: NOTE: 44 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.428 0.107 399.3 68: (ns/day) (hour/ns) 68: Performance: 4.033 5.952 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 68: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 68: < 0 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Pull group 1 'FirstWaterMolecule' has 3 atoms 68: Pull group 2 'SecondWaterMolecule' has 3 atoms 68: Number of degrees of freedom in T-Coupling group rest is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 3 2 68: 2 3 5 1.112 nm 1.000 nm 68: 68: There was 1 NOTE 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 68: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 68: Can not increase nstlist because an NVE ensemble is used 68: 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 4 steps, 0.0 ps. 68: Setting the LD random seed to 2144860861 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 32 % of the run time was spent in domain decomposition, 68: 0 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: NOTE: 23 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.853 0.217 393.9 68: (ns/day) (hour/ns) 68: Performance: 1.995 12.032 68: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 68: 68: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (1194 ms) 68: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (1194 ms total) 68: 68: [----------] 12 tests from FreezeWorks/FreezeGroupTest 68: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 68: There are 5 atoms that are fully frozen and part of COMM removal 68: group(s), removing these atoms from the COMM removal group(s) 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 68: There are 3 atoms that are frozen along less then 3 dimensions and part 68: of COMM removal group(s), due to limitations in the code these still 68: contribute to the mass of the COM along frozen dimensions and therefore 68: the COMM correction will be too small. 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 246.451 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: 68: There was 1 WARNING 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 8 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: 68: Dynamic load balancing report: 68: DLB was off during the run due to low measured imbalance. 68: Average load imbalance: 19.2%. 68: The balanceable part of the MD step is 1%, load imbalance is computed from this. 68: Part of the total run time spent waiting due to load imbalance: 0.3%. 68: 68: 68: NOTE: 15 % of the run time was spent in domain decomposition, 68: 0 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: NOTE: 42 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.497 0.140 354.6 68: (ns/day) (hour/ns) 68: Performance: 5.552 4.323 68: 68: 68: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (358 ms) 68: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 68: There are 5 atoms that are fully frozen and part of COMM removal 68: group(s), removing these atoms from the COMM removal group(s) 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 68: There are 3 atoms that are frozen along less then 3 dimensions and part 68: of COMM removal group(s), due to limitations in the code these still 68: contribute to the mass of the COM along frozen dimensions and therefore 68: the COMM correction will be too small. 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 246.451 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: 68: There was 1 WARNING 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 8 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: 68: Dynamic load balancing report: 68: DLB was off during the run due to low measured imbalance. 68: Average load imbalance: 20.3%. 68: The balanceable part of the MD step is 6%, load imbalance is computed from this. 68: Part of the total run time spent waiting due to load imbalance: 1.2%. 68: 68: 68: NOTE: 46 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.365 0.092 398.1 68: (ns/day) (hour/ns) 68: Performance: 8.472 2.833 68: 68: 68: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (182 ms) 68: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 68: There are 5 atoms that are fully frozen and part of COMM removal 68: group(s), removing these atoms from the COMM removal group(s) 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 68: There are 3 atoms that are frozen along less then 3 dimensions and part 68: of COMM removal group(s), due to limitations in the code these still 68: contribute to the mass of the COM along frozen dimensions and therefore 68: the COMM correction will be too small. 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 68: NVE simulation: will use the initial temperature of 246.451 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: 68: There was 1 WARNING 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 8 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: 68: Dynamic load balancing report: 68: DLB was off during the run due to low measured imbalance. 68: Average load imbalance: 14.3%. 68: The balanceable part of the MD step is 4%, load imbalance is computed from this. 68: Part of the total run time spent waiting due to load imbalance: 0.6%. 68: 68: 68: NOTE: 53 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.299 0.078 384.1 68: (ns/day) (hour/ns) 68: Performance: 9.985 2.404 68: 68: 68: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (150 ms) 68: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 68: There are 5 atoms that are fully frozen and part of COMM removal 68: group(s), removing these atoms from the COMM removal group(s) 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 68: There are 3 atoms that are frozen along less then 3 dimensions and part 68: of COMM removal group(s), due to limitations in the code these still 68: contribute to the mass of the COM along frozen dimensions and therefore 68: the COMM correction will be too small. 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 68: NVE simulation: will use the initial temperature of 246.451 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: 68: There was 1 WARNING 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 8 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: 68: Dynamic load balancing report: 68: DLB was off during the run due to low measured imbalance. 68: Average load imbalance: 7.2%. 68: The balanceable part of the MD step is 52%, load imbalance is computed from this. 68: Part of the total run time spent waiting due to load imbalance: 3.8%. 68: 68: 68: NOTE: 42 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.127 0.032 397.3 68: (ns/day) (hour/ns) 68: Performance: 24.281 0.988 68: 68: 68: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 (111 ms) 68: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 68: There are 5 atoms that are fully frozen and part of COMM removal 68: group(s), removing these atoms from the COMM removal group(s) 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 68: There are 3 atoms that are frozen along less then 3 dimensions and part 68: of COMM removal group(s), due to limitations in the code these still 68: contribute to the mass of the COM along frozen dimensions and therefore 68: the COMM correction will be too small. 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 68: NVE simulation: will use the initial temperature of 246.451 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: 68: There was 1 WARNING 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 8 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: 68: Dynamic load balancing report: 68: DLB was off during the run due to low measured imbalance. 68: Average load imbalance: 0.1%. 68: The balanceable part of the MD step is 40%, load imbalance is computed from this. 68: Part of the total run time spent waiting due to load imbalance: 0.0%. 68: 68: 68: NOTE: 37 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.317 0.084 376.5 68: (ns/day) (hour/ns) 68: Performance: 9.248 2.595 68: 68: 68: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (157 ms) 68: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 68: ./src/programs/mdrun/tests/freezegroups.cpp:209: Skipped 68: Parrinello-Rahman is not implemented in md-vv. 68: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (0 ms) 68: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 68: There are 5 atoms that are fully frozen and part of COMM removal 68: group(s), removing these atoms from the COMM removal group(s) 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 68: There are 3 atoms that are frozen along less then 3 dimensions and part 68: of COMM removal group(s), due to limitations in the code these still 68: contribute to the mass of the COM along frozen dimensions and therefore 68: the COMM correction will be too small. 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: There was 1 WARNING 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 68: Changing nstlist from 8 to 20, rlist from 0.756 to 0.861 68: 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 8 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 33 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.293 0.078 374.8 68: (ns/day) (hour/ns) 68: Performance: 9.936 2.416 68: 68: 68: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (191 ms) 68: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 68: There are 5 atoms that are fully frozen and part of COMM removal 68: group(s), removing these atoms from the COMM removal group(s) 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 68: There are 3 atoms that are frozen along less then 3 dimensions and part 68: of COMM removal group(s), due to limitations in the code these still 68: contribute to the mass of the COM along frozen dimensions and therefore 68: the COMM correction will be too small. 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: There was 1 WARNING 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 68: Changing nstlist from 8 to 20, rlist from 0.756 to 0.861 68: 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 8 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 45 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.221 0.075 294.3 68: (ns/day) (hour/ns) 68: Performance: 10.351 2.319 68: 68: 68: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (241 ms) 68: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 68: There are 5 atoms that are fully frozen and part of COMM removal 68: group(s), removing these atoms from the COMM removal group(s) 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 68: There are 3 atoms that are frozen along less then 3 dimensions and part 68: of COMM removal group(s), due to limitations in the code these still 68: contribute to the mass of the COM along frozen dimensions and therefore 68: the COMM correction will be too small. 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: There was 1 WARNING 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 68: Changing nstlist from 8 to 20, rlist from 0.756 to 0.861 68: 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 8 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 62 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.222 0.059 374.6 68: (ns/day) (hour/ns) 68: Performance: 13.126 1.829 68: 68: 68: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 (183 ms) 68: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 68: There are 5 atoms that are fully frozen and part of COMM removal 68: group(s), removing these atoms from the COMM removal group(s) 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 68: There are 3 atoms that are frozen along less then 3 dimensions and part 68: of COMM removal group(s), due to limitations in the code these still 68: contribute to the mass of the COM along frozen dimensions and therefore 68: the COMM correction will be too small. 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: There was 1 WARNING 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 68: Changing nstlist from 8 to 100, rlist from 0.735 to 0.832 68: 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 8 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 63 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.261 0.087 299.7 68: (ns/day) (hour/ns) 68: Performance: 8.935 2.686 68: 68: 68: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 (367 ms) 68: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 68: There are 5 atoms that are fully frozen and part of COMM removal 68: group(s), removing these atoms from the COMM removal group(s) 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 68: There are 3 atoms that are frozen along less then 3 dimensions and part 68: of COMM removal group(s), due to limitations in the code these still 68: contribute to the mass of the COM along frozen dimensions and therefore 68: the COMM correction will be too small. 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: There was 1 WARNING 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 68: Changing nstlist from 8 to 100, rlist from 0.735 to 0.832 68: 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 8 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 43 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.239 0.068 348.6 68: (ns/day) (hour/ns) 68: Performance: 11.356 2.113 68: 68: 68: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 (271 ms) 68: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 68: There are 5 atoms that are fully frozen and part of COMM removal 68: group(s), removing these atoms from the COMM removal group(s) 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 68: There are 3 atoms that are frozen along less then 3 dimensions and part 68: of COMM removal group(s), due to limitations in the code these still 68: contribute to the mass of the COM along frozen dimensions and therefore 68: the COMM correction will be too small. 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: There was 1 WARNING 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 68: Changing nstlist from 8 to 100, rlist from 0.735 to 0.832 68: 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 8 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 44 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.193 0.059 325.5 68: (ns/day) (hour/ns) 68: Performance: 13.098 1.832 68: 68: 68: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 (359 ms) 68: [----------] 12 tests from FreezeWorks/FreezeGroupTest (2576 ms total) 68: 68: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest 68: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 68: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 68: < 0 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 68: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: Net Acceleration in X direction, will not be corrected 68: Net Acceleration in Y direction, will not be corrected 68: Net Acceleration in Z direction, will not be corrected 68: 68: There were 3 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Setting gen_seed to -1363150214 68: 68: Velocities were taken from a Maxwell distribution at 0 K 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: 68: Dynamic load balancing report: 68: DLB was off during the run due to low measured imbalance. 68: Average load imbalance: 0.4%. 68: The balanceable part of the MD step is 32%, load imbalance is computed from this. 68: Part of the total run time spent waiting due to load imbalance: 0.1%. 68: 68: 68: NOTE: 49 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.178 0.045 398.9 68: (ns/day) (hour/ns) 68: Performance: 34.860 0.688 68: 68: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (132 ms) 68: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 68: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 68: < 0 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 68: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 68: Net Acceleration in X direction, will not be corrected 68: Net Acceleration in Y direction, will not be corrected 68: Net Acceleration in Z direction, will not be corrected 68: 68: There were 3 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 68: Can not increase nstlist because verlet-buffer-tolerance is not set or used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Setting gen_seed to -193466370 68: 68: Velocities were taken from a Maxwell distribution at 0 K 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: 68: Dynamic load balancing report: 68: DLB was off during the run due to low measured imbalance. 68: Average load imbalance: 32.4%. 68: The balanceable part of the MD step is 19%, load imbalance is computed from this. 68: Part of the total run time spent waiting due to load imbalance: 6.3%. 68: 68: NOTE: 6.3 % of the available CPU time was lost due to load imbalance 68: in the domain decomposition. 68: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 68: You can also consider manually changing the decomposition (option -dd); 68: e.g. by using fewer domains along the box dimension in which there is 68: considerable inhomogeneity in the simulated system. 68: 68: NOTE: 25 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.435 0.109 399.2 68: (ns/day) (hour/ns) 68: Performance: 14.280 1.681 68: 68: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (184 ms) 68: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 68: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 68: < 0 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 68: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: Net Acceleration in X direction, will not be corrected 68: Net Acceleration in Y direction, will not be corrected 68: Net Acceleration in Z direction, will not be corrected 68: 68: There were 3 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Setting gen_seed to -1121976361 68: 68: Velocities were taken from a Maxwell distribution at 0 K 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: 68: Dynamic load balancing report: 68: DLB was off during the run due to low measured imbalance. 68: Average load imbalance: 0.1%. 68: The balanceable part of the MD step is 47%, load imbalance is computed from this. 68: Part of the total run time spent waiting due to load imbalance: 0.1%. 68: 68: 68: NOTE: 37 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.266 0.070 376.7 68: (ns/day) (hour/ns) 68: Performance: 22.063 1.088 68: 68: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 (159 ms) 68: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 68: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 68: < 0 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 68: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 68: Net Acceleration in X direction, will not be corrected 68: Net Acceleration in Y direction, will not be corrected 68: Net Acceleration in Z direction, will not be corrected 68: 68: There were 3 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 68: Can not increase nstlist because verlet-buffer-tolerance is not set or used 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Setting gen_seed to 1610568639 68: 68: Velocities were taken from a Maxwell distribution at 0 K 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: 68: Dynamic load balancing report: 68: DLB was off during the run due to low measured imbalance. 68: Average load imbalance: 5.4%. 68: The balanceable part of the MD step is 44%, load imbalance is computed from this. 68: Part of the total run time spent waiting due to load imbalance: 2.4%. 68: 68: 68: NOTE: 28 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.631 0.162 390.0 68: (ns/day) (hour/ns) 68: Performance: 9.616 2.496 68: 68: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (239 ms) 68: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (716 ms total) 68: 68: [----------] Global test environment tear-down 68: [==========] 29 tests from 8 test suites ran. (20217 ms total) 68: [ PASSED ] 28 tests. 68: [ SKIPPED ] 1 test, listed below: 68: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 68/90 Test #68: MdrunTestsTwoRanks ........................ Passed 20.29 sec test 69 Start 69: MdrunSingleRankAlgorithmsTests 69: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/mdrun-single-rank-algorithms-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/MdrunSingleRankAlgorithmsTests.xml" 69: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests 69: Test timeout computed to be: 600 69: [==========] Running 5 tests from 3 test suites. 69: [----------] Global test environment set-up. 69: [----------] 1 test from DispersionCorrectionTest 69: [ RUN ] DispersionCorrectionTest.DispersionCorrectionCanRun 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 30.00 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]: 69: There are 9 non-linear virtual site constructions. Their contribution to 69: the energy error is approximated. In most cases this does not affect the 69: error significantly. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 2 NOTEs 69: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 69: Changing nstlist from 10 to 40, rlist from 1.027 to 1.175 69: 69: Update groups can not be used for this system because an incompatible virtual site type is used 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine dipeptide in vacuo' 69: 200 steps, 0.4 ps. 69: Setting the LD random seed to -308396674 69: 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 69: 69: Cleaning up constraints and constant bonded interactions with virtual sites 69: 69: Converted 3 Bonds with virtual sites to connections, 7 left 69: 69: Removed 18 Angles with virtual sites, 21 left 69: 69: Removed 10 Proper Dih.s with virtual sites, 44 left 69: 69: Converted 12 Constraints with virtual sites to connections, 0 left 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 69: 69: Calculated rlist for 1x1 atom pair-list as 1.038 nm, buffer size 0.038 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 1.023 nm, buffer size 0.023 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.092 0.046 199.5 69: (ns/day) (hour/ns) 69: Performance: 751.075 0.032 69: [ OK ] DispersionCorrectionTest.DispersionCorrectionCanRun (119 ms) 69: [----------] 1 test from DispersionCorrectionTest (119 ms total) 69: 69: [----------] 1 test from OriresTest 69: [ RUN ] OriresTest.OriresCanRun 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 518.00 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There was 1 NOTE 69: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 69: Orientation restraints only supports a single rank. Choosing to use only a single thread-MPI rank. 69: Changing nstlist from 10 to 25, rlist from 1.076 to 1.219 69: 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-1' 69: 10 steps, 0.0 ps. 69: Setting the LD random seed to 1590165493 69: 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/orires_1lvz.gro' 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 69: 69: Calculated rlist for 1x1 atom pair-list as 1.093 nm, buffer size 0.093 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 1.070 nm, buffer size 0.070 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.750 0.383 196.0 69: (ns/day) (hour/ns) 69: Performance: 4.964 4.835 69: [ OK ] OriresTest.OriresCanRun (1313 ms) 69: [----------] 1 test from OriresTest (1313 ms total) 69: 69: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest 69: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 69: Number of degrees of freedom in T-Coupling group rest is 10.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]: 69: NVE simulation with an initial temperature of zero: will use a Verlet 69: buffer of 10%. Check your energy drift! 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]: 69: The optimal PME mesh load for parallel simulations is below 0.5 69: and for highly parallel simulations between 0.25 and 0.33, 69: for higher performance, increase the cut-off and the PME grid spacing. 69: 69: 69: 69: There were 2 NOTEs 69: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Dipoles' 69: 20 steps, 0.1 ps. 69: Setting the LD random seed to 1742007007 69: 69: Generated 1 of the 1 non-bonded parameter combinations 69: 69: Excluding 1 bonded neighbours molecule type 'Dipole' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/dipoles.gro', all velocities are zero 69: 69: Searching the wall atom type(s) 69: 69: The largest distance between excluded atoms is 0.344 nm between atom 1 and 2 69: Calculating fourier grid dimensions for X Y Z 69: Using a fourier grid of 20x20x40, spacing 0.200 0.200 0.200 69: 69: Estimate for the relative computational load of the PME mesh part: 1.00 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.194 0.097 199.6 69: (ns/day) (hour/ns) 69: Performance: 46.619 0.515 69: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Last energy frame read 5 time 0.050 trr version: GMX_trn_file (double precision) 69: 69: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 (1087 ms) 69: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 69: Test system 'epsilon-surface-constraint' cannot run with 1 ranks. 69: The supported numbers are > 1. 69: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 (0 ms) 69: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 69: With epsilon_surface > 0 all molecules should be neutral. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 69: With epsilon_surface > 0 you can only use domain decomposition when there 69: are only small molecules with all bonds constrained (mdrun will check for 69: this). 69: 69: Number of degrees of freedom in T-Coupling group rest is 9.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 69: NVE simulation with an initial temperature of zero: will use a Verlet 69: buffer of 10%. Check your energy drift! 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 69: The optimal PME mesh load for parallel simulations is below 0.5 69: and for highly parallel simulations between 0.25 and 0.33, 69: for higher performance, increase the cut-off and the PME grid spacing. 69: 69: 69: 69: There were 4 NOTEs 69: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Dipoles' 69: 20 steps, 0.1 ps. 69: Setting the LD random seed to -1375997990 69: 69: Generated 1 of the 1 non-bonded parameter combinations 69: 69: Excluding 1 bonded neighbours molecule type 'Dipole' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/dipoles.gro', all velocities are zero 69: 69: The largest distance between excluded atoms is 0.344 nm between atom 1 and 2 69: Calculating fourier grid dimensions for X Y Z 69: Using a fourier grid of 20x20x20, spacing 0.200 0.200 0.200 69: 69: Estimate for the relative computational load of the PME mesh part: 1.00 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.118 0.059 199.6 69: (ns/day) (hour/ns) 69: Performance: 76.619 0.313 69: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Last energy frame read 5 time 0.050 69: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 (478 ms) 69: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest (1566 ms total) 69: 69: [----------] Global test environment tear-down 69: [==========] 5 tests from 3 test suites ran. (3582 ms total) 69: [ PASSED ] 5 tests. 69/90 Test #69: MdrunSingleRankAlgorithmsTests ............ Passed 3.63 sec test 70 Start 70: Minimize1RankTests 70: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/minimize-test "-ntomp" "2" "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/Minimize1RankTests.xml" 70: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests 70: Test timeout computed to be: 600 70: [==========] Running 12 tests from 2 test suites. 70: [----------] Global test environment set-up. 70: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 70: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group System is 27.00 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 4 NOTEs 70: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 70: Using 1 MPI thread 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Steepest Descents: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: 70: Energy minimization reached the maximum number of steps before the forces 70: reached the requested precision Fmax < 10. 70: 70: writing lowest energy coordinates. 70: 70: Steepest Descents did not converge to Fmax < 10 in 5 steps. 70: Potential Energy = -4.79910463671056e+01 70: Maximum force = 1.86297359432216e+02 on atom 13 70: Norm of force = 8.77219865482116e+01 70: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 70: 70: Generated 330891 of the 330891 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (1407 ms) 70: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group System is 27.00 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 4 NOTEs 70: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 70: Using 1 MPI thread 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Polak-Ribiere Conjugate Gradients: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: F-max = 3.02331e+02 on atom 3 70: F-Norm = 1.18024e+02 70: 70: 70: Energy minimization reached the maximum number of steps before the forces 70: reached the requested precision Fmax < 10. 70: 70: writing lowest energy coordinates. 70: 70: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 70: Potential Energy = -5.58622538633291e+01 70: Maximum force = 4.27274822366516e+02 on atom 13 70: Norm of force = 1.84530029253834e+02 70: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 70: 70: Generated 330891 of the 330891 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (1835 ms) 70: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: Generating 1-4 interactions: fudge = 1 70: Number of degrees of freedom in T-Coupling group System is 22.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 4 NOTEs 70: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 70: Using 1 MPI thread 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Steepest Descents: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: 70: Energy minimization reached the maximum number of steps before the forces 70: reached the requested precision Fmax < 10. 70: 70: writing lowest energy coordinates. 70: 70: Steepest Descents did not converge to Fmax < 10 in 5 steps. 70: Potential Energy = 3.19376899751522e+02 70: Maximum force = 9.99884921009767e+03 on atom 9 70: Norm of force = 4.61669565054298e+03 70: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 70: 70: Generated 17396 of the 20503 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Glycine' 70: 70: turning H bonds into constraints... 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (175 ms) 70: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: Generating 1-4 interactions: fudge = 1 70: 70: NOTE 3 [file glycine_vacuo.top, line 12]: 70: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 70: 70: Number of degrees of freedom in T-Coupling group System is 22.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 5 NOTEs 70: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 70: Using 1 MPI thread 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Polak-Ribiere Conjugate Gradients: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: F-max = 2.41575e+04 on atom 10 70: F-Norm = 1.18451e+04 70: 70: 70: Energy minimization reached the maximum number of steps before the forces 70: reached the requested precision Fmax < 10. 70: 70: writing lowest energy coordinates. 70: 70: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 70: Potential Energy = 1.51743018140927e+02 70: Maximum force = 7.42089573409110e+03 on atom 9 70: Norm of force = 3.56929298615738e+03 70: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 70: 70: Generated 17396 of the 20503 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Glycine' 70: 70: turning H bonds into constraints... 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (243 ms) 70: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file unknown]: 70: You are using constraints on all bonds, whereas the forcefield has been 70: parametrized only with constraints involving hydrogen atoms. We suggest 70: using constraints = h-bonds instead, this will also improve performance. 70: 70: Number of degrees of freedom in T-Coupling group System is 23.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 5 NOTEs 70: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 70: Update groups can not be used for this system because an incompatible virtual site type is used 70: 70: Using 1 MPI thread 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Steepest Descents: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: 70: Energy minimization reached the maximum number of steps before the forces 70: reached the requested precision Fmax < 10. 70: 70: writing lowest energy coordinates. 70: 70: Steepest Descents did not converge to Fmax < 10 in 5 steps. 70: Potential Energy = -1.56984193848274e+02 70: Maximum force = 4.56923624626478e+02 on atom 17 70: Norm of force = 1.83258377168370e+02 70: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 70: 70: turning all bonds into constraints... 70: 70: Cleaning up constraints and constant bonded interactions with virtual sites 70: 70: Removed 18 Angles with virtual sites, 21 left 70: 70: Removed 10 Proper Dih.s with virtual sites, 44 left 70: 70: Converted 15 Constraints with virtual sites to connections, 7 left 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (97 ms) 70: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file unknown]: 70: You are using constraints on all bonds, whereas the forcefield has been 70: parametrized only with constraints involving hydrogen atoms. We suggest 70: using constraints = h-bonds instead, this will also improve performance. 70: 70: 70: NOTE 4 [file unknown]: 70: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 70: 70: Number of degrees of freedom in T-Coupling group System is 23.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 6 NOTEs 70: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 70: Update groups can not be used for this system because an incompatible virtual site type is used 70: 70: Using 1 MPI thread 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Polak-Ribiere Conjugate Gradients: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: F-max = 1.06800e+03 on atom 28 70: F-Norm = 4.26922e+02 70: 70: 70: Energy minimization reached the maximum number of steps before the forces 70: reached the requested precision Fmax < 10. 70: 70: writing lowest energy coordinates. 70: 70: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 70: Potential Energy = -1.69410778678185e+02 70: Maximum force = 2.18225948474112e+02 on atom 17 70: Norm of force = 7.92068036537837e+01 70: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 70: 70: turning all bonds into constraints... 70: 70: Cleaning up constraints and constant bonded interactions with virtual sites 70: 70: Removed 18 Angles with virtual sites, 21 left 70: 70: Removed 10 Proper Dih.s with virtual sites, 44 left 70: 70: Converted 15 Constraints with virtual sites to connections, 7 left 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (97 ms) 70: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (3857 ms total) 70: 70: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 70: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 3 NOTEs 70: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 70: Using 1 MPI thread 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Steepest Descents: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: 70: writing lowest energy coordinates. 70: 70: Steepest Descents converged to Fmax < 10 in 1 steps 70: Potential Energy = -9.74257075835447e-01 70: Maximum force = 4.01322929015133e+00 on atom 1 70: Norm of force = 1.63839399694378e+00 70: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file 70: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (19 ms) 70: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 3 NOTEs 70: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 70: Using 1 MPI thread 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Polak-Ribiere Conjugate Gradients: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: F-max = 4.01323e+00 on atom 1 70: F-Norm = 1.63839e+00 70: 70: 70: writing lowest energy coordinates. 70: 70: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 70: Potential Energy = -9.90642313893969e-01 70: Maximum force = 2.57812909490791e+00 on atom 1 70: Norm of force = 1.05251679559130e+00 70: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (28 ms) 70: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 70: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 3 NOTEs 70: 70: There was 1 WARNING 70: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 70: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. 70: 70: Using 1 MPI thread 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Low-Memory BFGS Minimizer: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: Using 10 BFGS correction steps. 70: 70: F-max = 4.01323e+00 on atom 1 70: F-Norm = 1.63839e+00 70: 70: 70: writing lowest energy coordinates. 70: 70: Low-Memory BFGS Minimizer converged to Fmax < 10 in -1 steps 70: Potential Energy = -9.90642313893969e-01 70: Maximum force = 2.57812909490791e+00 on atom 1 70: Norm of force = 1.05251679559130e+00 70: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (16 ms) 70: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: Generating 1-4 interactions: fudge = 1 70: Number of degrees of freedom in T-Coupling group System is 27.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 4 NOTEs 70: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 70: Using 1 MPI thread 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Steepest Descents: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: 70: Energy minimization reached the maximum number of steps before the forces 70: reached the requested precision Fmax < 10. 70: 70: writing lowest energy coordinates. 70: 70: Steepest Descents did not converge to Fmax < 10 in 5 steps. 70: Potential Energy = 3.19395484891518e+02 70: Maximum force = 9.97041707197910e+03 on atom 9 70: Norm of force = 4.62274878665467e+03 70: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 70: 70: Generated 17396 of the 20503 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Glycine' 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (220 ms) 70: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: Generating 1-4 interactions: fudge = 1 70: Number of degrees of freedom in T-Coupling group System is 27.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 4 NOTEs 70: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 70: Using 1 MPI thread 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Polak-Ribiere Conjugate Gradients: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: F-max = 2.41672e+04 on atom 10 70: F-Norm = 1.19357e+04 70: 70: 70: Energy minimization reached the maximum number of steps before the forces 70: reached the requested precision Fmax < 10. 70: 70: writing lowest energy coordinates. 70: 70: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 70: Potential Energy = 1.56258793899480e+02 70: Maximum force = 7.50181017480396e+03 on atom 9 70: Norm of force = 3.61390332564874e+03 70: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 70: 70: Generated 17396 of the 20503 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Glycine' 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (315 ms) 70: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 70: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 70: 70: Generating 1-4 interactions: fudge = 1 70: Number of degrees of freedom in T-Coupling group System is 27.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 4 NOTEs 70: 70: There was 1 WARNING 70: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 70: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. 70: 70: Using 1 MPI thread 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Low-Memory BFGS Minimizer: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: Using 10 BFGS correction steps. 70: 70: F-max = 2.41672e+04 on atom 10 70: F-Norm = 1.19357e+04 70: 70: 70: Energy minimization has stopped, but the forces have not converged to the 70: requested precision Fmax < 10 (which may not be possible for your system). It 70: stopped because the algorithm tried to make a new step whose size was too 70: small, or there was no change in the energy since last step. Either way, we 70: regard the minimization as converged to within the available machine 70: precision, given your starting configuration and EM parameters. 70: 70: writing lowest energy coordinates. 70: 70: Low-Memory BFGS Minimizer converged to machine precision in 0 steps, 70: but did not reach the requested Fmax < 10. 70: Potential Energy = 5.61116097794204e+02 70: Maximum force = 1.26854826291223e+04 on atom 10 70: Norm of force = 6.06436286976271e+03 70: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 70: 70: Generated 17396 of the 20503 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Glycine' 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (216 ms) 70: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (816 ms total) 70: 70: [----------] Global test environment tear-down 70: [==========] 12 tests from 2 test suites ran. (5002 ms total) 70: [ PASSED ] 12 tests. 70/90 Test #70: Minimize1RankTests ........................ Passed 5.07 sec test 71 Start 71: Minimize2RankTests 71: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/minimize-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/Minimize2RankTests.xml" 71: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests 71: Test timeout computed to be: 600 71: [==========] Running 12 tests from 2 test suites. 71: [----------] Global test environment set-up. 71: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 71: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 71: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 71: setting nstcomm equal to nstcalcenergy for less overhead 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 27.00 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 71: COM removal frequency is set to (4). 71: Other settings require a global communication frequency of 100. 71: Note that this will require additional global communication steps, 71: which will reduce performance when using multiple ranks. 71: Consider setting nstcomm to a multiple of 100. 71: 71: 71: There were 4 NOTEs 71: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: 71: Steepest Descents: 71: Tolerance (Fmax) = 1.00000e+01 71: Number of steps = 4 71: 71: Energy minimization reached the maximum number of steps before the forces 71: reached the requested precision Fmax < 10. 71: 71: writing lowest energy coordinates. 71: 71: Steepest Descents did not converge to Fmax < 10 in 5 steps. 71: Potential Energy = -4.79910463671057e+01 71: Maximum force = 1.86297359432216e+02 on atom 13 71: Norm of force = 8.77219865482118e+01 71: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 71: 71: Generated 330891 of the 330891 1-4 parameter combinations 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (1145 ms) 71: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 71: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 71: setting nstcomm equal to nstcalcenergy for less overhead 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 27.00 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 71: COM removal frequency is set to (4). 71: Other settings require a global communication frequency of 100. 71: Note that this will require additional global communication steps, 71: which will reduce performance when using multiple ranks. 71: Consider setting nstcomm to a multiple of 100. 71: 71: 71: There were 4 NOTEs 71: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: 71: Polak-Ribiere Conjugate Gradients: 71: Tolerance (Fmax) = 1.00000e+01 71: Number of steps = 4 71: F-max = 3.02331e+02 on atom 3 71: F-Norm = 1.18024e+02 71: 71: 71: Energy minimization reached the maximum number of steps before the forces 71: reached the requested precision Fmax < 10. 71: 71: writing lowest energy coordinates. 71: 71: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 71: Potential Energy = -5.58622538633291e+01 71: Maximum force = 4.27274822366504e+02 on atom 13 71: Norm of force = 1.84530029253830e+02 71: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 71: 71: Generated 330891 of the 330891 1-4 parameter combinations 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (1185 ms) 71: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 71: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 71: setting nstcomm equal to nstcalcenergy for less overhead 71: 71: Generating 1-4 interactions: fudge = 1 71: Number of degrees of freedom in T-Coupling group System is 22.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 71: COM removal frequency is set to (4). 71: Other settings require a global communication frequency of 100. 71: Note that this will require additional global communication steps, 71: which will reduce performance when using multiple ranks. 71: Consider setting nstcomm to a multiple of 100. 71: 71: 71: There were 4 NOTEs 71: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: 71: Steepest Descents: 71: Tolerance (Fmax) = 1.00000e+01 71: Number of steps = 4 71: 71: Energy minimization reached the maximum number of steps before the forces 71: reached the requested precision Fmax < 10. 71: 71: writing lowest energy coordinates. 71: 71: Steepest Descents did not converge to Fmax < 10 in 5 steps. 71: Potential Energy = 3.19376899751522e+02 71: Maximum force = 9.99884921009767e+03 on atom 9 71: Norm of force = 4.61669565054298e+03 71: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 71: 71: Generated 17396 of the 20503 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Glycine' 71: 71: turning H bonds into constraints... 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (329 ms) 71: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 71: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 71: setting nstcomm equal to nstcalcenergy for less overhead 71: 71: Generating 1-4 interactions: fudge = 1 71: 71: NOTE 3 [file glycine_vacuo.top, line 12]: 71: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 71: 71: Number of degrees of freedom in T-Coupling group System is 22.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 71: COM removal frequency is set to (4). 71: Other settings require a global communication frequency of 100. 71: Note that this will require additional global communication steps, 71: which will reduce performance when using multiple ranks. 71: Consider setting nstcomm to a multiple of 100. 71: 71: 71: There were 5 NOTEs 71: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: 71: Polak-Ribiere Conjugate Gradients: 71: Tolerance (Fmax) = 1.00000e+01 71: Number of steps = 4 71: F-max = 2.41575e+04 on atom 10 71: F-Norm = 1.18451e+04 71: 71: 71: Energy minimization reached the maximum number of steps before the forces 71: reached the requested precision Fmax < 10. 71: 71: writing lowest energy coordinates. 71: 71: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 71: Potential Energy = 1.51743018140927e+02 71: Maximum force = 7.42089573409110e+03 on atom 9 71: Norm of force = 3.56929298615739e+03 71: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 71: 71: Generated 17396 of the 20503 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Glycine' 71: 71: turning H bonds into constraints... 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (372 ms) 71: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 71: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 71: setting nstcomm equal to nstcalcenergy for less overhead 71: 71: Generating 1-4 interactions: fudge = 0.5 71: 71: NOTE 3 [file unknown]: 71: You are using constraints on all bonds, whereas the forcefield has been 71: parametrized only with constraints involving hydrogen atoms. We suggest 71: using constraints = h-bonds instead, this will also improve performance. 71: 71: Number of degrees of freedom in T-Coupling group System is 23.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 71: COM removal frequency is set to (4). 71: Other settings require a global communication frequency of 100. 71: Note that this will require additional global communication steps, 71: which will reduce performance when using multiple ranks. 71: Consider setting nstcomm to a multiple of 100. 71: 71: 71: There were 5 NOTEs 71: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 71: Update groups can not be used for this system because an incompatible virtual site type is used 71: 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: 71: Steepest Descents: 71: Tolerance (Fmax) = 1.00000e+01 71: Number of steps = 4 71: 71: Energy minimization reached the maximum number of steps before the forces 71: reached the requested precision Fmax < 10. 71: 71: writing lowest energy coordinates. 71: 71: Steepest Descents did not converge to Fmax < 10 in 5 steps. 71: Potential Energy = -1.56984193848273e+02 71: Maximum force = 4.56923624626478e+02 on atom 17 71: Norm of force = 1.83258377168370e+02 71: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 Generated 2145 of the 2145 non-bonded parameter combinations 71: 71: Generated 2145 of the 2145 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 71: 71: turning all bonds into constraints... 71: 71: Cleaning up constraints and constant bonded interactions with virtual sites 71: 71: Removed 18 Angles with virtual sites, 21 left 71: 71: Removed 10 Proper Dih.s with virtual sites, 44 left 71: 71: Converted 15 Constraints with virtual sites to connections, 7 left 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (123 ms) 71: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 71: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 71: setting nstcomm equal to nstcalcenergy for less overhead 71: 71: Generating 1-4 interactions: fudge = 0.5 71: 71: NOTE 3 [file unknown]: 71: You are using constraints on all bonds, whereas the forcefield has been 71: parametrized only with constraints involving hydrogen atoms. We suggest 71: using constraints = h-bonds instead, this will also improve performance. 71: 71: 71: NOTE 4 [file unknown]: 71: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 71: 71: Number of degrees of freedom in T-Coupling group System is 23.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 71: COM removal frequency is set to (4). 71: Other settings require a global communication frequency of 100. 71: Note that this will require additional global communication steps, 71: which will reduce performance when using multiple ranks. 71: Consider setting nstcomm to a multiple of 100. 71: 71: 71: There were 6 NOTEs 71: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 71: Update groups can not be used for this system because an incompatible virtual site type is used 71: 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: 71: Polak-Ribiere Conjugate Gradients: 71: Tolerance (Fmax) = 1.00000e+01 71: Number of steps = 4 71: F-max = 1.06800e+03 on atom 28 71: F-Norm = 4.26922e+02 71: 71: 71: Energy minimization reached the maximum number of steps before the forces 71: reached the requested precision Fmax < 10. 71: 71: writing lowest energy coordinates. 71: 71: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 71: Potential Energy = -1.69410778678185e+02 71: Maximum force = 2.18225948474111e+02 on atom 17 71: Norm of force = 7.92068036537837e+01 71: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 2145 of the 2145 non-bonded parameter combinations 71: 71: Generated 2145 of the 2145 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 71: 71: turning all bonds into constraints... 71: 71: Cleaning up constraints and constant bonded interactions with virtual sites 71: 71: Removed 18 Angles with virtual sites, 21 left 71: 71: Removed 10 Proper Dih.s with virtual sites, 44 left 71: 71: Converted 15 Constraints with virtual sites to connections, 7 left 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (2085 ms) 71: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (5242 ms total) 71: 71: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 71: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 71: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 71: setting nstcomm equal to nstcalcenergy for less overhead 71: 71: Number of degrees of freedom in T-Coupling group System is 33.00 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 71: COM removal frequency is set to (4). 71: Other settings require a global communication frequency of 100. 71: Note that this will require additional global communication steps, 71: which will reduce performance when using multiple ranks. 71: Consider setting nstcomm to a multiple of 100. 71: 71: 71: There were 3 NOTEs 71: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: 71: Steepest Descents: 71: Tolerance (Fmax) = 1.00000e+01 71: Number of steps = 4 71: 71: writing lowest energy coordinates. 71: 71: Steepest Descents converged to Fmax < 10 in 1 steps 71: Potential Energy = -9.74257075835447e-01 71: Maximum force = 4.01322929015133e+00 on atom 3 71: Norm of force = 1.63839399694378e+00 71: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file 71: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 71: 71: Excluding 1 bonded neighbours molecule type 'Argon' 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (85 ms) 71: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 71: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 71: setting nstcomm equal to nstcalcenergy for less overhead 71: 71: Number of degrees of freedom in T-Coupling group System is 33.00 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 71: COM removal frequency is set to (4). 71: Other settings require a global communication frequency of 100. 71: Note that this will require additional global communication steps, 71: which will reduce performance when using multiple ranks. 71: Consider setting nstcomm to a multiple of 100. 71: 71: 71: There were 3 NOTEs 71: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: 71: Polak-Ribiere Conjugate Gradients: 71: Tolerance (Fmax) = 1.00000e+01 71: Number of steps = 4 71: F-max = 4.01323e+00 on atom 3 71: F-Norm = 1.63839e+00 71: 71: 71: writing lowest energy coordinates. 71: 71: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 71: Potential Energy = -9.90642313893969e-01 71: Maximum force = 2.57812909490791e+00 on atom 3 71: Norm of force = 1.05251679559130e+00 71: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 71: 71: Excluding 1 bonded neighbours molecule type 'Argon' 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (290 ms) 71: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 71: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 71: setting nstcomm equal to nstcalcenergy for less overhead 71: 71: 71: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 71: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 71: 71: Number of degrees of freedom in T-Coupling group System is 33.00 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 71: COM removal frequency is set to (4). 71: Other settings require a global communication frequency of 100. 71: Note that this will require additional global communication steps, 71: which will reduce performance when using multiple ranks. 71: Consider setting nstcomm to a multiple of 100. 71: 71: 71: There were 3 NOTEs 71: 71: There was 1 WARNING 71: Generated 1 of the 1 non-bonded parameter combinations 71: 71: Excluding 1 bonded neighbours molecule type 'Argon' 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (16 ms) 71: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 71: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 71: setting nstcomm equal to nstcalcenergy for less overhead 71: 71: Generating 1-4 interactions: fudge = 1 71: Number of degrees of freedom in T-Coupling group System is 27.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 71: COM removal frequency is set to (4). 71: Other settings require a global communication frequency of 100. 71: Note that this will require additional global communication steps, 71: which will reduce performance when using multiple ranks. 71: Consider setting nstcomm to a multiple of 100. 71: 71: 71: There were 4 NOTEs 71: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: 71: Steepest Descents: 71: Tolerance (Fmax) = 1.00000e+01 71: Number of steps = 4 71: 71: Energy minimization reached the maximum number of steps before the forces 71: reached the requested precision Fmax < 10. 71: 71: writing lowest energy coordinates. 71: 71: Steepest Descents did not converge to Fmax < 10 in 5 steps. 71: Potential Energy = 3.19395484891519e+02 71: Maximum force = 9.97041707197910e+03 on atom 9 71: Norm of force = 4.62274878665467e+03 71: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 71: 71: Generated 17396 of the 20503 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Glycine' 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (449 ms) 71: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 71: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 71: setting nstcomm equal to nstcalcenergy for less overhead 71: 71: Generating 1-4 interactions: fudge = 1 71: Number of degrees of freedom in T-Coupling group System is 27.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 71: COM removal frequency is set to (4). 71: Other settings require a global communication frequency of 100. 71: Note that this will require additional global communication steps, 71: which will reduce performance when using multiple ranks. 71: Consider setting nstcomm to a multiple of 100. 71: 71: 71: There were 4 NOTEs 71: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: 71: Polak-Ribiere Conjugate Gradients: 71: Tolerance (Fmax) = 1.00000e+01 71: Number of steps = 4 71: F-max = 2.41672e+04 on atom 10 71: F-Norm = 1.19357e+04 71: 71: 71: Energy minimization reached the maximum number of steps before the forces 71: reached the requested precision Fmax < 10. 71: 71: writing lowest energy coordinates. 71: 71: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 71: Potential Energy = 1.56258793899480e+02 71: Maximum force = 7.50181017480397e+03 on atom 9 71: Norm of force = 3.61390332564874e+03 71: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 71: 71: Generated 17396 of the 20503 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Glycine' 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (2627 ms) 71: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 71: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 71: setting nstcomm equal to nstcalcenergy for less overhead 71: 71: 71: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 71: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 71: 71: Generating 1-4 interactions: fudge = 1 71: Number of degrees of freedom in T-Coupling group System is 27.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 71: COM removal frequency is set to (4). 71: Other settings require a global communication frequency of 100. 71: Note that this will require additional global communication steps, 71: which will reduce performance when using multiple ranks. 71: Consider setting nstcomm to a multiple of 100. 71: 71: 71: There were 4 NOTEs 71: 71: There was 1 WARNING 71: Generated 20503 of the 20503 non-bonded parameter combinations 71: 71: Generated 17396 of the 20503 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Glycine' 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (302 ms) 71: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (3772 ms total) 71: 71: [----------] Global test environment tear-down 71: [==========] 12 tests from 2 test suites ran. (9409 ms total) 71: [ PASSED ] 12 tests. 71/90 Test #71: Minimize2RankTests ........................ Passed 9.49 sec test 72 Start 72: MdrunNonIntegratorTests 72: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/mdrun-non-integrator-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/MdrunNonIntegratorTests.xml" 72: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests 72: Test timeout computed to be: 600 72: [==========] Running 53 tests from 5 test suites. 72: [----------] Global test environment set-up. 72: [----------] 1 test from NonbondedBenchTest 72: [ RUN ] NonbondedBenchTest.BasicEndToEndTest 72: SIMD width: 2 72: System size: 3000 atoms 72: Cut-off radius: 1 nm 72: Number of threads: 1 72: Number of iterations: 1 72: Compute energies: no 72: Ewald excl. corr.: analytical 72: 72: Coulomb LJ comb. SIMD Mcycles Mcycles/it. pairs/cycle 72: total useful 72: Ewald all geom. 4xM 88.006 88.0056 0.0120 0.0072 72: [ OK ] NonbondedBenchTest.BasicEndToEndTest (99 ms) 72: [----------] 1 test from NonbondedBenchTest (99 ms total) 72: 72: [----------] 5 tests from NormalModesWorks/NormalModesTest 72: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/0 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 15.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 4 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Small system size (N=6), using full Hessian format. 72: Allocating Hessian memory... 72: 72: starting normal mode calculation '2 scaled waters' 72: 12 steps. 72: 72: Maximum force: 9.96989e-06 72: 72: 72: Writing Hessian... 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Reading double precision matrix generated by GROMACS 2025.0-Debian_2025.0_2 72: 72: Diagonalizing to find vectors 7 through 18... 72: Writing eigenvalues... 72: 72: Writing average structure & eigenvectors 7--18 to eigenvec.trr 72: Generated 3 of the 3 non-bonded parameter combinations 72: 72: Generated 3 of the 3 1-4 parameter combinations 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: This run will generate roughly 0 Mb of data 72: There are: 6 Atoms 72: Using begin = 7 and end = 18 72: Full matrix storage format, nrow=18, ncols=18 72: Writing eigenfrequencies - negative eigenvalues will be set to zero. 72: Cannot compute entropy when -first = 7 72: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/0 (50 ms) 72: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/1 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Generating 1-4 interactions: fudge = 1 72: 72: NOTE 3 [file villin.top, line 2452]: 72: System has non-zero total charge: -2.000000 72: Total charge should normally be an integer. See 72: https://manual.gromacs.org/current/user-guide/floating-point.html 72: for discussion on how close it should be to an integer. 72: 72: 72: 72: Number of degrees of freedom in T-Coupling group System is 765.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 5 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Small system size (N=256), using full Hessian format. 72: Allocating Hessian memory... 72: 72: starting normal mode calculation 'AMYLOID BETA A4 PROTEIN' 72: 512 steps. 72: 72: Maximum force: 6.97568e-04 72: 72: 72: Writing Hessian... 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Reading double precision matrix generated by GROMACS 2025.0-Debian_2025.0_2 72: 72: Diagonalizing to find vectors 7 through 50... 72: Writing eigenvalues... 72: 72: Writing average structure & eigenvectors 7--50 to eigenvec.trr 72: Generated 20503 of the 20503 non-bonded parameter combinations 72: 72: Generated 17396 of the 20503 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 72: 72: This run will generate roughly 0 Mb of data 72: There are: 256 Atoms 72: Using begin = 7 and end = 50 72: Full matrix storage format, nrow=768, ncols=768 72: Writing eigenfrequencies - negative eigenvalues will be set to zero. 72: Cannot compute entropy when -first = 7 72: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/1 (4265 ms) 72: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/2 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 15.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 4 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Small system size (N=6), using full Hessian format. 72: Allocating Hessian memory... 72: 72: starting normal mode calculation 'flex spc dimer' 72: 12 steps. 72: 72: Maximum force: 3.36401e-04 72: 72: 72: Writing Hessian... 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Reading double precision matrix generated by GROMACS 2025.0-Debian_2025.0_2 72: 72: Diagonalizing to find vectors 7 through 18... 72: Writing eigenvalues... 72: 72: Writing average structure & eigenvectors 7--18 to eigenvec.trr 72: Generated 330891 of the 330891 non-bonded parameter combinations 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: This run will generate roughly 0 Mb of data 72: There are: 6 Atoms 72: Using begin = 7 and end = 18 72: Full matrix storage format, nrow=18, ncols=18 72: Writing eigenfrequencies - negative eigenvalues will be set to zero. 72: Cannot compute entropy when -first = 7 72: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/2 (905 ms) 72: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/3 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 6.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 4 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Update groups can not be used for this system because an incompatible virtual site type is used 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Small system size (N=3), using full Hessian format. 72: Allocating Hessian memory... 72: 72: starting normal mode calculation '1 TIP5P' 72: 6 steps. 72: 72: Maximum force: 2.42882e-04 72: 72: 72: Writing Hessian... 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Reading double precision matrix generated by GROMACS 2025.0-Debian_2025.0_2 72: 72: Diagonalizing to find vectors 7 through 9... 72: Writing eigenvalues... 72: 72: Writing average structure & eigenvectors 7--9 to eigenvec.trr 72: Generated 330891 of the 330891 non-bonded parameter combinations 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: Cleaning up constraints and constant bonded interactions with virtual sites 72: 72: This run will generate roughly 0 Mb of data 72: There are: 3 Atoms 72: There are: 2 VSites 72: Using begin = 7 and end = 9 72: Full matrix storage format, nrow=9, ncols=9 72: Writing eigenfrequencies - negative eigenvalues will be set to zero. 72: Cannot compute entropy when -first = 7 72: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/3 (665 ms) 72: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/4 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: Number of degrees of freedom in T-Coupling group System is 15.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 2 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Update groups can not be used for this system because the construction atoms of a virtual site are only partly with a group of constrained atoms 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Small system size (N=6), using full Hessian format. 72: Allocating Hessian memory... 72: 72: starting normal mode calculation 'sw dimer' 72: 12 steps. 72: 72: Maximum force: 1.07599e-03 72: The force is probably not small enough to ensure that you are at a minimum. 72: Be aware that negative eigenvalues may occur 72: when the resulting matrix is diagonalized. 72: 72: 72: Writing Hessian... 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Reading double precision matrix generated by GROMACS 2025.0-Debian_2025.0_2 72: 72: Diagonalizing to find vectors 7 through 18... 72: Writing eigenvalues... 72: 72: Writing average structure & eigenvectors 7--18 to eigenvec.trr 72: Generated 6 of the 10 non-bonded parameter combinations 72: 72: Excluding 2 bonded neighbours molecule type 'SW' 72: 72: Cleaning up constraints and constant bonded interactions with virtual sites 72: 72: This run will generate roughly 0 Mb of data 72: There are: 6 Atoms 72: There are: 2 Shells 72: There are: 2 VSites 72: 72: NOTE: in the current version shell prediction during the crun is disabled 72: 72: Using begin = 7 and end = 18 72: Full matrix storage format, nrow=18, ncols=18 72: Writing eigenfrequencies - negative eigenvalues will be set to zero. 72: Cannot compute entropy when -first = 7 72: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/4 (163 ms) 72: [----------] 5 tests from NormalModesWorks/NormalModesTest (6050 ms total) 72: 72: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest 72: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Number of degrees of freedom in T-Coupling group System is 33.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 72: NVE simulation: will use the initial temperature of 68.810 K for 72: determining the Verlet buffer size 72: 72: 72: There were 3 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'Argon' 72: 16 steps, 0.0 ps. 72: Generated 1 of the 1 non-bonded parameter combinations 72: 72: Excluding 1 bonded neighbours molecule type 'Argon' 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.583 0.292 199.9 72: (ns/day) (hour/ns) 72: Performance: 5.036 4.766 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.trr' 72: 72: trr version: GMX_trn_file (double precision) 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 29 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.002 0.001 193.1 72: (ns/day) (hour/ns) 72: Performance: 1657.856 0.014 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim2.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 (362 ms) 72: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Number of degrees of freedom in T-Coupling group System is 33.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 72: NVE simulation: will use the initial temperature of 68.810 K for 72: determining the Verlet buffer size 72: 72: 72: There were 3 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'Argon' 72: 16 steps, 0.0 ps. 72: Generated 1 of the 1 non-bonded parameter combinations 72: 72: Excluding 1 bonded neighbours molecule type 'Argon' 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 2.250 1.125 200.0 72: (ns/day) (hour/ns) 72: Performance: 1.305 18.386 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 23 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.002 0.001 188.6 72: (ns/day) (hour/ns) 72: Performance: 1490.586 0.016 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim2.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 (1214 ms) 72: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Number of degrees of freedom in T-Coupling group System is 33.00 72: 72: There were 2 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 100, rlist from 0.712 to 0.746 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'Argon' 72: 16 steps, 0.0 ps. 72: Generated 1 of the 1 non-bonded parameter combinations 72: 72: Excluding 1 bonded neighbours molecule type 'Argon' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 1.316 0.658 200.0 72: (ns/day) (hour/ns) 72: Performance: 2.231 10.755 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 100, rlist from 0.712 to 0.746 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 27 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.002 0.001 191.9 72: (ns/day) (hour/ns) 72: Performance: 1504.051 0.016 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim2.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 (832 ms) 72: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Number of degrees of freedom in T-Coupling group System is 33.00 72: 72: There were 2 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'Argon' 72: 16 steps, 0.0 ps. 72: Generated 1 of the 1 non-bonded parameter combinations 72: 72: Excluding 1 bonded neighbours molecule type 'Argon' 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 1.709 0.855 200.0 72: (ns/day) (hour/ns) 72: Performance: 1.719 13.965 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 26 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.002 0.001 194.5 72: (ns/day) (hour/ns) 72: Performance: 1394.746 0.017 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim2.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 (916 ms) 72: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 27.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 72: NVE simulation: will use the initial temperature of 398.997 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'spc2' 72: 16 steps, 0.0 ps. 72: Generated 330891 of the 330891 non-bonded parameter combinations 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.095 0.048 199.3 72: (ns/day) (hour/ns) 72: Performance: 30.661 0.783 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 30 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.002 0.001 194.2 72: (ns/day) (hour/ns) 72: Performance: 1375.133 0.017 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim2.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 (816 ms) 72: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 27.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 72: NVE simulation: will use the initial temperature of 398.997 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'spc2' 72: 16 steps, 0.0 ps. 72: Generated 330891 of the 330891 non-bonded parameter combinations 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.061 0.030 199.4 72: (ns/day) (hour/ns) 72: Performance: 48.289 0.497 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 24 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.002 0.001 194.7 72: (ns/day) (hour/ns) 72: Performance: 1639.328 0.015 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim2.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 (841 ms) 72: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 27.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 3 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 100, rlist from 0.736 to 0.834 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'spc2' 72: 16 steps, 0.0 ps. 72: Generated 330891 of the 330891 non-bonded parameter combinations 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.738 nm, buffer size 0.038 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.037 0.018 199.1 72: (ns/day) (hour/ns) 72: Performance: 79.533 0.302 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 100, rlist from 0.736 to 0.834 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 26 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.002 0.001 193.0 72: (ns/day) (hour/ns) 72: Performance: 1605.157 0.015 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim2.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 (826 ms) 72: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 27.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 3 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'spc2' 72: 16 steps, 0.0 ps. 72: Generated 330891 of the 330891 non-bonded parameter combinations 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.075 0.038 199.6 72: (ns/day) (hour/ns) 72: Performance: 39.114 0.614 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.021 0.011 198.6 72: (ns/day) (hour/ns) 72: Performance: 139.380 0.172 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim2.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 (805 ms) 72: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: 72: NOTE 3 [file unknown]: 72: You are using constraints on all bonds, whereas the forcefield has been 72: parametrized only with constraints involving hydrogen atoms. We suggest 72: using constraints = h-bonds instead, this will also improve performance. 72: 72: Number of degrees of freedom in T-Coupling group System is 23.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 72: NVE simulation: will use the initial temperature of 456.887 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 72: There are 9 non-linear virtual site constructions. Their contribution to 72: the energy error is approximated. In most cases this does not affect the 72: error significantly. 72: 72: 72: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 6 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Update groups can not be used for this system because an incompatible virtual site type is used 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'Alanine dipeptide in vacuo' 72: 16 steps, 0.0 ps. 72: Generated 2145 of the 2145 non-bonded parameter combinations 72: 72: Generated 2145 of the 2145 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 72: 72: turning all bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 72: 72: Cleaning up constraints and constant bonded interactions with virtual sites 72: 72: Removed 18 Angles with virtual sites, 21 left 72: 72: Removed 10 Proper Dih.s with virtual sites, 44 left 72: 72: Converted 15 Constraints with virtual sites to connections, 7 left 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: NOTE: 21 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.079 0.040 199.0 72: (ns/day) (hour/ns) 72: Performance: 37.038 0.648 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Update groups can not be used for this system because an incompatible virtual site type is used 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 21 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.007 0.004 196.3 72: (ns/day) (hour/ns) 72: Performance: 418.974 0.057 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim2.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 (116 ms) 72: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: 72: NOTE 3 [file unknown]: 72: You are using constraints on all bonds, whereas the forcefield has been 72: parametrized only with constraints involving hydrogen atoms. We suggest 72: using constraints = h-bonds instead, this will also improve performance. 72: 72: Number of degrees of freedom in T-Coupling group System is 23.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 72: NVE simulation: will use the initial temperature of 456.887 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 72: There are 9 non-linear virtual site constructions. Their contribution to 72: the energy error is approximated. In most cases this does not affect the 72: error significantly. 72: 72: 72: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 6 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Update groups can not be used for this system because an incompatible virtual site type is used 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'Alanine dipeptide in vacuo' 72: 16 steps, 0.0 ps. 72: Generated 2145 of the 2145 non-bonded parameter combinations 72: 72: Generated 2145 of the 2145 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 72: 72: turning all bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 72: 72: Cleaning up constraints and constant bonded interactions with virtual sites 72: 72: Removed 18 Angles with virtual sites, 21 left 72: 72: Removed 10 Proper Dih.s with virtual sites, 44 left 72: 72: Converted 15 Constraints with virtual sites to connections, 7 left 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: NOTE: 28 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.060 0.030 199.0 72: (ns/day) (hour/ns) 72: Performance: 48.357 0.496 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Update groups can not be used for this system because an incompatible virtual site type is used 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 12 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.006 0.003 195.7 72: (ns/day) (hour/ns) 72: Performance: 489.324 0.049 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim2.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 (129 ms) 72: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: 72: NOTE 3 [file unknown]: 72: You are using constraints on all bonds, whereas the forcefield has been 72: parametrized only with constraints involving hydrogen atoms. We suggest 72: using constraints = h-bonds instead, this will also improve performance. 72: 72: Number of degrees of freedom in T-Coupling group System is 23.00 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 72: There are 9 non-linear virtual site constructions. Their contribution to 72: the energy error is approximated. In most cases this does not affect the 72: error significantly. 72: 72: 72: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 5 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 80, rlist from 0.75 to 0.871 72: 72: Update groups can not be used for this system because an incompatible virtual site type is used 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'Alanine dipeptide in vacuo' 72: 16 steps, 0.0 ps. 72: Generated 2145 of the 2145 non-bonded parameter combinations 72: 72: Generated 2145 of the 2145 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 72: 72: turning all bonds into constraints... 72: 72: Cleaning up constraints and constant bonded interactions with virtual sites 72: 72: Removed 18 Angles with virtual sites, 21 left 72: 72: Removed 10 Proper Dih.s with virtual sites, 44 left 72: 72: Converted 15 Constraints with virtual sites to connections, 7 left 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.061 0.031 197.9 72: (ns/day) (hour/ns) 72: Performance: 47.738 0.503 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 80, rlist from 0.75 to 0.871 72: 72: Update groups can not be used for this system because an incompatible virtual site type is used 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 20 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.004 0.002 194.7 72: (ns/day) (hour/ns) 72: Performance: 696.585 0.034 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim2.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 (363 ms) 72: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: 72: NOTE 3 [file unknown]: 72: You are using constraints on all bonds, whereas the forcefield has been 72: parametrized only with constraints involving hydrogen atoms. We suggest 72: using constraints = h-bonds instead, this will also improve performance. 72: 72: Number of degrees of freedom in T-Coupling group System is 23.00 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 72: There are 9 non-linear virtual site constructions. Their contribution to 72: the energy error is approximated. In most cases this does not affect the 72: error significantly. 72: 72: 72: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 5 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 25, rlist from 0.73 to 0.814 72: 72: Update groups can not be used for this system because an incompatible virtual site type is used 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'Alanine dipeptide in vacuo' 72: 16 steps, 0.0 ps. 72: Generated 2145 of the 2145 non-bonded parameter combinations 72: 72: Generated 2145 of the 2145 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 72: 72: turning all bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 72: 72: Cleaning up constraints and constant bonded interactions with virtual sites 72: 72: Removed 18 Angles with virtual sites, 21 left 72: 72: Removed 10 Proper Dih.s with virtual sites, 44 left 72: 72: Converted 15 Constraints with virtual sites to connections, 7 left 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.057 0.029 199.2 72: (ns/day) (hour/ns) 72: Performance: 51.356 0.467 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 25, rlist from 0.73 to 0.814 72: 72: Update groups can not be used for this system because an incompatible virtual site type is used 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 19 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.004 0.002 195.6 72: (ns/day) (hour/ns) 72: Performance: 693.995 0.035 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim2.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 (145 ms) 72: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest (7371 ms total) 72: 72: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.103 0.052 197.7 72: (ns/day) (hour/ns) 72: Performance: 28.277 0.849 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.016 0.046 35.8 72: (ns/day) (hour/ns) 72: Performance: 32.255 0.744 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim2.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 (158 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.045 0.023 198.9 72: (ns/day) (hour/ns) 72: Performance: 65.120 0.369 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.010 0.005 192.1 72: (ns/day) (hour/ns) 72: Performance: 272.340 0.088 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim2.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 (72 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.083 0.042 199.3 72: (ns/day) (hour/ns) 72: Performance: 35.309 0.680 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.012 0.006 193.9 72: (ns/day) (hour/ns) 72: Performance: 233.692 0.103 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim2.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 (106 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.114 0.057 199.4 72: (ns/day) (hour/ns) 72: Performance: 25.753 0.932 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 21 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.008 0.004 192.3 72: (ns/day) (hour/ns) 72: Performance: 366.397 0.066 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim2.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 (118 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.050 0.025 198.7 72: (ns/day) (hour/ns) 72: Performance: 58.726 0.409 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 17 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.004 0.002 185.0 72: (ns/day) (hour/ns) 72: Performance: 716.932 0.033 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim2.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 (67 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.137 0.069 199.5 72: (ns/day) (hour/ns) 72: Performance: 21.361 1.124 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 20 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.004 0.002 183.5 72: (ns/day) (hour/ns) 72: Performance: 638.403 0.038 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim2.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 (133 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.196 0.098 199.5 72: (ns/day) (hour/ns) 72: Performance: 14.918 1.609 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 18 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.004 0.002 186.8 72: (ns/day) (hour/ns) 72: Performance: 656.850 0.037 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim2.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 (144 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.093 0.047 199.5 72: (ns/day) (hour/ns) 72: Performance: 31.391 0.765 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.045 0.023 198.2 72: (ns/day) (hour/ns) 72: Performance: 65.243 0.368 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim2.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 (143 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.049 0.025 198.9 72: (ns/day) (hour/ns) 72: Performance: 59.396 0.404 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 22 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.004 0.002 183.2 72: (ns/day) (hour/ns) 72: Performance: 673.068 0.036 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim2.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 (71 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.089 0.046 194.9 72: (ns/day) (hour/ns) 72: Performance: 32.145 0.747 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.007 0.004 190.8 72: (ns/day) (hour/ns) 72: Performance: 378.183 0.063 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim2.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 (87 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.053 0.027 199.0 72: (ns/day) (hour/ns) 72: Performance: 55.021 0.436 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 17 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.003 0.002 162.4 72: (ns/day) (hour/ns) 72: Performance: 733.579 0.033 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim2.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 (75 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.088 0.044 199.7 72: (ns/day) (hour/ns) 72: Performance: 33.227 0.722 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.007 0.004 190.3 72: (ns/day) (hour/ns) 72: Performance: 381.225 0.063 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim2.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 (90 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.100 0.050 199.6 72: (ns/day) (hour/ns) 72: Performance: 29.381 0.817 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 24 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.008 0.005 182.4 72: (ns/day) (hour/ns) 72: Performance: 322.510 0.074 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim2.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 (106 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.129 0.065 199.7 72: (ns/day) (hour/ns) 72: Performance: 22.766 1.054 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 26 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.004 0.002 185.1 72: (ns/day) (hour/ns) 72: Performance: 664.860 0.036 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim2.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 (128 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.080 0.040 199.6 72: (ns/day) (hour/ns) 72: Performance: 36.582 0.656 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 18 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.004 0.002 185.0 72: (ns/day) (hour/ns) 72: Performance: 771.038 0.031 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim2.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 (94 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.121 0.060 199.7 72: (ns/day) (hour/ns) 72: Performance: 24.331 0.986 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.011 0.006 193.5 72: (ns/day) (hour/ns) 72: Performance: 254.633 0.094 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim2.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 (189 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: NOTE: 15 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.194 0.097 199.8 72: (ns/day) (hour/ns) 72: Performance: 15.143 1.585 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.004 0.008 45.0 72: (ns/day) (hour/ns) 72: Performance: 177.421 0.135 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim2.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 (179 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.326 0.163 199.9 72: (ns/day) (hour/ns) 72: Performance: 9.006 2.665 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.024 0.013 181.5 72: (ns/day) (hour/ns) 72: Performance: 113.438 0.212 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim2.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 (257 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.126 0.063 199.5 72: (ns/day) (hour/ns) 72: Performance: 23.179 1.035 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 17 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.004 0.002 178.3 72: (ns/day) (hour/ns) 72: Performance: 606.955 0.040 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim2.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 (201 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.126 0.063 198.9 72: (ns/day) (hour/ns) 72: Performance: 23.140 1.037 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.023 0.012 196.9 72: (ns/day) (hour/ns) 72: Performance: 123.575 0.194 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim2.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 (190 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.614 0.308 199.4 72: (ns/day) (hour/ns) 72: Performance: 4.771 5.031 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.025 0.013 195.9 72: (ns/day) (hour/ns) 72: Performance: 114.639 0.209 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim2.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 (399 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 72: NVE simulation: will use the initial temperature of 294.908 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.154 0.077 199.8 72: (ns/day) (hour/ns) 72: Performance: 19.111 1.256 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 21 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.005 0.003 185.3 72: (ns/day) (hour/ns) 72: Performance: 581.957 0.041 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim2.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 (183 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 3 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.168 0.084 199.7 72: (ns/day) (hour/ns) 72: Performance: 17.484 1.373 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 22 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.005 0.003 183.5 72: (ns/day) (hour/ns) 72: Performance: 587.003 0.041 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim2.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 (546 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 3 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.093 0.047 199.3 72: (ns/day) (hour/ns) 72: Performance: 31.454 0.763 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.029 0.015 196.4 72: (ns/day) (hour/ns) 72: Performance: 98.117 0.245 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim2.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 (193 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 3 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.093 0.047 199.3 72: (ns/day) (hour/ns) 72: Performance: 31.417 0.764 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 14 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.006 0.003 185.8 72: (ns/day) (hour/ns) 72: Performance: 471.426 0.051 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim2.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 (145 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 3 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.114 0.057 199.4 72: (ns/day) (hour/ns) 72: Performance: 25.768 0.931 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 18 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.004 0.002 184.1 72: (ns/day) (hour/ns) 72: Performance: 693.214 0.035 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim2.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 (143 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 3 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.116 0.058 199.1 72: (ns/day) (hour/ns) 72: Performance: 25.269 0.950 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 45 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.012 0.006 191.8 72: (ns/day) (hour/ns) 72: Performance: 235.092 0.102 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim2.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 (167 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 3 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.058 0.029 199.1 72: (ns/day) (hour/ns) 72: Performance: 50.264 0.477 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.011 0.006 190.7 72: (ns/day) (hour/ns) 72: Performance: 257.249 0.093 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim2.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 (116 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 3 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.076 0.038 199.3 72: (ns/day) (hour/ns) 72: Performance: 38.332 0.626 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 12 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.009 0.005 189.0 72: (ns/day) (hour/ns) 72: Performance: 311.597 0.077 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim2.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 (120 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 3 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.119 0.060 199.4 72: (ns/day) (hour/ns) 72: Performance: 24.565 0.977 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.029 0.015 196.6 72: (ns/day) (hour/ns) 72: Performance: 99.061 0.242 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim2.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 (166 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 3 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.096 0.048 199.4 72: (ns/day) (hour/ns) 72: Performance: 30.664 0.783 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 17 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.012 0.006 194.7 72: (ns/day) (hour/ns) 72: Performance: 235.335 0.102 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim2.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 (171 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 3 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.212 0.106 199.5 72: (ns/day) (hour/ns) 72: Performance: 13.853 1.733 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.005 0.118 4.5 72: (ns/day) (hour/ns) 72: Performance: 12.498 1.920 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim2.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 (564 ms) 72: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 79.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 3 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun '30 atom system in water' 72: 16 steps, 0.0 ps. 72: Generated 2485 of the 2485 non-bonded parameter combinations 72: 72: Generated 2485 of the 2485 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'nonanol' 72: 72: turning H bonds into constraints... 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: turning H bonds into constraints... 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.178 0.089 199.4 72: (ns/day) (hour/ns) 72: Performance: 16.473 1.457 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 72: 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.trr' 72: 72: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 72: 72: NOTE: 18 % of the run time was spent in pair search, 72: you might want to increase nstlist (this has no effect on accuracy) 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.006 0.003 178.3 72: (ns/day) (hour/ns) 72: Performance: 431.324 0.056 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim2.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 72: 72: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 (314 ms) 72: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest (5855 ms total) 72: 72: [----------] 2 tests from Angles1/SimpleMdrunTest 72: [ RUN ] Angles1/SimpleMdrunTest.WithinTolerances/0 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file angles1.top, line 72]: 72: In moleculetype 'butane' 4 atoms are not bound by a potential or 72: constraint to any other atom in the same moleculetype. Although 72: technically this might not cause issues in a simulation, this often means 72: that the user forgot to add a bond/potential/constraint or put multiple 72: molecules in the same moleculetype definition by mistake. Run with -v to 72: get information for each atom. 72: 72: Number of degrees of freedom in T-Coupling group System is 9.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0_input.mdp]: 72: NVE simulation: will use the initial temperature of 238.919 K for 72: determining the Verlet buffer size 72: 72: 72: There were 3 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'This_incredible_box_of_butane' 72: 50 steps, 0.1 ps. 72: Generated 3 of the 3 non-bonded parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'butane' 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/angles1.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 238.919 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.700 nm, buffer size 0.000 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.700 nm, buffer size 0.000 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.096 0.050 192.4 72: (ns/day) (hour/ns) 72: Performance: 88.142 0.272 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 5 time 0.020 Reading energy frame 6 time 0.024 Reading energy frame 7 time 0.028 Reading energy frame 8 time 0.032 Reading energy frame 9 time 0.036 Reading energy frame 10 time 0.040 Reading energy frame 11 time 0.044 Reading energy frame 12 time 0.048 Reading energy frame 13 time 0.050 Last energy frame read 13 time 0.050 72: [ OK ] Angles1/SimpleMdrunTest.WithinTolerances/0 (71 ms) 72: [ RUN ] Angles1/SimpleMdrunTest.WithinTolerances/1 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file angles1.top, line 72]: 72: In moleculetype 'butane' 4 atoms are not bound by a potential or 72: constraint to any other atom in the same moleculetype. Although 72: technically this might not cause issues in a simulation, this often means 72: that the user forgot to add a bond/potential/constraint or put multiple 72: molecules in the same moleculetype definition by mistake. Run with -v to 72: get information for each atom. 72: 72: Number of degrees of freedom in T-Coupling group System is 9.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1_input.mdp]: 72: NVE simulation: will use the initial temperature of 238.919 K for 72: determining the Verlet buffer size 72: 72: 72: There were 3 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: starting mdrun 'This_incredible_box_of_butane' 72: 50 steps, 0.1 ps. 72: Generated 3 of the 3 non-bonded parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'butane' 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/angles1.gro' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 238.919 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.700 nm, buffer size 0.000 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.700 nm, buffer size 0.000 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.038 0.019 199.0 72: (ns/day) (hour/ns) 72: Performance: 228.035 0.105 72: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 5 time 0.020 Reading energy frame 6 time 0.024 Reading energy frame 7 time 0.028 Reading energy frame 8 time 0.032 Reading energy frame 9 time 0.036 Reading energy frame 10 time 0.040 Reading energy frame 11 time 0.044 Reading energy frame 12 time 0.048 Reading energy frame 13 time 0.050 Last energy frame read 13 time 0.050 72: [ OK ] Angles1/SimpleMdrunTest.WithinTolerances/1 (43 ms) 72: [----------] 2 tests from Angles1/SimpleMdrunTest (115 ms total) 72: 72: [----------] Global test environment tear-down 72: [==========] 53 tests from 5 test suites ran. (20184 ms total) 72: [ PASSED ] 53 tests. 72/90 Test #72: MdrunNonIntegratorTests ................... Passed 20.24 sec test 73 Start 73: MdrunTpiTests 73: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/mdrun-tpi-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/MdrunTpiTests.xml" 73: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests 73: Test timeout computed to be: 600 73: [==========] Running 3 tests from 1 test suite. 73: [----------] Global test environment set-up. 73: [----------] 3 tests from Simple/TpiTest 73: [ RUN ] Simple/TpiTest.ReproducesOutput/0 73: Generating 1-4 interactions: fudge = 0.5 73: Number of degrees of freedom in T-Coupling group System is 1308.00 73: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 73: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 73: TPI is not implemented for GPUs. 73: 73: Using 1 MPI thread 73: Using 1 OpenMP thread 73: 73: 73: NOTE: Thread affinity was not set. 73: Reading frames from gro file '216 water molecules', 648 atoms. 73: Reading frame 0 time 0.000 mu 6.291e+01 6.291e+01 73: Last frame 0 time 0.000 73: Generated 331705 of the 331705 non-bonded parameter combinations 73: 73: Generated 331705 of the 331705 1-4 parameter combinations 73: 73: Excluding 2 bonded neighbours molecule type 'SOL' 73: 73: Excluding 3 bonded neighbours molecule type 'methane' 73: Analysing residue names: 73: There are: 216 Water residues 73: There are: 1 Other residues 73: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 73: 73: This run will generate roughly 0 Mb of data 73: [ OK ] Simple/TpiTest.ReproducesOutput/0 (662 ms) 73: [ RUN ] Simple/TpiTest.ReproducesOutput/1 73: Generating 1-4 interactions: fudge = 0.5 73: Number of degrees of freedom in T-Coupling group System is 1308.00 73: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 73: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 73: TPI is not implemented for GPUs. 73: 73: Using 1 MPI thread 73: Using 1 OpenMP thread 73: 73: 73: NOTE: Thread affinity was not set. 73: Reading frames from gro file '216 water molecules', 648 atoms. 73: Reading frame 0 time 0.000 mu 4.535e+01 4.535e+01 73: Last frame 0 time 0.000 73: Generated 331705 of the 331705 non-bonded parameter combinations 73: 73: Generated 331705 of the 331705 1-4 parameter combinations 73: 73: Excluding 2 bonded neighbours molecule type 'SOL' 73: 73: Excluding 3 bonded neighbours molecule type 'methane' 73: Analysing residue names: 73: There are: 216 Water residues 73: There are: 1 Other residues 73: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 73: 73: This run will generate roughly 0 Mb of data 73: [ OK ] Simple/TpiTest.ReproducesOutput/1 (594 ms) 73: [ RUN ] Simple/TpiTest.ReproducesOutput/2 73: Generating 1-4 interactions: fudge = 0.5 73: Number of degrees of freedom in T-Coupling group System is 1308.00 73: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 73: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 73: TPI is not implemented for GPUs. 73: 73: Using 1 MPI thread 73: Using 1 OpenMP thread 73: 73: 73: NOTE: Thread affinity was not set. 73: Reading frames from gro file '216 water molecules', 648 atoms. 73: Reading frame 0 time 0.000 mu 6.203e+01 6.203e+01 73: Last frame 0 time 0.000 73: Generated 331705 of the 331705 non-bonded parameter combinations 73: 73: Generated 331705 of the 331705 1-4 parameter combinations 73: 73: Excluding 2 bonded neighbours molecule type 'SOL' 73: 73: Excluding 3 bonded neighbours molecule type 'methane' 73: Analysing residue names: 73: There are: 216 Water residues 73: There are: 1 Other residues 73: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 73: 73: This run will generate roughly 0 Mb of data 73: [ OK ] Simple/TpiTest.ReproducesOutput/2 (840 ms) 73: [----------] 3 tests from Simple/TpiTest (2097 ms total) 73: 73: [----------] Global test environment tear-down 73: [==========] 3 tests from 1 test suite ran. (2215 ms total) 73: [ PASSED ] 3 tests. 73/90 Test #73: MdrunTpiTests ............................. Passed 2.24 sec test 74 Start 74: MdrunMpiTests 74: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/mdrun-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/MdrunMpiTests.xml" 74: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests 74: Test timeout computed to be: 600 74: [==========] Running 16 tests from 2 test suites. 74: [----------] Global test environment set-up. 74: [----------] 4 tests from MimicTest 74: [ RUN ] MimicTest.OneQuantumMol 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 74: For a correct single-point energy evaluation with nsteps = 0, use 74: continuation = yes to avoid constraining the input coordinates. 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group rest is 21.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 74: NVE simulation with an initial temperature of zero: will use a Verlet 74: buffer of 10%. Check your energy drift! 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 2 MPI threads 74: Using 2 OpenMP threads per tMPI thread 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro' 74: 74: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 74: Reading frame 0 time 0.000 Last frame 0 time 0.000 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.018 0.005 391.3 74: (ns/day) (hour/ns) 74: Performance: 19.071 1.258 74: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -809517577 74: 74: Generated 10 of the 10 non-bonded parameter combinations 74: 74: Generated 10 of the 10 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 74: 74: This run will generate roughly 0 Mb of data 74: [ OK ] MimicTest.OneQuantumMol (40 ms) 74: [ RUN ] MimicTest.AllQuantumMol 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 74: For a correct single-point energy evaluation with nsteps = 0, use 74: continuation = yes to avoid constraining the input coordinates. 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group rest is 21.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 74: NVE simulation with an initial temperature of zero: will use a Verlet 74: buffer of 10%. Check your energy drift! 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 2 MPI threads 74: Using 2 OpenMP threads per tMPI thread 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro' 74: 74: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 74: Reading frame 0 time 0.000 Last frame 0 time 0.000 74: 74: NOTE: 26 % of the run time was spent in domain decomposition, 74: 16 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: NOTE: 5 % of the run time was spent communicating energies, 74: you might want to increase some nst* mdp options 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.001 381.2 74: (ns/day) (hour/ns) 74: Performance: 127.691 0.188 74: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 1559748543 74: 74: Generated 10 of the 10 non-bonded parameter combinations 74: 74: Generated 10 of the 10 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 74: 74: This run will generate roughly 0 Mb of data 74: [ OK ] MimicTest.AllQuantumMol (30 ms) 74: [ RUN ] MimicTest.TwoQuantumMol 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 74: For a correct single-point energy evaluation with nsteps = 0, use 74: continuation = yes to avoid constraining the input coordinates. 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group rest is 21.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 74: NVE simulation with an initial temperature of zero: will use a Verlet 74: buffer of 10%. Check your energy drift! 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 2 MPI threads 74: Using 2 OpenMP threads per tMPI thread 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro' 74: 74: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 74: Reading frame 0 time 0.000 Last frame 0 time 0.000 74: 74: NOTE: 23 % of the run time was spent in domain decomposition, 74: 15 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: NOTE: 5 % of the run time was spent communicating energies, 74: you might want to increase some nst* mdp options 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.001 377.0 74: (ns/day) (hour/ns) 74: Performance: 116.262 0.206 74: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -942276769 74: 74: Generated 10 of the 10 non-bonded parameter combinations 74: 74: Generated 10 of the 10 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 74: 74: This run will generate roughly 0 Mb of data 74: [ OK ] MimicTest.TwoQuantumMol (27 ms) 74: [ RUN ] MimicTest.BondCuts 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 74: For a correct single-point energy evaluation with nsteps = 0, use 74: continuation = yes to avoid constraining the input coordinates. 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group rest is 66.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 74: NVE simulation: will use the initial temperature of 300.368 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 2 MPI threads 74: Using 2 OpenMP threads per tMPI thread 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 74: 74: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 74: Reading frame 0 time 0.000 Last frame 0 time 0.000 74: 74: NOTE: 23 % of the run time was spent in domain decomposition, 74: 14 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.005 0.001 386.2 74: (ns/day) (hour/ns) 74: Performance: 66.499 0.361 74: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -610402313 74: 74: Generated 2211 of the 2211 non-bonded parameter combinations 74: 74: Generated 2211 of the 2211 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 74: 74: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 74: 74: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: [ OK ] MimicTest.BondCuts (98 ms) 74: [----------] 4 tests from MimicTest (196 ms total) 74: 74: [----------] 12 tests from DomainDecomposition/DomDecSpecialCasesTest 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group rest is 9.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 74: NVE simulation with an initial temperature of zero: will use a Verlet 74: buffer of 10%. Check your energy drift! 74: 74: 74: There was 1 NOTE 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 9.00 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group rest is 9.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 74: NVE simulation with an initial temperature of zero: will use a Verlet 74: buffer of 10%. Check your energy drift! 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 74: The optimal PME mesh load for parallel simulations is below 0.5 74: and for highly parallel simulations between 0.25 and 0.33, 74: for higher performance, increase the cut-off and the PME grid spacing. 74: 74: 74: 74: There were 2 NOTEs 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 9.00 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 74: The optimal PME mesh load for parallel simulations is below 0.5 74: and for highly parallel simulations between 0.25 and 0.33, 74: for higher performance, increase the cut-off and the PME grid spacing. 74: 74: 74: 74: There was 1 NOTE 74: Setting the LD random seed to -944054274 74: 74: Generated 3 of the 3 non-bonded parameter combinations 74: 74: Generated 3 of the 3 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 74: 74: This run will generate roughly 0 Mb of data 74: Setting the LD random seed to 2074902015 74: 74: Generated 3 of the 3 non-bonded parameter combinations 74: 74: Generated 3 of the 3 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 74: 74: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 1.017 nm, buffer size 0.017 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 1.005 nm, buffer size 0.005 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: Setting the LD random seed to -545268870 74: 74: Generated 3 of the 3 non-bonded parameter combinations 74: 74: Generated 3 of the 3 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 74: 74: The largest distance between excluded atoms is 0.164 nm between atom 2 and 3 74: Calculating fourier grid dimensions for X Y Z 74: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107 74: 74: Estimate for the relative computational load of the PME mesh part: 1.00 74: 74: This run will generate roughly 0 Mb of data 74: Setting the LD random seed to -305698945 74: 74: Generated 3 of the 3 non-bonded parameter combinations 74: 74: Generated 3 of the 3 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 74: 74: The largest distance between excluded atoms is 0.164 nm between atom 2 and 3 74: 74: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: Calculating fourier grid dimensions for X Y Z 74: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107 74: 74: Estimate for the relative computational load of the PME mesh part: 1.00 74: 74: This run will generate roughly 0 Mb of data 74: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme0 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_RF_No.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 2 MPI threads 74: Using 2 OpenMP threads per tMPI thread 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 20 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: 74: Dynamic load balancing report: 74: DLB was off during the run due to low measured imbalance. 74: Average load imbalance: 7.6%. 74: The balanceable part of the MD step is 15%, load imbalance is computed from this. 74: Part of the total run time spent waiting due to load imbalance: 1.2%. 74: 74: 74: NOTE: 25 % of the run time was spent communicating energies, 74: you might want to increase some nst* mdp options 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.139 0.035 398.7 74: (ns/day) (hour/ns) 74: Performance: 51.901 0.462 74: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme0 (55 ms) 74: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 74: ./src/programs/mdrun/tests/domain_decomposition.cpp:385: Skipped 74: Test configuration is invalid: 74: Cannot have separate PME ranks when PME is not used 74: 74: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 (0 ms) 74: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 74: ./src/programs/mdrun/tests/domain_decomposition.cpp:385: Skipped 74: Test configuration is invalid: 74: Cannot have separate PME ranks when PME is not used 74: Cannot use two separate PME ranks when there are less than four ranks total 74: 74: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 74: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_RF_TemperatureAndPressure.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 74: Changing nstlist from 10 to 50, rlist from 1.009 to 1.15 74: 74: Using 2 MPI threads 74: Using 2 OpenMP threads per tMPI thread 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 20 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: NOTE: 35 % of the run time was spent communicating energies, 74: you might want to increase some nst* mdp options 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.075 0.019 397.6 74: (ns/day) (hour/ns) 74: Performance: 96.487 0.249 74: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 (41 ms) 74: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 74: ./src/programs/mdrun/tests/domain_decomposition.cpp:385: Skipped 74: Test configuration is invalid: 74: Cannot have separate PME ranks when PME is not used 74: 74: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 (0 ms) 74: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 74: ./src/programs/mdrun/tests/domain_decomposition.cpp:385: Skipped 74: Test configuration is invalid: 74: Cannot have separate PME ranks when PME is not used 74: Cannot use two separate PME ranks when there are less than four ranks total 74: 74: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 74: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme0 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_No.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 2 MPI threads 74: Using 2 OpenMP threads per tMPI thread 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 20 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: 74: Dynamic load balancing report: 74: DLB was off during the run due to low measured imbalance. 74: Average load imbalance: 1.4%. 74: The balanceable part of the MD step is 4%, load imbalance is computed from this. 74: Part of the total run time spent waiting due to load imbalance: 0.1%. 74: 74: 74: NOTE: 14 % of the run time was spent communicating energies, 74: you might want to increase some nst* mdp options 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.233 0.058 399.1 74: (ns/day) (hour/ns) 74: Performance: 31.017 0.774 74: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme0 (285 ms) 74: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme1 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_No.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 2 MPI threads 74: Using 2 OpenMP threads per tMPI thread 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 20 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.211 0.053 397.1 74: (ns/day) (hour/ns) 74: Performance: 34.166 0.702 74: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme1 (160 ms) 74: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 74: ./src/programs/mdrun/tests/domain_decomposition.cpp:385: Skipped 74: Test configuration is invalid: 74: Cannot use two separate PME ranks when there are less than four ranks total 74: 74: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 74: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_TemperatureAndPressure.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 74: Changing nstlist from 10 to 100, rlist from 1 to 1 74: 74: Using 2 MPI threads 74: Using 2 OpenMP threads per tMPI thread 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 20 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: NOTE: 14 % of the run time was spent communicating energies, 74: you might want to increase some nst* mdp options 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.158 0.040 394.9 74: (ns/day) (hour/ns) 74: Performance: 45.237 0.531 74: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 (122 ms) 74: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_TemperatureAndPressure.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 74: Changing nstlist from 10 to 100, rlist from 1 to 1 74: 74: Using 2 MPI threads 74: Using 2 OpenMP threads per tMPI thread 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 20 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.122 0.031 397.2 74: (ns/day) (hour/ns) 74: Performance: 59.182 0.406 74: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 (85 ms) 74: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 74: ./src/programs/mdrun/tests/domain_decomposition.cpp:385: Skipped 74: Test configuration is invalid: 74: Cannot use two separate PME ranks when there are less than four ranks total 74: 74: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 74: [----------] 12 tests from DomainDecomposition/DomDecSpecialCasesTest (753 ms total) 74: 74: [----------] Global test environment tear-down 74: [==========] 16 tests from 2 test suites ran. (1226 ms total) 74: [ PASSED ] 10 tests. 74: [ SKIPPED ] 6 tests, listed below: 74: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 74: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 74: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 74: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 74: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 74: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 74/90 Test #74: MdrunMpiTests ............................. Passed 1.25 sec test 75 Start 75: MdrunMultiSimTests 75: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/mdrun-multisim-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/MdrunMultiSimTests.xml" 75: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests 75: Test timeout computed to be: 600 75: [==========] Running 2 tests from 1 test suite. 75: [----------] Global test environment set-up. 75: [----------] 2 tests from InNvt/MultiSimTerminationTest 75: [ RUN ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 75: [ OK ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 (0 ms) 75: [ RUN ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/1 75: [ OK ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/1 (0 ms) 75: [----------] 2 tests from InNvt/MultiSimTerminationTest (0 ms total) 75: 75: [----------] Global test environment tear-down 75: [==========] 2 tests from 1 test suite ran. (100 ms total) 75: [ PASSED ] 2 tests. 75: 75: YOU HAVE 4 DISABLED TESTS 75: 75/90 Test #75: MdrunMultiSimTests ........................ Passed 0.13 sec test 76 Start 76: MdrunMultiSimReplexTests 76: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/mdrun-multisim-replex-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/MdrunMultiSimReplexTests.xml" 76: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests 76: Test timeout computed to be: 600 76: [==========] Running 1 test from 1 test suite. 76: [----------] Global test environment set-up. 76: [----------] 1 test from InNvt/ReplicaExchangeTerminationTest 76: [ RUN ] InNvt/ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 76: [ OK ] InNvt/ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 (0 ms) 76: [----------] 1 test from InNvt/ReplicaExchangeTerminationTest (0 ms total) 76: 76: [----------] Global test environment tear-down 76: [==========] 1 test from 1 test suite ran. (120 ms total) 76: [ PASSED ] 1 test. 76: 76: YOU HAVE 4 DISABLED TESTS 76: 76/90 Test #76: MdrunMultiSimReplexTests .................. Passed 0.14 sec test 77 Start 77: MdrunMultiSimReplexEquivalenceTests 77: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/mdrun-multisim-replex-equivalence-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/MdrunMultiSimReplexEquivalenceTests.xml" 77: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests 77: Test timeout computed to be: 600 77: [==========] Running 0 tests from 0 test suites. 77: [==========] 0 tests from 0 test suites ran. (0 ms total) 77: [ PASSED ] 0 tests. 77: 77: YOU HAVE 10 DISABLED TESTS 77: 77/90 Test #77: MdrunMultiSimReplexEquivalenceTests ....... Passed 0.04 sec test 78 Start 78: MdrunMpi1RankPmeTests 78: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/mdrun-mpi-pme-test "-ntomp" "2" "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/MdrunMpi1RankPmeTests.xml" 78: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests 78: Test timeout computed to be: 600 78: [==========] Running 19 tests from 1 test suite. 78: [----------] Global test environment set-up. 78: [----------] 19 tests from ReproducesEnergies/PmeTest 78: Number of degrees of freedom in T-Coupling group rest is 12.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 78: NVE simulation: will use the initial temperature of 1046.791 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 78: The optimal PME mesh load for parallel simulations is below 0.5 78: and for highly parallel simulations between 0.25 and 0.33, 78: for higher performance, increase the cut-off and the PME grid spacing. 78: 78: 78: 78: There were 2 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 78: For a correct single-point energy evaluation with nsteps = 0, use 78: continuation = yes to avoid constraining the input coordinates. 78: 78: Number of degrees of freedom in T-Coupling group rest is 13.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 78: NVE simulation: will use the initial temperature of 966.268 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 78: The optimal PME mesh load for parallel simulations is below 0.5 78: and for highly parallel simulations between 0.25 and 0.33, 78: for higher performance, increase the cut-off and the PME grid spacing. 78: 78: 78: 78: There were 3 NOTEs 78: Setting the LD random seed to 1835384829 78: 78: Generated 8 of the 10 non-bonded parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'Methanol' 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 78: 78: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: Calculating fourier grid dimensions for X Y Z 78: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107 78: 78: Estimate for the relative computational load of the PME mesh part: 1.00 78: 78: This run will generate roughly 0 Mb of data 78: Setting the LD random seed to -304087875 78: 78: Generated 8 of the 10 non-bonded parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'Methanol' 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 78: 78: Searching the wall atom type(s) 78: 78: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: Calculating fourier grid dimensions for X Y Z 78: Using a fourier grid of 28x28x128, spacing 0.107 0.107 0.118 78: 78: Estimate for the relative computational load of the PME mesh part: 1.00 78: 78: This run will generate roughly 0 Mb of data 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu 78: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 78: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc-and-methanol' 78: 20 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.105 0.053 199.5 78: (ns/day) (hour/ns) 78: Performance: 34.362 0.698 78: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_cpu.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu (280 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto 78: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 78: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc-and-methanol' 78: 20 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.084 0.042 199.3 78: (ns/day) (hour/ns) 78: Performance: 42.937 0.559 78: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_auto.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto (58 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 78: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 78: Test is being skipped because: 78: it targets GPU execution, but no compatible devices were detected 78: PME GPU does not support: 78: Double-precision build of GROMACS. 78: Non-GPU build of GROMACS. 78: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 78: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 78: Test is being skipped because: 78: it targets GPU execution, but no compatible devices were detected 78: PME GPU does not support: 78: Double-precision build of GROMACS. 78: Non-GPU build of GROMACS. 78: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 78: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 78: Test is being skipped because: 78: it targets GPU execution, but no compatible devices were detected 78: PME GPU does not support: 78: Double-precision build of GROMACS. 78: Non-GPU build of GROMACS. 78: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu 78: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 78: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc-and-methanol' 78: 0 steps, 0.0 ps. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.400 0.200 199.8 78: (ns/day) (hour/ns) 78: Performance: 0.431 55.625 78: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_0__pme_cpu.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu (853 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 78: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 78: Test is being skipped because: 78: it targets GPU execution, but no compatible devices were detected 78: PME GPU does not support: 78: Double-precision build of GROMACS. 78: Non-GPU build of GROMACS. 78: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 78: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 78: Test is being skipped because: 78: it targets GPU execution, but no compatible devices were detected 78: PME GPU does not support: 78: Double-precision build of GROMACS. 78: Non-GPU build of GROMACS. 78: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu 78: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 78: Test is being skipped because: 78: it targets using PME rank(s) but the simulation is using only one rank 78: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto 78: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 78: Test is being skipped because: 78: it targets using PME rank(s) but the simulation is using only one rank 78: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 78: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 78: Test is being skipped because: 78: it targets using PME rank(s) but the simulation is using only one rank 78: it targets GPU execution, but no compatible devices were detected 78: PME GPU does not support: 78: Double-precision build of GROMACS. 78: Non-GPU build of GROMACS. 78: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 78: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 78: Test is being skipped because: 78: it targets using PME rank(s) but the simulation is using only one rank 78: it targets GPU execution, but no compatible devices were detected 78: PME GPU does not support: 78: Double-precision build of GROMACS. 78: Non-GPU build of GROMACS. 78: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 78: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 78: Test is being skipped because: 78: it targets using PME rank(s) but the simulation is using only one rank 78: it targets GPU execution, but no compatible devices were detected 78: PME GPU does not support: 78: Double-precision build of GROMACS. 78: Non-GPU build of GROMACS. 78: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu 78: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 78: Test is being skipped because: 78: it targets using PME rank(s) but the simulation is using only one rank 78: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 78: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 78: Test is being skipped because: 78: it targets using PME rank(s) but the simulation is using only one rank 78: it targets GPU execution, but no compatible devices were detected 78: PME GPU does not support: 78: Double-precision build of GROMACS. 78: Non-GPU build of GROMACS. 78: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 78: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 78: Test is being skipped because: 78: it targets using PME rank(s) but the simulation is using only one rank 78: it targets GPU execution, but no compatible devices were detected 78: PME GPU does not support: 78: Double-precision build of GROMACS. 78: Non-GPU build of GROMACS. 78: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu 78: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 78: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc-and-methanol' 78: 20 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.095 0.048 199.5 78: (ns/day) (hour/ns) 78: Performance: 38.177 0.629 78: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__tunepme__npme_0__pme_cpu.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu (60 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 78: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 78: Test is being skipped because: 78: it targets GPU execution, but no compatible devices were detected 78: PME GPU does not support: 78: Double-precision build of GROMACS. 78: Non-GPU build of GROMACS. 78: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 78: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 78: Test is being skipped because: 78: it targets GPU execution, but no compatible devices were detected 78: PME GPU does not support: 78: Double-precision build of GROMACS. 78: Non-GPU build of GROMACS. 78: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 78: [----------] 19 tests from ReproducesEnergies/PmeTest (1255 ms total) 78: 78: [----------] Global test environment tear-down 78: [==========] 19 tests from 1 test suite ran. (1426 ms total) 78: [ PASSED ] 4 tests. 78: [ SKIPPED ] 15 tests, listed below: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 78/90 Test #78: MdrunMpi1RankPmeTests ..................... Passed 1.47 sec test 79 Start 79: MdrunMpi2RankPmeTests 79: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/mdrun-mpi-pme-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/MdrunMpi2RankPmeTests.xml" 79: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests 79: Test timeout computed to be: 600 79: [==========] Running 19 tests from 1 test suite. 79: [----------] Global test environment set-up. 79: [----------] 19 tests from ReproducesEnergies/PmeTest 79: Number of degrees of freedom in T-Coupling group rest is 12.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 79: NVE simulation: will use the initial temperature of 1046.791 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 79: The optimal PME mesh load for parallel simulations is below 0.5 79: and for highly parallel simulations between 0.25 and 0.33, 79: for higher performance, increase the cut-off and the PME grid spacing. 79: 79: 79: 79: There were 2 NOTEs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 79: For a correct single-point energy evaluation with nsteps = 0, use 79: continuation = yes to avoid constraining the input coordinates. 79: 79: Number of degrees of freedom in T-Coupling group rest is 13.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 79: NVE simulation: will use the initial temperature of 966.268 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 79: The optimal PME mesh load for parallel simulations is below 0.5 79: and for highly parallel simulations between 0.25 and 0.33, 79: for higher performance, increase the cut-off and the PME grid spacing. 79: 79: 79: 79: There were 3 NOTEs 79: Setting the LD random seed to -939658270 79: 79: Generated 8 of the 10 non-bonded parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'Methanol' 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 79: 79: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: Calculating fourier grid dimensions for X Y Z 79: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107 79: 79: Estimate for the relative computational load of the PME mesh part: 1.00 79: 79: This run will generate roughly 0 Mb of data 79: Setting the LD random seed to -2297877 79: 79: Generated 8 of the 10 non-bonded parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'Methanol' 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 79: 79: Searching the wall atom type(s) 79: 79: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: Calculating fourier grid dimensions for X Y Z 79: Using a fourier grid of 28x28x128, spacing 0.107 0.107 0.118 79: 79: Estimate for the relative computational load of the PME mesh part: 1.00 79: 79: This run will generate roughly 0 Mb of data 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu 79: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 2 MPI threads 79: Using 2 OpenMP threads per tMPI thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc-and-methanol' 79: 20 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: 79: Dynamic load balancing report: 79: DLB was off during the run due to low measured imbalance. 79: Average load imbalance: 4.4%. 79: The balanceable part of the MD step is 15%, load imbalance is computed from this. 79: Part of the total run time spent waiting due to load imbalance: 0.7%. 79: 79: 79: NOTE: 19 % of the run time was spent communicating energies, 79: you might want to increase some nst* mdp options 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.224 0.056 398.8 79: (ns/day) (hour/ns) 79: Performance: 32.271 0.744 79: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_cpu.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu (202 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto 79: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 2 MPI threads 79: Using 2 OpenMP threads per tMPI thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc-and-methanol' 79: 20 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: 79: Dynamic load balancing report: 79: DLB was off during the run due to low measured imbalance. 79: Average load imbalance: 8.3%. 79: The balanceable part of the MD step is 4%, load imbalance is computed from this. 79: Part of the total run time spent waiting due to load imbalance: 0.4%. 79: 79: 79: NOTE: 13 % of the run time was spent communicating energies, 79: you might want to increase some nst* mdp options 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.227 0.057 398.9 79: (ns/day) (hour/ns) 79: Performance: 31.951 0.751 79: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_auto.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto (79 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 79: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 79: Test is being skipped because: 79: it targets GPU execution, but no compatible devices were detected 79: it targets PME decomposition, but that is not supported 79: PME GPU does not support: 79: Double-precision build of GROMACS. 79: Non-GPU build of GROMACS. 79: 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 79: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 79: Test is being skipped because: 79: it targets GPU execution, but no compatible devices were detected 79: it targets PME decomposition, but that is not supported 79: PME GPU does not support: 79: Double-precision build of GROMACS. 79: Non-GPU build of GROMACS. 79: 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 79: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 79: Test is being skipped because: 79: it targets GPU execution, but no compatible devices were detected 79: it targets PME decomposition, but that is not supported 79: PME GPU does not support: 79: Double-precision build of GROMACS. 79: Non-GPU build of GROMACS. 79: 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto (0 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu 79: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 2 MPI threads 79: Using 2 OpenMP threads per tMPI thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc-and-methanol' 79: 0 steps, 0.0 ps. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.023 0.006 381.3 79: (ns/day) (hour/ns) 79: Performance: 14.548 1.650 79: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_0__pme_cpu.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu (463 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 79: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 79: Test is being skipped because: 79: it targets GPU execution, but no compatible devices were detected 79: it targets PME decomposition, but that is not supported 79: PME GPU does not support: 79: Double-precision build of GROMACS. 79: Non-GPU build of GROMACS. 79: 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 79: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 79: Test is being skipped because: 79: it targets GPU execution, but no compatible devices were detected 79: it targets PME decomposition, but that is not supported 79: PME GPU does not support: 79: Double-precision build of GROMACS. 79: Non-GPU build of GROMACS. 79: 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu 79: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 2 MPI threads 79: Using 2 OpenMP threads per tMPI thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc-and-methanol' 79: 20 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 1.584 0.396 399.6 79: (ns/day) (hour/ns) 79: Performance: 4.578 5.242 79: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_1__pme_cpu.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu (502 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto 79: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 2 MPI threads 79: Using 2 OpenMP threads per tMPI thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc-and-methanol' 79: 20 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 3.790 0.948 399.9 79: (ns/day) (hour/ns) 79: Performance: 1.914 12.537 79: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_1__pme_auto.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto (960 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 79: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 79: Test is being skipped because: 79: it targets GPU execution, but no compatible devices were detected 79: PME GPU does not support: 79: Double-precision build of GROMACS. 79: Non-GPU build of GROMACS. 79: 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 79: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 79: Test is being skipped because: 79: it targets GPU execution, but no compatible devices were detected 79: PME GPU does not support: 79: Double-precision build of GROMACS. 79: Non-GPU build of GROMACS. 79: 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 79: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 79: Test is being skipped because: 79: it targets GPU execution, but no compatible devices were detected 79: PME GPU does not support: 79: Double-precision build of GROMACS. 79: Non-GPU build of GROMACS. 79: 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto (0 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu 79: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 2 MPI threads 79: Using 2 OpenMP threads per tMPI thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc-and-methanol' 79: 0 steps, 0.0 ps. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.018 0.005 385.5 79: (ns/day) (hour/ns) 79: Performance: 18.018 1.332 79: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_1__pme_cpu.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu (420 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 79: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 79: Test is being skipped because: 79: it targets GPU execution, but no compatible devices were detected 79: PME GPU does not support: 79: Double-precision build of GROMACS. 79: Non-GPU build of GROMACS. 79: 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 79: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 79: Test is being skipped because: 79: it targets GPU execution, but no compatible devices were detected 79: PME GPU does not support: 79: Double-precision build of GROMACS. 79: Non-GPU build of GROMACS. 79: 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu 79: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 2 MPI threads 79: Using 2 OpenMP threads per tMPI thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc-and-methanol' 79: 20 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: 79: Dynamic load balancing report: 79: DLB was off during the run due to low measured imbalance. 79: Average load imbalance: 7.8%. 79: The balanceable part of the MD step is 6%, load imbalance is computed from this. 79: Part of the total run time spent waiting due to load imbalance: 0.5%. 79: 79: 79: NOTE: 49 % of the run time was spent communicating energies, 79: you might want to increase some nst* mdp options 79: 79: Core t (s) Wall t (s) (%) 79: Time: 3.624 0.906 399.9 79: (ns/day) (hour/ns) 79: Performance: 2.002 11.987 79: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__tunepme__npme_0__pme_cpu.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu (942 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 79: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 79: Test is being skipped because: 79: it targets GPU execution, but no compatible devices were detected 79: it targets PME decomposition, but that is not supported 79: PME GPU does not support: 79: Double-precision build of GROMACS. 79: Non-GPU build of GROMACS. 79: 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu (4 ms) 79: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 79: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 79: Test is being skipped because: 79: it targets GPU execution, but no compatible devices were detected 79: it targets PME decomposition, but that is not supported 79: PME GPU does not support: 79: Double-precision build of GROMACS. 79: Non-GPU build of GROMACS. 79: 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 79: [----------] 19 tests from ReproducesEnergies/PmeTest (3578 ms total) 79: 79: [----------] Global test environment tear-down 79: [==========] 19 tests from 1 test suite ran. (3707 ms total) 79: [ PASSED ] 7 tests. 79: [ SKIPPED ] 12 tests, listed below: 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 79: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 79/90 Test #79: MdrunMpi2RankPmeTests ..................... Passed 3.75 sec test 80 Start 80: MdrunCoordinationBasicTests1Rank 80: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/mdrun-coordination-basic-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/MdrunCoordinationBasicTests1Rank.xml" 80: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests 80: Test timeout computed to be: 1920 80: [==========] Running 1 test from 1 test suite. 80: [----------] Global test environment set-up. 80: [----------] 1 test from BasicPropagators/PeriodicActionsTest 80: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 1 OpenMP thread 80: 80: 80: NOTE: Thread affinity was not set. 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 1.098 1.098 100.0 80: (ns/day) (hour/ns) 80: Performance: 1.338 17.937 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 1 OpenMP thread 80: 80: 80: NOTE: Thread affinity was not set. 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.785 0.785 100.0 80: (ns/day) (hour/ns) 80: Performance: 1.872 12.820 80: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: COM removal frequency is set to (1). 80: Other settings require a global communication frequency of 4. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 4. 80: 80: 80: There were 5 NOTEs 80: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 1 OpenMP thread 80: 80: 80: NOTE: Thread affinity was not set. 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 1.028 1.028 100.0 80: (ns/day) (hour/ns) 80: Performance: 1.428 16.802 80: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: COM removal frequency is set to (1). 80: Other settings require a global communication frequency of 100. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 100. 80: 80: 80: There were 4 NOTEs 80: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 1 OpenMP thread 80: 80: 80: NOTE: Thread affinity was not set. 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 1.742 1.742 100.0 80: (ns/day) (hour/ns) 80: Performance: 0.843 28.469 80: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: COM removal frequency is set to (1). 80: Other settings require a global communication frequency of 100. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 100. 80: 80: 80: There were 4 NOTEs 80: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 1 OpenMP thread 80: 80: 80: NOTE: Thread affinity was not set. 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 1.042 1.042 100.0 80: (ns/day) (hour/ns) 80: Performance: 1.409 17.028 80: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: COM removal frequency is set to (1). 80: Other settings require a global communication frequency of 100. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 100. 80: 80: 80: There were 4 NOTEs 80: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 1 OpenMP thread 80: 80: 80: NOTE: Thread affinity was not set. 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.691 0.691 100.0 80: (ns/day) (hour/ns) 80: Performance: 2.124 11.298 80: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 80: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (7108 ms) 80: [----------] 1 test from BasicPropagators/PeriodicActionsTest (7108 ms total) 80: 80: [----------] Global test environment tear-down 80: [==========] 1 test from 1 test suite ran. (7247 ms total) 80: [ PASSED ] 1 test. 80/90 Test #80: MdrunCoordinationBasicTests1Rank .......... Passed 7.30 sec test 81 Start 81: MdrunCoordinationBasicTests2Ranks 81: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/mdrun-coordination-basic-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/MdrunCoordinationBasicTests2Ranks.xml" 81: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests 81: Test timeout computed to be: 1920 81: [==========] Running 1 test from 1 test suite. 81: [----------] Global test environment set-up. 81: [----------] 1 test from BasicPropagators/PeriodicActionsTest 81: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 1 OpenMP thread per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 2.3%. 81: The balanceable part of the MD step is 53%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 1.2%. 81: 81: 81: NOTE: 50 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 1.696 0.848 200.0 81: (ns/day) (hour/ns) 81: Performance: 1.732 13.858 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 1 OpenMP thread per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 1.8%. 81: The balanceable part of the MD step is 31%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 0.6%. 81: 81: 81: NOTE: 50 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 1.516 0.758 200.0 81: (ns/day) (hour/ns) 81: Performance: 1.937 12.388 81: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: COM removal frequency is set to (1). 81: Other settings require a global communication frequency of 4. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 4. 81: 81: 81: There were 5 NOTEs 81: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 1 OpenMP thread per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was turned on during the run due to measured imbalance. 81: Average load imbalance: 4.9%. 81: The balanceable part of the MD step is 43%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 2.1%. 81: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 81: 81: 81: NOTE: 49 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.577 0.292 197.6 81: (ns/day) (hour/ns) 81: Performance: 5.031 4.771 81: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: COM removal frequency is set to (1). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 1 OpenMP thread per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 2.4%. 81: The balanceable part of the MD step is 44%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 1.0%. 81: 81: 81: NOTE: 50 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 1.492 0.746 200.0 81: (ns/day) (hour/ns) 81: Performance: 1.969 12.190 81: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: COM removal frequency is set to (1). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 1 OpenMP thread per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 1.8%. 81: The balanceable part of the MD step is 24%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 0.4%. 81: 81: 81: NOTE: 48 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.047 0.023 198.8 81: (ns/day) (hour/ns) 81: Performance: 62.674 0.383 81: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: COM removal frequency is set to (1). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 4 NOTEs 81: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 1 OpenMP thread per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 0.9%. 81: The balanceable part of the MD step is 39%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 0.4%. 81: 81: 81: NOTE: 47 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.028 0.014 198.2 81: (ns/day) (hour/ns) 81: Performance: 105.676 0.227 81: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 81: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (3681 ms) 81: [----------] 1 test from BasicPropagators/PeriodicActionsTest (3681 ms total) 81: 81: [----------] Global test environment tear-down 81: [==========] 1 test from 1 test suite ran. (3752 ms total) 81: [ PASSED ] 1 test. 81/90 Test #81: MdrunCoordinationBasicTests2Ranks ......... Passed 3.77 sec test 82 Start 82: MdrunCoordinationCouplingTests1Rank 82: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/mdrun-coordination-coupling-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/MdrunCoordinationCouplingTests1Rank.xml" 82: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests 82: Test timeout computed to be: 1920 82: [==========] Running 25 tests from 1 test suite. 82: [----------] Global test environment set-up. 82: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.021 0.021 99.6 82: (ns/day) (hour/ns) 82: Performance: 70.020 0.343 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.014 0.014 99.4 82: (ns/day) (hour/ns) 82: Performance: 105.867 0.227 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 4. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 4. 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.011 0.011 99.1 82: (ns/day) (hour/ns) 82: Performance: 137.161 0.175 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.027 0.027 99.7 82: (ns/day) (hour/ns) 82: Performance: 53.752 0.446 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.019 0.019 99.6 82: (ns/day) (hour/ns) 82: Performance: 76.338 0.314 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.032 0.032 99.5 82: (ns/day) (hour/ns) 82: Performance: 45.727 0.525 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (204 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.022 0.022 99.7 82: (ns/day) (hour/ns) 82: Performance: 65.523 0.366 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.013 0.013 99.4 82: (ns/day) (hour/ns) 82: Performance: 110.383 0.217 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.011 0.011 99.4 82: (ns/day) (hour/ns) 82: Performance: 133.673 0.180 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.024 0.024 99.7 82: (ns/day) (hour/ns) 82: Performance: 61.545 0.390 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.178 0.179 99.9 82: (ns/day) (hour/ns) 82: Performance: 8.226 2.918 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.020 0.020 99.6 82: (ns/day) (hour/ns) 82: Performance: 73.170 0.328 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (347 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.018 0.018 99.5 82: (ns/day) (hour/ns) 82: Performance: 80.214 0.299 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.019 0.019 99.5 82: (ns/day) (hour/ns) 82: Performance: 76.466 0.314 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.011 0.011 99.2 82: (ns/day) (hour/ns) 82: Performance: 136.007 0.176 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.019 0.019 99.6 82: (ns/day) (hour/ns) 82: Performance: 77.912 0.308 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.032 0.032 99.7 82: (ns/day) (hour/ns) 82: Performance: 46.136 0.520 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.028 0.028 99.6 82: (ns/day) (hour/ns) 82: Performance: 51.951 0.462 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (225 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.025 0.025 99.7 82: (ns/day) (hour/ns) 82: Performance: 58.189 0.412 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.031 0.031 99.7 82: (ns/day) (hour/ns) 82: Performance: 47.914 0.501 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.021 0.022 97.2 82: (ns/day) (hour/ns) 82: Performance: 66.464 0.361 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.036 0.036 99.7 82: (ns/day) (hour/ns) 82: Performance: 41.169 0.583 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.040 0.040 99.8 82: (ns/day) (hour/ns) 82: Performance: 36.897 0.650 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.015 0.015 99.5 82: (ns/day) (hour/ns) 82: Performance: 95.737 0.251 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (305 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.020 0.020 99.7 82: (ns/day) (hour/ns) 82: Performance: 73.508 0.326 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.026 0.026 99.7 82: (ns/day) (hour/ns) 82: Performance: 56.545 0.424 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.022 0.022 99.7 82: (ns/day) (hour/ns) 82: Performance: 67.336 0.356 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.033 0.033 99.8 82: (ns/day) (hour/ns) 82: Performance: 44.876 0.535 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.016 0.016 99.4 82: (ns/day) (hour/ns) 82: Performance: 90.241 0.266 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.028 0.028 99.7 82: (ns/day) (hour/ns) 82: Performance: 52.312 0.459 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (249 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.034 0.034 99.8 82: (ns/day) (hour/ns) 82: Performance: 43.118 0.557 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.012 0.012 99.4 82: (ns/day) (hour/ns) 82: Performance: 124.580 0.193 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.035 0.036 99.6 82: (ns/day) (hour/ns) 82: Performance: 41.271 0.582 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.028 0.028 99.5 82: (ns/day) (hour/ns) 82: Performance: 52.659 0.456 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.025 0.025 99.4 82: (ns/day) (hour/ns) 82: Performance: 58.969 0.407 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.036 0.036 99.6 82: (ns/day) (hour/ns) 82: Performance: 40.945 0.586 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (338 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.019 0.019 98.9 82: (ns/day) (hour/ns) 82: Performance: 77.866 0.308 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.026 0.026 99.6 82: (ns/day) (hour/ns) 82: Performance: 56.435 0.425 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.036 0.036 99.7 82: (ns/day) (hour/ns) 82: Performance: 40.444 0.593 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.022 0.022 99.1 82: (ns/day) (hour/ns) 82: Performance: 65.771 0.365 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.033 0.033 99.7 82: (ns/day) (hour/ns) 82: Performance: 44.179 0.543 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.024 0.024 99.6 82: (ns/day) (hour/ns) 82: Performance: 61.218 0.392 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (287 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.036 0.036 99.7 82: (ns/day) (hour/ns) 82: Performance: 40.256 0.596 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.021 0.021 99.6 82: (ns/day) (hour/ns) 82: Performance: 68.745 0.349 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.029 0.029 99.7 82: (ns/day) (hour/ns) 82: Performance: 50.238 0.478 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.032 0.032 99.7 82: (ns/day) (hour/ns) 82: Performance: 46.105 0.521 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.045 0.045 99.8 82: (ns/day) (hour/ns) 82: Performance: 32.936 0.729 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.020 0.020 99.5 82: (ns/day) (hour/ns) 82: Performance: 72.518 0.331 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (312 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.019 0.019 99.4 82: (ns/day) (hour/ns) 82: Performance: 77.193 0.311 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.018 0.018 99.2 82: (ns/day) (hour/ns) 82: Performance: 79.982 0.300 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.020 0.021 99.7 82: (ns/day) (hour/ns) 82: Performance: 71.616 0.335 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.019 0.019 99.6 82: (ns/day) (hour/ns) 82: Performance: 75.942 0.316 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.021 0.021 99.6 82: (ns/day) (hour/ns) 82: Performance: 70.454 0.341 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.041 0.041 99.8 82: (ns/day) (hour/ns) 82: Performance: 35.944 0.668 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (248 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.020 0.020 99.2 82: (ns/day) (hour/ns) 82: Performance: 74.091 0.324 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.011 0.011 99.4 82: (ns/day) (hour/ns) 82: Performance: 129.476 0.185 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.013 0.013 99.1 82: (ns/day) (hour/ns) 82: Performance: 114.350 0.210 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.022 0.022 99.6 82: (ns/day) (hour/ns) 82: Performance: 67.520 0.355 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.016 0.016 99.5 82: (ns/day) (hour/ns) 82: Performance: 89.701 0.268 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.020 0.020 99.5 82: (ns/day) (hour/ns) 82: Performance: 73.338 0.327 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (202 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.019 0.019 99.5 82: (ns/day) (hour/ns) 82: Performance: 76.628 0.313 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.018 0.018 99.5 82: (ns/day) (hour/ns) 82: Performance: 81.349 0.295 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.010 0.010 99.1 82: (ns/day) (hour/ns) 82: Performance: 152.237 0.158 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.038 0.038 99.7 82: (ns/day) (hour/ns) 82: Performance: 38.864 0.618 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.020 0.020 99.0 82: (ns/day) (hour/ns) 82: Performance: 73.376 0.327 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.027 0.027 99.6 82: (ns/day) (hour/ns) 82: Performance: 54.538 0.440 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (242 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.032 0.032 99.7 82: (ns/day) (hour/ns) 82: Performance: 45.509 0.527 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.016 0.016 99.5 82: (ns/day) (hour/ns) 82: Performance: 93.555 0.257 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.015 0.015 99.5 82: (ns/day) (hour/ns) 82: Performance: 99.638 0.241 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.031 0.031 99.7 82: (ns/day) (hour/ns) 82: Performance: 47.760 0.503 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.044 0.045 99.7 82: (ns/day) (hour/ns) 82: Performance: 32.965 0.728 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.025 0.025 99.6 82: (ns/day) (hour/ns) 82: Performance: 58.076 0.413 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (290 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.018 0.018 99.5 82: (ns/day) (hour/ns) 82: Performance: 82.091 0.292 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.018 0.018 99.5 82: (ns/day) (hour/ns) 82: Performance: 83.050 0.289 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 4. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 4. 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.010 0.010 99.3 82: (ns/day) (hour/ns) 82: Performance: 140.441 0.171 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.027 0.027 99.5 82: (ns/day) (hour/ns) 82: Performance: 53.982 0.445 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.030 0.031 99.8 82: (ns/day) (hour/ns) 82: Performance: 48.073 0.499 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.032 0.032 99.7 82: (ns/day) (hour/ns) 82: Performance: 46.189 0.520 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (268 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.030 0.031 99.7 82: (ns/day) (hour/ns) 82: Performance: 48.034 0.500 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.032 0.033 99.5 82: (ns/day) (hour/ns) 82: Performance: 45.139 0.532 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.037 0.037 99.8 82: (ns/day) (hour/ns) 82: Performance: 39.369 0.610 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.024 0.024 99.5 82: (ns/day) (hour/ns) 82: Performance: 61.321 0.391 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.026 0.026 99.6 82: (ns/day) (hour/ns) 82: Performance: 57.231 0.419 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.021 0.021 99.7 82: (ns/day) (hour/ns) 82: Performance: 68.353 0.351 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (266 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.015 0.015 99.5 82: (ns/day) (hour/ns) 82: Performance: 96.249 0.249 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.020 0.021 99.5 82: (ns/day) (hour/ns) 82: Performance: 71.522 0.336 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.027 0.027 99.6 82: (ns/day) (hour/ns) 82: Performance: 55.053 0.436 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.035 0.035 99.8 82: (ns/day) (hour/ns) 82: Performance: 41.528 0.578 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.020 0.020 99.6 82: (ns/day) (hour/ns) 82: Performance: 73.713 0.326 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.019 0.019 99.6 82: (ns/day) (hour/ns) 82: Performance: 78.238 0.307 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (250 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.022 0.022 99.6 82: (ns/day) (hour/ns) 82: Performance: 66.695 0.360 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.023 0.023 99.5 82: (ns/day) (hour/ns) 82: Performance: 63.431 0.378 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.019 0.019 99.2 82: (ns/day) (hour/ns) 82: Performance: 78.588 0.305 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.022 0.022 98.7 82: (ns/day) (hour/ns) 82: Performance: 67.327 0.356 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.027 0.027 99.6 82: (ns/day) (hour/ns) 82: Performance: 53.955 0.445 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.023 0.023 99.6 82: (ns/day) (hour/ns) 82: Performance: 64.103 0.374 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (232 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.035 0.035 99.8 82: (ns/day) (hour/ns) 82: Performance: 41.823 0.574 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.027 0.027 99.6 82: (ns/day) (hour/ns) 82: Performance: 54.271 0.442 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 4. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 4. 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.019 0.020 99.4 82: (ns/day) (hour/ns) 82: Performance: 75.120 0.319 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.023 0.023 99.7 82: (ns/day) (hour/ns) 82: Performance: 62.618 0.383 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.022 0.022 99.7 82: (ns/day) (hour/ns) 82: Performance: 67.700 0.355 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.024 0.024 99.6 82: (ns/day) (hour/ns) 82: Performance: 60.127 0.399 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (228 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.026 0.026 99.6 82: (ns/day) (hour/ns) 82: Performance: 57.314 0.419 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.023 0.023 99.7 82: (ns/day) (hour/ns) 82: Performance: 63.721 0.377 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.026 0.026 99.7 82: (ns/day) (hour/ns) 82: Performance: 56.076 0.428 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.032 0.032 99.7 82: (ns/day) (hour/ns) 82: Performance: 46.231 0.519 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.047 0.047 99.8 82: (ns/day) (hour/ns) 82: Performance: 31.021 0.774 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.030 0.030 99.7 82: (ns/day) (hour/ns) 82: Performance: 48.268 0.497 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (305 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.055 0.055 99.9 82: (ns/day) (hour/ns) 82: Performance: 26.765 0.897 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.020 0.020 99.6 82: (ns/day) (hour/ns) 82: Performance: 72.034 0.333 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.017 0.017 99.6 82: (ns/day) (hour/ns) 82: Performance: 87.934 0.273 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.024 0.024 99.7 82: (ns/day) (hour/ns) 82: Performance: 60.474 0.397 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.034 0.034 99.8 82: (ns/day) (hour/ns) 82: Performance: 43.505 0.552 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.028 0.028 99.8 82: (ns/day) (hour/ns) 82: Performance: 52.347 0.458 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (276 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.020 0.020 99.5 82: (ns/day) (hour/ns) 82: Performance: 74.210 0.323 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.016 0.016 99.4 82: (ns/day) (hour/ns) 82: Performance: 93.117 0.258 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.103 0.103 99.6 82: (ns/day) (hour/ns) 82: Performance: 14.216 1.688 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 1.213 1.213 100.0 82: (ns/day) (hour/ns) 82: Performance: 1.211 19.821 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 1.166 1.166 100.0 82: (ns/day) (hour/ns) 82: Performance: 1.259 19.058 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 1.272 1.272 100.0 82: (ns/day) (hour/ns) 82: Performance: 1.155 20.779 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (4578 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 1.336 1.336 100.0 82: (ns/day) (hour/ns) 82: Performance: 1.099 21.829 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.848 0.848 100.0 82: (ns/day) (hour/ns) 82: Performance: 1.732 13.860 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.025 0.025 99.5 82: (ns/day) (hour/ns) 82: Performance: 58.916 0.407 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.022 0.023 99.0 82: (ns/day) (hour/ns) 82: Performance: 64.690 0.371 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.032 0.032 99.7 82: (ns/day) (hour/ns) 82: Performance: 45.270 0.530 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.021 0.021 99.4 82: (ns/day) (hour/ns) 82: Performance: 69.445 0.346 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (3471 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.019 0.019 99.5 82: (ns/day) (hour/ns) 82: Performance: 75.479 0.318 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.015 0.015 99.3 82: (ns/day) (hour/ns) 82: Performance: 100.445 0.239 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.011 0.011 99.0 82: (ns/day) (hour/ns) 82: Performance: 130.336 0.184 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.031 0.031 99.7 82: (ns/day) (hour/ns) 82: Performance: 46.740 0.513 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.034 0.034 99.6 82: (ns/day) (hour/ns) 82: Performance: 42.595 0.563 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.031 0.031 99.7 82: (ns/day) (hour/ns) 82: Performance: 47.301 0.507 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (254 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.026 0.026 99.1 82: (ns/day) (hour/ns) 82: Performance: 56.203 0.427 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.013 0.014 99.3 82: (ns/day) (hour/ns) 82: Performance: 108.641 0.221 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.030 0.030 99.6 82: (ns/day) (hour/ns) 82: Performance: 49.202 0.488 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.043 0.043 98.6 82: (ns/day) (hour/ns) 82: Performance: 33.799 0.710 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 1.103 1.103 100.0 82: (ns/day) (hour/ns) 82: Performance: 1.332 18.018 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 1.575 1.575 100.0 82: (ns/day) (hour/ns) 82: Performance: 0.933 25.732 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 (2981 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: MTTK coupling is deprecated and will soon be removed 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: for current Trotter decomposition methods with vv, nsttcouple and 82: nstpcouple must be equal. Both have been reset to 82: min(nsttcouple,nstpcouple) = 2 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 1.193 1.193 100.0 82: (ns/day) (hour/ns) 82: Performance: 1.231 19.499 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: MTTK coupling is deprecated and will soon be removed 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: for current Trotter decomposition methods with vv, nsttcouple and 82: nstpcouple must be equal. Both have been reset to 82: min(nsttcouple,nstpcouple) = 2 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 2.749 2.749 100.0 82: (ns/day) (hour/ns) 82: Performance: 0.534 44.916 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: MTTK coupling is deprecated and will soon be removed 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: for current Trotter decomposition methods with vv, nsttcouple and 82: nstpcouple must be equal. Both have been reset to 82: min(nsttcouple,nstpcouple) = 2 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 5 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 1.135 1.135 100.0 82: (ns/day) (hour/ns) 82: Performance: 1.294 18.545 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: MTTK coupling is deprecated and will soon be removed 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: for current Trotter decomposition methods with vv, nsttcouple and 82: nstpcouple must be equal. Both have been reset to 82: min(nsttcouple,nstpcouple) = 2 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 5 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.765 0.765 100.0 82: (ns/day) (hour/ns) 82: Performance: 1.919 12.504 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: MTTK coupling is deprecated and will soon be removed 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: for current Trotter decomposition methods with vv, nsttcouple and 82: nstpcouple must be equal. Both have been reset to 82: min(nsttcouple,nstpcouple) = 2 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 5 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 1.176 1.176 100.0 82: (ns/day) (hour/ns) 82: Performance: 1.248 19.223 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: MTTK coupling is deprecated and will soon be removed 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: for current Trotter decomposition methods with vv, nsttcouple and 82: nstpcouple must be equal. Both have been reset to 82: min(nsttcouple,nstpcouple) = 2 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 5 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.757 0.757 100.0 82: (ns/day) (hour/ns) 82: Performance: 1.940 12.371 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 (8907 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.052 0.052 99.7 82: (ns/day) (hour/ns) 82: Performance: 28.327 0.847 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.051 0.051 99.8 82: (ns/day) (hour/ns) 82: Performance: 28.964 0.829 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.059 0.059 99.8 82: (ns/day) (hour/ns) 82: Performance: 24.907 0.964 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.044 0.044 99.7 82: (ns/day) (hour/ns) 82: Performance: 33.069 0.726 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.059 0.060 99.8 82: (ns/day) (hour/ns) 82: Performance: 24.661 0.973 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 82: 82: Using 1 MPI thread 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.035 0.035 99.7 82: (ns/day) (hour/ns) 82: Performance: 42.022 0.571 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 (450 ms) 82: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest (25730 ms total) 82: 82: [----------] Global test environment tear-down 82: [==========] 25 tests from 1 test suite ran. (25841 ms total) 82: [ PASSED ] 25 tests. 82/90 Test #82: MdrunCoordinationCouplingTests1Rank ....... Passed 25.87 sec test 83 Start 83: MdrunCoordinationCouplingTests2Ranks 83: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/mdrun-coordination-coupling-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/MdrunCoordinationCouplingTests2Ranks.xml" 83: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests 83: Test timeout computed to be: 1920 83: [==========] Running 25 tests from 1 test suite. 83: [----------] Global test environment set-up. 83: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.1%. 83: The balanceable part of the MD step is 49%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.0%. 83: 83: 83: NOTE: 49 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.112 0.056 199.6 83: (ns/day) (hour/ns) 83: Performance: 26.063 0.921 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 0.9%. 83: The balanceable part of the MD step is 2%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.0%. 83: 83: 83: NOTE: 40 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.139 0.070 199.7 83: (ns/day) (hour/ns) 83: Performance: 21.033 1.141 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 4. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 4. 83: 83: 83: There were 4 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 3.0%. 83: The balanceable part of the MD step is 42%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.3%. 83: 83: 83: NOTE: 51 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.099 0.050 199.5 83: (ns/day) (hour/ns) 83: Performance: 29.457 0.815 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 4 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 5.1%. 83: The balanceable part of the MD step is 35%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.8%. 83: 83: 83: NOTE: 49 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.097 0.048 199.4 83: (ns/day) (hour/ns) 83: Performance: 30.304 0.792 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 4 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was turned on during the run due to measured imbalance. 83: Average load imbalance: 6.8%. 83: The balanceable part of the MD step is 34%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 2.3%. 83: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 83: 83: 83: NOTE: 49 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.130 0.065 199.5 83: (ns/day) (hour/ns) 83: Performance: 22.581 1.063 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 4 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 3.3%. 83: The balanceable part of the MD step is 35%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.2%. 83: 83: 83: NOTE: 51 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.086 0.043 199.3 83: (ns/day) (hour/ns) 83: Performance: 34.134 0.703 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (729 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was turned on during the run due to measured imbalance. 83: Average load imbalance: 6.1%. 83: The balanceable part of the MD step is 33%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 2.0%. 83: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 83: 83: 83: NOTE: 22 % of the run time was spent in domain decomposition, 83: 0 % of the run time was spent in pair search, 83: you might want to increase nstlist (this has no effect on accuracy) 83: 83: NOTE: 37 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.134 0.086 155.7 83: (ns/day) (hour/ns) 83: Performance: 17.057 1.407 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was turned on during the run due to measured imbalance. 83: Average load imbalance: 20.8%. 83: The balanceable part of the MD step is 44%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 9.1%. 83: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 83: 83: NOTE: 9.1 % of the available CPU time was lost due to load imbalance 83: in the domain decomposition. 83: You can consider manually changing the decomposition (option -dd); 83: e.g. by using fewer domains along the box dimension in which there is 83: considerable inhomogeneity in the simulated system. 83: 83: NOTE: 43 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.241 0.135 177.9 83: (ns/day) (hour/ns) 83: Performance: 10.864 2.209 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.1%. 83: The balanceable part of the MD step is 40%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.5%. 83: 83: 83: NOTE: 49 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.107 0.054 199.4 83: (ns/day) (hour/ns) 83: Performance: 27.306 0.879 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 0.3%. 83: The balanceable part of the MD step is 42%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.1%. 83: 83: 83: NOTE: 48 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.075 0.038 198.0 83: (ns/day) (hour/ns) 83: Performance: 38.646 0.621 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was turned on during the run due to measured imbalance. 83: Average load imbalance: 7.4%. 83: The balanceable part of the MD step is 39%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 2.9%. 83: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 83: 83: 83: NOTE: 59 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.159 0.085 186.4 83: (ns/day) (hour/ns) 83: Performance: 17.204 1.395 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.5%. 83: The balanceable part of the MD step is 43%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.1%. 83: 83: 83: NOTE: 47 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.095 0.053 180.3 83: (ns/day) (hour/ns) 83: Performance: 27.846 0.862 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (1398 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.2%. 83: The balanceable part of the MD step is 45%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.5%. 83: 83: 83: NOTE: 53 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.700 0.381 183.6 83: (ns/day) (hour/ns) 83: Performance: 3.853 6.229 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was turned on during the run due to measured imbalance. 83: Average load imbalance: 24.5%. 83: The balanceable part of the MD step is 35%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 8.5%. 83: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 83: 83: NOTE: 8.5 % of the available CPU time was lost due to load imbalance 83: in the domain decomposition. 83: You can consider manually changing the decomposition (option -dd); 83: e.g. by using fewer domains along the box dimension in which there is 83: considerable inhomogeneity in the simulated system. 83: 83: NOTE: 38 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.803 0.455 176.2 83: (ns/day) (hour/ns) 83: Performance: 3.225 7.442 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was turned on during the run due to measured imbalance. 83: Average load imbalance: 31.0%. 83: The balanceable part of the MD step is 21%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 6.4%. 83: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 83: 83: NOTE: 6.4 % of the available CPU time was lost due to load imbalance 83: in the domain decomposition. 83: You can consider manually changing the decomposition (option -dd); 83: e.g. by using fewer domains along the box dimension in which there is 83: considerable inhomogeneity in the simulated system. 83: 83: NOTE: 22 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.313 0.157 199.8 83: (ns/day) (hour/ns) 83: Performance: 9.368 2.562 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 0.9%. 83: The balanceable part of the MD step is 41%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.4%. 83: 83: 83: NOTE: 48 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.065 0.033 198.4 83: (ns/day) (hour/ns) 83: Performance: 44.821 0.535 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 0.8%. 83: The balanceable part of the MD step is 4%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.0%. 83: 83: 83: NOTE: 34 % of the run time was spent in domain decomposition, 83: 2 % of the run time was spent in pair search, 83: you might want to increase nstlist (this has no effect on accuracy) 83: 83: NOTE: 30 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.057 0.028 199.3 83: (ns/day) (hour/ns) 83: Performance: 51.563 0.465 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 11.1%. 83: The balanceable part of the MD step is 2%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.2%. 83: 83: 83: NOTE: 43 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.190 0.095 199.6 83: (ns/day) (hour/ns) 83: Performance: 15.415 1.557 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (1770 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 3.3%. 83: The balanceable part of the MD step is 4%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.1%. 83: 83: 83: NOTE: 37 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.157 0.079 199.4 83: (ns/day) (hour/ns) 83: Performance: 18.674 1.285 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.0%. 83: The balanceable part of the MD step is 2%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.0%. 83: 83: 83: NOTE: 35 % of the run time was spent in domain decomposition, 83: 0 % of the run time was spent in pair search, 83: you might want to increase nstlist (this has no effect on accuracy) 83: 83: NOTE: 31 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.151 0.075 199.5 83: (ns/day) (hour/ns) 83: Performance: 19.471 1.233 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 14.0%. 83: The balanceable part of the MD step is 10%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.4%. 83: 83: 83: NOTE: 55 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.305 0.172 176.7 83: (ns/day) (hour/ns) 83: Performance: 8.522 2.816 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 5.0%. 83: The balanceable part of the MD step is 8%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.4%. 83: 83: 83: NOTE: 48 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.084 0.042 199.5 83: (ns/day) (hour/ns) 83: Performance: 34.782 0.690 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was turned on during the run due to measured imbalance. 83: Average load imbalance: 16.2%. 83: The balanceable part of the MD step is 28%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 4.5%. 83: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 83: 83: 83: NOTE: 57 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.314 0.157 199.7 83: (ns/day) (hour/ns) 83: Performance: 9.346 2.568 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.4%. 83: The balanceable part of the MD step is 43%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.6%. 83: 83: 83: NOTE: 49 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.093 0.046 199.5 83: (ns/day) (hour/ns) 83: Performance: 31.608 0.759 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (1218 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 73 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.192 0.129 148.9 83: (ns/day) (hour/ns) 83: Performance: 11.379 2.109 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 48 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.048 0.024 198.8 83: (ns/day) (hour/ns) 83: Performance: 60.282 0.398 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 47 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.093 0.047 199.2 83: (ns/day) (hour/ns) 83: Performance: 31.529 0.761 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 62 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.105 0.057 185.3 83: (ns/day) (hour/ns) 83: Performance: 25.877 0.927 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 47 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 1.525 0.763 200.0 83: (ns/day) (hour/ns) 83: Performance: 1.926 12.463 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 49 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.080 0.040 199.2 83: (ns/day) (hour/ns) 83: Performance: 36.669 0.655 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (2512 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 53 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.075 0.038 199.3 83: (ns/day) (hour/ns) 83: Performance: 39.074 0.614 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 60 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.077 0.039 198.4 83: (ns/day) (hour/ns) 83: Performance: 38.074 0.630 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 25 % of the run time was spent in domain decomposition, 83: 0 % of the run time was spent in pair search, 83: you might want to increase nstlist (this has no effect on accuracy) 83: 83: NOTE: 36 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.083 0.041 199.5 83: (ns/day) (hour/ns) 83: Performance: 35.450 0.677 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 49 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.088 0.044 199.2 83: (ns/day) (hour/ns) 83: Performance: 33.136 0.724 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 49 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.111 0.060 186.2 83: (ns/day) (hour/ns) 83: Performance: 24.665 0.973 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 40 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.090 0.054 166.7 83: (ns/day) (hour/ns) 83: Performance: 27.048 0.887 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (522 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 36 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.141 0.070 199.6 83: (ns/day) (hour/ns) 83: Performance: 20.837 1.152 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 30 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.061 0.032 192.3 83: (ns/day) (hour/ns) 83: Performance: 46.257 0.519 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 47 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.040 0.020 198.9 83: (ns/day) (hour/ns) 83: Performance: 73.801 0.325 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 49 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.085 0.043 198.8 83: (ns/day) (hour/ns) 83: Performance: 34.337 0.699 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 52 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.116 0.058 199.3 83: (ns/day) (hour/ns) 83: Performance: 25.213 0.952 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 57 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.113 0.078 144.2 83: (ns/day) (hour/ns) 83: Performance: 18.772 1.279 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (890 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 53 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.095 0.048 199.2 83: (ns/day) (hour/ns) 83: Performance: 30.640 0.783 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 50 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.065 0.033 198.9 83: (ns/day) (hour/ns) 83: Performance: 45.034 0.533 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 38 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.070 0.036 195.3 83: (ns/day) (hour/ns) 83: Performance: 40.908 0.587 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 49 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.084 0.042 199.3 83: (ns/day) (hour/ns) 83: Performance: 35.033 0.685 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 46 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.079 0.042 185.7 83: (ns/day) (hour/ns) 83: Performance: 34.712 0.691 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 57 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.191 0.096 199.5 83: (ns/day) (hour/ns) 83: Performance: 15.367 1.562 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (669 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 50 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.114 0.057 199.4 83: (ns/day) (hour/ns) 83: Performance: 25.609 0.937 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 48 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.057 0.029 199.1 83: (ns/day) (hour/ns) 83: Performance: 51.511 0.466 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 4 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 45 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.100 0.058 171.7 83: (ns/day) (hour/ns) 83: Performance: 25.249 0.951 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 4 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 49 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.136 0.068 199.5 83: (ns/day) (hour/ns) 83: Performance: 21.616 1.110 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 4 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 53 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.104 0.052 199.6 83: (ns/day) (hour/ns) 83: Performance: 28.211 0.851 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 4 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 49 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.087 0.044 199.5 83: (ns/day) (hour/ns) 83: Performance: 33.674 0.713 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (1042 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 57 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.126 0.063 199.4 83: (ns/day) (hour/ns) 83: Performance: 23.180 1.035 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 48 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.072 0.036 199.3 83: (ns/day) (hour/ns) 83: Performance: 40.876 0.587 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 49 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.104 0.052 199.4 83: (ns/day) (hour/ns) 83: Performance: 28.069 0.855 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 53 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.071 0.036 198.7 83: (ns/day) (hour/ns) 83: Performance: 40.964 0.586 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 49 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.063 0.032 199.2 83: (ns/day) (hour/ns) 83: Performance: 46.622 0.515 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 49 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.088 0.044 199.4 83: (ns/day) (hour/ns) 83: Performance: 33.273 0.721 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (594 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 53 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.069 0.035 199.1 83: (ns/day) (hour/ns) 83: Performance: 42.258 0.568 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 48 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.048 0.024 198.6 83: (ns/day) (hour/ns) 83: Performance: 60.766 0.395 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 53 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.073 0.037 199.2 83: (ns/day) (hour/ns) 83: Performance: 40.150 0.598 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 65 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.093 0.065 142.5 83: (ns/day) (hour/ns) 83: Performance: 22.459 1.069 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 57 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.098 0.049 199.4 83: (ns/day) (hour/ns) 83: Performance: 29.862 0.804 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 50 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.085 0.043 199.1 83: (ns/day) (hour/ns) 83: Performance: 34.446 0.697 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (561 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 43 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.101 0.051 198.8 83: (ns/day) (hour/ns) 83: Performance: 29.018 0.827 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 48 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.064 0.032 199.0 83: (ns/day) (hour/ns) 83: Performance: 45.705 0.525 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 53 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.077 0.039 199.1 83: (ns/day) (hour/ns) 83: Performance: 37.789 0.635 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 60 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.084 0.042 198.7 83: (ns/day) (hour/ns) 83: Performance: 34.906 0.688 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 46 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.065 0.033 199.2 83: (ns/day) (hour/ns) 83: Performance: 45.073 0.532 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 83: 1 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 49 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.095 0.047 199.5 83: (ns/day) (hour/ns) 83: Performance: 30.945 0.776 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (578 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 46 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.114 0.057 199.7 83: (ns/day) (hour/ns) 83: Performance: 25.737 0.933 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 48 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.047 0.024 198.9 83: (ns/day) (hour/ns) 83: Performance: 61.997 0.387 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 4. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 4. 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 49 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.062 0.031 199.3 83: (ns/day) (hour/ns) 83: Performance: 47.504 0.505 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 49 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.078 0.039 199.1 83: (ns/day) (hour/ns) 83: Performance: 37.530 0.639 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 43 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.107 0.054 198.2 83: (ns/day) (hour/ns) 83: Performance: 27.206 0.882 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 51 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.172 0.086 199.7 83: (ns/day) (hour/ns) 83: Performance: 17.079 1.405 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (591 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 47 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.093 0.047 199.0 83: (ns/day) (hour/ns) 83: Performance: 31.490 0.762 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 49 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.079 0.040 199.4 83: (ns/day) (hour/ns) 83: Performance: 37.059 0.648 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 75 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.091 0.052 173.6 83: (ns/day) (hour/ns) 83: Performance: 28.119 0.854 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 48 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.120 0.064 186.7 83: (ns/day) (hour/ns) 83: Performance: 22.863 1.050 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 53 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.072 0.039 183.6 83: (ns/day) (hour/ns) 83: Performance: 37.227 0.645 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 46 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.073 0.037 199.0 83: (ns/day) (hour/ns) 83: Performance: 40.148 0.598 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (600 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 43 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.097 0.049 199.6 83: (ns/day) (hour/ns) 83: Performance: 30.164 0.796 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 48 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.091 0.045 199.5 83: (ns/day) (hour/ns) 83: Performance: 32.305 0.743 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 39 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.071 0.036 199.3 83: (ns/day) (hour/ns) 83: Performance: 41.141 0.583 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 48 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.084 0.044 189.2 83: (ns/day) (hour/ns) 83: Performance: 33.222 0.722 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 49 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.057 0.028 199.3 83: (ns/day) (hour/ns) 83: Performance: 51.603 0.465 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 46 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.030 0.016 192.2 83: (ns/day) (hour/ns) 83: Performance: 92.933 0.258 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (439 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 49 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.678 0.339 200.0 83: (ns/day) (hour/ns) 83: Performance: 4.333 5.539 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 49 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 2.342 1.198 195.5 83: (ns/day) (hour/ns) 83: Performance: 1.226 19.570 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 50 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.759 0.380 199.9 83: (ns/day) (hour/ns) 83: Performance: 3.867 6.206 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 50 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 1.741 0.871 200.0 83: (ns/day) (hour/ns) 83: Performance: 1.687 14.226 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 50 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 2.542 1.271 200.0 83: (ns/day) (hour/ns) 83: Performance: 1.155 20.774 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: NOTE: 53 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.393 0.213 184.9 83: (ns/day) (hour/ns) 83: Performance: 6.901 3.478 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (6940 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.9%. 83: The balanceable part of the MD step is 50%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.4%. 83: 83: 83: Core t (s) Wall t (s) (%) 83: Time: 2.904 1.452 200.0 83: (ns/day) (hour/ns) 83: Performance: 1.011 23.730 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 0.3%. 83: The balanceable part of the MD step is 58%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.2%. 83: 83: 83: Core t (s) Wall t (s) (%) 83: Time: 1.816 0.912 199.2 83: (ns/day) (hour/ns) 83: Performance: 1.611 14.901 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 4. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 4. 83: 83: 83: There were 4 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 3.0%. 83: The balanceable part of the MD step is 47%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.4%. 83: 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.673 0.356 189.4 83: (ns/day) (hour/ns) 83: Performance: 4.132 5.809 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 4 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.3%. 83: The balanceable part of the MD step is 45%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.6%. 83: 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.103 0.052 198.4 83: (ns/day) (hour/ns) 83: Performance: 28.361 0.846 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 4 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was turned on during the run due to measured imbalance. 83: Average load imbalance: 5.3%. 83: The balanceable part of the MD step is 45%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 2.4%. 83: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 83: 83: 83: NOTE: 6 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.137 0.069 199.4 83: (ns/day) (hour/ns) 83: Performance: 21.358 1.124 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 4 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 0.6%. 83: The balanceable part of the MD step is 3%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.0%. 83: 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.186 0.093 199.5 83: (ns/day) (hour/ns) 83: Performance: 15.737 1.525 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (3429 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 0.9%. 83: The balanceable part of the MD step is 12%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.1%. 83: 83: 83: NOTE: 14 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.130 0.065 198.9 83: (ns/day) (hour/ns) 83: Performance: 22.538 1.065 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.2%. 83: The balanceable part of the MD step is 55%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.7%. 83: 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.089 0.044 199.0 83: (ns/day) (hour/ns) 83: Performance: 33.016 0.727 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 3.8%. 83: The balanceable part of the MD step is 51%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.9%. 83: 83: 83: NOTE: 9 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.085 0.043 197.9 83: (ns/day) (hour/ns) 83: Performance: 34.100 0.704 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.1%. 83: The balanceable part of the MD step is 33%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.4%. 83: 83: 83: NOTE: 6 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.163 0.082 198.8 83: (ns/day) (hour/ns) 83: Performance: 17.872 1.343 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.1%. 83: The balanceable part of the MD step is 49%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.0%. 83: 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.081 0.045 180.4 83: (ns/day) (hour/ns) 83: Performance: 32.586 0.737 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.2%. 83: The balanceable part of the MD step is 2%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.0%. 83: 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.144 0.072 199.3 83: (ns/day) (hour/ns) 83: Performance: 20.269 1.184 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (743 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 0.9%. 83: The balanceable part of the MD step is 24%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.2%. 83: 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.069 0.035 198.9 83: (ns/day) (hour/ns) 83: Performance: 42.200 0.569 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 0.3%. 83: The balanceable part of the MD step is 15%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.0%. 83: 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.090 0.046 196.1 83: (ns/day) (hour/ns) 83: Performance: 31.856 0.753 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was turned on during the run due to measured imbalance. 83: Average load imbalance: 37.9%. 83: The balanceable part of the MD step is 32%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 11.9%. 83: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 83: 83: NOTE: 11.9 % of the available CPU time was lost due to load imbalance 83: in the domain decomposition. 83: You can consider manually changing the decomposition (option -dd); 83: e.g. by using fewer domains along the box dimension in which there is 83: considerable inhomogeneity in the simulated system. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.049 0.025 198.5 83: (ns/day) (hour/ns) 83: Performance: 59.672 0.402 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.7%. 83: The balanceable part of the MD step is 50%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.8%. 83: 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.139 0.071 196.6 83: (ns/day) (hour/ns) 83: Performance: 20.826 1.152 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 4.6%. 83: The balanceable part of the MD step is 19%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.9%. 83: 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.110 0.056 196.8 83: (ns/day) (hour/ns) 83: Performance: 26.322 0.912 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.0%. 83: The balanceable part of the MD step is 48%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.5%. 83: 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.106 0.053 198.8 83: (ns/day) (hour/ns) 83: Performance: 27.459 0.874 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (571 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.095 0.048 198.2 83: (ns/day) (hour/ns) 83: Performance: 30.756 0.780 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.062 0.031 198.4 83: (ns/day) (hour/ns) 83: Performance: 46.860 0.512 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.060 0.030 197.6 83: (ns/day) (hour/ns) 83: Performance: 48.487 0.495 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.101 0.051 198.9 83: (ns/day) (hour/ns) 83: Performance: 28.874 0.831 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.062 0.031 198.6 83: (ns/day) (hour/ns) 83: Performance: 46.951 0.511 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.115 0.058 199.2 83: (ns/day) (hour/ns) 83: Performance: 25.466 0.942 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (836 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.094 0.047 199.1 83: (ns/day) (hour/ns) 83: Performance: 31.014 0.774 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.109 0.057 192.1 83: (ns/day) (hour/ns) 83: Performance: 25.792 0.931 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.083 0.044 189.5 83: (ns/day) (hour/ns) 83: Performance: 33.417 0.718 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.098 0.051 191.8 83: (ns/day) (hour/ns) 83: Performance: 28.726 0.835 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.151 0.077 196.6 83: (ns/day) (hour/ns) 83: Performance: 19.131 1.255 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 83: The Berendsen barostat does not generate any strictly correct ensemble, 83: and should not be used for new production simulations (in our opinion). 83: We recommend using the C-rescale barostat instead. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.065 0.034 190.1 83: (ns/day) (hour/ns) 83: Performance: 42.715 0.562 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (541 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.078 0.039 199.0 83: (ns/day) (hour/ns) 83: Performance: 37.507 0.640 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.060 0.032 186.8 83: (ns/day) (hour/ns) 83: Performance: 45.646 0.526 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.034 0.017 197.2 83: (ns/day) (hour/ns) 83: Performance: 84.151 0.285 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.059 0.030 198.8 83: (ns/day) (hour/ns) 83: Performance: 49.448 0.485 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.075 0.038 198.6 83: (ns/day) (hour/ns) 83: Performance: 38.840 0.618 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.173 0.125 138.4 83: (ns/day) (hour/ns) 83: Performance: 11.743 2.044 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (460 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.111 0.060 184.3 83: (ns/day) (hour/ns) 83: Performance: 24.337 0.986 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.062 0.031 197.3 83: (ns/day) (hour/ns) 83: Performance: 46.927 0.511 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.114 0.057 199.1 83: (ns/day) (hour/ns) 83: Performance: 25.693 0.934 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.110 0.055 199.1 83: (ns/day) (hour/ns) 83: Performance: 26.506 0.905 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.089 0.045 199.0 83: (ns/day) (hour/ns) 83: Performance: 32.970 0.728 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.075 0.038 198.6 83: (ns/day) (hour/ns) 83: Performance: 39.110 0.614 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 (607 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: MTTK coupling is deprecated and will soon be removed 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: for current Trotter decomposition methods with vv, nsttcouple and 83: nstpcouple must be equal. Both have been reset to 83: min(nsttcouple,nstpcouple) = 2 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 4 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.102 0.051 198.8 83: (ns/day) (hour/ns) 83: Performance: 28.655 0.838 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: MTTK coupling is deprecated and will soon be removed 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: for current Trotter decomposition methods with vv, nsttcouple and 83: nstpcouple must be equal. Both have been reset to 83: min(nsttcouple,nstpcouple) = 2 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 4 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.130 0.068 192.8 83: (ns/day) (hour/ns) 83: Performance: 21.710 1.105 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: MTTK coupling is deprecated and will soon be removed 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: for current Trotter decomposition methods with vv, nsttcouple and 83: nstpcouple must be equal. Both have been reset to 83: min(nsttcouple,nstpcouple) = 2 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 5 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.078 0.039 198.7 83: (ns/day) (hour/ns) 83: Performance: 37.596 0.638 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: MTTK coupling is deprecated and will soon be removed 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: for current Trotter decomposition methods with vv, nsttcouple and 83: nstpcouple must be equal. Both have been reset to 83: min(nsttcouple,nstpcouple) = 2 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 5 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.087 0.044 198.8 83: (ns/day) (hour/ns) 83: Performance: 33.629 0.714 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: MTTK coupling is deprecated and will soon be removed 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: for current Trotter decomposition methods with vv, nsttcouple and 83: nstpcouple must be equal. Both have been reset to 83: min(nsttcouple,nstpcouple) = 2 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 5 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.088 0.045 195.2 83: (ns/day) (hour/ns) 83: Performance: 32.624 0.736 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: MTTK coupling is deprecated and will soon be removed 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: for current Trotter decomposition methods with vv, nsttcouple and 83: nstpcouple must be equal. Both have been reset to 83: min(nsttcouple,nstpcouple) = 2 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 5 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.091 0.046 198.8 83: (ns/day) (hour/ns) 83: Performance: 31.947 0.751 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 (479 ms) 83: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.078 0.039 198.9 83: (ns/day) (hour/ns) 83: Performance: 37.262 0.644 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.075 0.038 198.5 83: (ns/day) (hour/ns) 83: Performance: 38.875 0.617 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.078 0.039 198.9 83: (ns/day) (hour/ns) 83: Performance: 37.571 0.639 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.082 0.041 199.0 83: (ns/day) (hour/ns) 83: Performance: 35.787 0.671 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.133 0.067 197.6 83: (ns/day) (hour/ns) 83: Performance: 21.893 1.096 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: There were 2 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 83: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 83: 83: Using 2 MPI threads 83: Using 1 OpenMP thread per tMPI thread 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.052 0.027 197.3 83: (ns/day) (hour/ns) 83: Performance: 55.365 0.433 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 83: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 (469 ms) 83: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest (29200 ms total) 83: 83: [----------] Global test environment tear-down 83: [==========] 25 tests from 1 test suite ran. (29445 ms total) 83: [ PASSED ] 25 tests. 83/90 Test #83: MdrunCoordinationCouplingTests2Ranks ...... Passed 29.56 sec test 84 Start 84: MdrunCoordinationConstraintsTests1Rank 84: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/mdrun-coordination-constraints-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/MdrunCoordinationConstraintsTests1Rank.xml" 84: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests 84: Test timeout computed to be: 1920 84: [==========] Running 13 tests from 1 test suite. 84: [----------] Global test environment set-up. 84: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.033 0.033 99.7 84: (ns/day) (hour/ns) 84: Performance: 44.202 0.543 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.048 0.048 99.7 84: (ns/day) (hour/ns) 84: Performance: 30.612 0.784 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 4. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 4. 84: 84: 84: There were 5 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.020 0.020 99.6 84: (ns/day) (hour/ns) 84: Performance: 74.706 0.321 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 5 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.082 0.082 99.9 84: (ns/day) (hour/ns) 84: Performance: 17.948 1.337 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 5 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.040 0.040 99.8 84: (ns/day) (hour/ns) 84: Performance: 36.339 0.660 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 5 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.029 0.031 94.8 84: (ns/day) (hour/ns) 84: Performance: 47.899 0.501 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (5057 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.032 0.033 99.7 84: (ns/day) (hour/ns) 84: Performance: 45.174 0.531 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.040 0.041 99.4 84: (ns/day) (hour/ns) 84: Performance: 36.180 0.663 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.069 0.069 99.9 84: (ns/day) (hour/ns) 84: Performance: 21.298 1.127 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.370 0.370 100.0 84: (ns/day) (hour/ns) 84: Performance: 3.973 6.041 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.021 0.021 99.3 84: (ns/day) (hour/ns) 84: Performance: 69.596 0.345 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.288 0.288 100.0 84: (ns/day) (hour/ns) 84: Performance: 5.094 4.712 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (5265 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.019 0.019 99.6 84: (ns/day) (hour/ns) 84: Performance: 76.154 0.315 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.013 0.013 99.4 84: (ns/day) (hour/ns) 84: Performance: 113.505 0.211 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.011 0.011 99.2 84: (ns/day) (hour/ns) 84: Performance: 137.173 0.175 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.015 0.016 99.3 84: (ns/day) (hour/ns) 84: Performance: 94.362 0.254 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.024 0.024 99.4 84: (ns/day) (hour/ns) 84: Performance: 60.920 0.394 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.013 0.013 99.4 84: (ns/day) (hour/ns) 84: Performance: 113.238 0.212 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (3484 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.017 0.017 99.2 84: (ns/day) (hour/ns) 84: Performance: 87.314 0.275 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.023 0.023 99.6 84: (ns/day) (hour/ns) 84: Performance: 64.668 0.371 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.023 0.023 99.5 84: (ns/day) (hour/ns) 84: Performance: 64.342 0.373 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.052 0.052 99.7 84: (ns/day) (hour/ns) 84: Performance: 28.324 0.847 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.019 0.019 99.6 84: (ns/day) (hour/ns) 84: Performance: 76.129 0.315 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.012 0.012 98.7 84: (ns/day) (hour/ns) 84: Performance: 118.139 0.203 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (3982 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.032 0.033 99.8 84: (ns/day) (hour/ns) 84: Performance: 45.148 0.532 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.334 0.336 99.4 84: (ns/day) (hour/ns) 84: Performance: 4.368 5.495 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.009 0.009 99.1 84: (ns/day) (hour/ns) 84: Performance: 161.373 0.149 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.013 0.013 99.4 84: (ns/day) (hour/ns) 84: Performance: 111.474 0.215 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.036 0.036 99.7 84: (ns/day) (hour/ns) 84: Performance: 40.960 0.586 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.011 0.011 99.3 84: (ns/day) (hour/ns) 84: Performance: 131.457 0.183 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (4054 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.020 0.020 99.6 84: (ns/day) (hour/ns) 84: Performance: 73.954 0.325 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.011 0.011 99.2 84: (ns/day) (hour/ns) 84: Performance: 131.099 0.183 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.008 0.008 99.1 84: (ns/day) (hour/ns) 84: Performance: 192.989 0.124 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.014 0.014 99.4 84: (ns/day) (hour/ns) 84: Performance: 104.422 0.230 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.011 0.011 99.0 84: (ns/day) (hour/ns) 84: Performance: 135.944 0.177 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.010 0.010 98.9 84: (ns/day) (hour/ns) 84: Performance: 145.989 0.164 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (3577 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.011 0.011 99.3 84: (ns/day) (hour/ns) 84: Performance: 132.440 0.181 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.015 0.015 99.5 84: (ns/day) (hour/ns) 84: Performance: 98.942 0.243 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 4. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 4. 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.009 0.009 99.2 84: (ns/day) (hour/ns) 84: Performance: 156.666 0.153 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.039 0.039 99.7 84: (ns/day) (hour/ns) 84: Performance: 37.924 0.633 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.034 0.034 99.7 84: (ns/day) (hour/ns) 84: Performance: 42.712 0.562 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.030 0.030 99.6 84: (ns/day) (hour/ns) 84: Performance: 49.381 0.486 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (5799 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.044 0.044 99.7 84: (ns/day) (hour/ns) 84: Performance: 33.484 0.717 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.047 0.047 99.8 84: (ns/day) (hour/ns) 84: Performance: 31.362 0.765 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.028 0.028 99.6 84: (ns/day) (hour/ns) 84: Performance: 51.646 0.465 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.025 0.025 99.6 84: (ns/day) (hour/ns) 84: Performance: 59.064 0.406 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.042 0.043 99.7 84: (ns/day) (hour/ns) 84: Performance: 34.510 0.695 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.015 0.015 99.3 84: (ns/day) (hour/ns) 84: Performance: 96.297 0.249 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (6359 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.035 0.035 99.6 84: (ns/day) (hour/ns) 84: Performance: 41.638 0.576 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.018 0.018 99.5 84: (ns/day) (hour/ns) 84: Performance: 82.385 0.291 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.012 0.012 99.3 84: (ns/day) (hour/ns) 84: Performance: 125.693 0.191 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.216 0.216 100.0 84: (ns/day) (hour/ns) 84: Performance: 6.795 3.532 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.040 0.040 99.7 84: (ns/day) (hour/ns) 84: Performance: 36.424 0.659 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.035 0.035 99.8 84: (ns/day) (hour/ns) 84: Performance: 41.574 0.577 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (5428 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.039 0.039 99.8 84: (ns/day) (hour/ns) 84: Performance: 37.236 0.645 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.028 0.028 99.7 84: (ns/day) (hour/ns) 84: Performance: 51.598 0.465 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 4. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 4. 84: 84: 84: There were 5 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.730 0.730 100.0 84: (ns/day) (hour/ns) 84: Performance: 2.012 11.931 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 5 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.023 0.023 99.8 84: (ns/day) (hour/ns) 84: Performance: 63.778 0.376 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 5 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.032 0.032 99.8 84: (ns/day) (hour/ns) 84: Performance: 46.395 0.517 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 5 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.058 0.059 99.9 84: (ns/day) (hour/ns) 84: Performance: 25.097 0.956 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (6250 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.055 0.055 99.9 84: (ns/day) (hour/ns) 84: Performance: 26.824 0.895 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.033 0.033 99.8 84: (ns/day) (hour/ns) 84: Performance: 44.617 0.538 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.048 0.048 99.8 84: (ns/day) (hour/ns) 84: Performance: 30.643 0.783 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 1.160 1.160 100.0 84: (ns/day) (hour/ns) 84: Performance: 1.266 18.962 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 1.599 1.599 100.0 84: (ns/day) (hour/ns) 84: Performance: 0.918 26.135 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.038 0.038 99.7 84: (ns/day) (hour/ns) 84: Performance: 38.225 0.628 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (8121 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.036 0.037 99.8 84: (ns/day) (hour/ns) 84: Performance: 40.200 0.597 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.024 0.024 99.7 84: (ns/day) (hour/ns) 84: Performance: 61.573 0.390 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.023 0.023 99.7 84: (ns/day) (hour/ns) 84: Performance: 63.123 0.380 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.040 0.041 99.8 84: (ns/day) (hour/ns) 84: Performance: 36.211 0.663 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.055 0.055 99.8 84: (ns/day) (hour/ns) 84: Performance: 26.607 0.902 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.037 0.037 99.8 84: (ns/day) (hour/ns) 84: Performance: 40.143 0.598 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (4089 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.051 0.052 99.8 84: (ns/day) (hour/ns) 84: Performance: 28.515 0.842 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.024 0.024 99.7 84: (ns/day) (hour/ns) 84: Performance: 61.378 0.391 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.014 0.015 99.5 84: (ns/day) (hour/ns) 84: Performance: 100.997 0.238 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.034 0.034 99.7 84: (ns/day) (hour/ns) 84: Performance: 42.841 0.560 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.034 0.034 99.7 84: (ns/day) (hour/ns) 84: Performance: 43.619 0.550 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 84: 84: Using 1 MPI thread 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.047 0.047 99.8 84: (ns/day) (hour/ns) 84: Performance: 31.155 0.770 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (4615 ms) 84: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest (66087 ms total) 84: 84: [----------] Global test environment tear-down 84: [==========] 13 tests from 1 test suite ran. (66248 ms total) 84: [ PASSED ] 13 tests. 84/90 Test #84: MdrunCoordinationConstraintsTests1Rank .... Passed 66.28 sec test 85 Start 85: MdrunCoordinationConstraintsTests2Ranks 85: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/mdrun-coordination-constraints-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/MdrunCoordinationConstraintsTests2Ranks.xml" 85: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests 85: Test timeout computed to be: 1920 85: [==========] Running 13 tests from 1 test suite. 85: [----------] Global test environment set-up. 85: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest 85: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.2%. 85: The balanceable part of the MD step is 40%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.5%. 85: 85: 85: NOTE: 60 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.078 0.039 199.0 85: (ns/day) (hour/ns) 85: Performance: 37.621 0.638 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 3.1%. 85: The balanceable part of the MD step is 49%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.5%. 85: 85: 85: NOTE: 12 % of the run time was spent in domain decomposition, 85: 0 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: NOTE: 43 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.543 0.272 199.9 85: (ns/day) (hour/ns) 85: Performance: 5.409 4.437 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 4. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 4. 85: 85: 85: There were 5 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 3.1%. 85: The balanceable part of the MD step is 36%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.1%. 85: 85: 85: NOTE: 48 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.065 0.033 199.2 85: (ns/day) (hour/ns) 85: Performance: 45.061 0.533 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 5 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 0.7%. 85: The balanceable part of the MD step is 36%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.3%. 85: 85: 85: NOTE: 50 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.802 0.401 199.9 85: (ns/day) (hour/ns) 85: Performance: 3.661 6.555 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 5 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.4%. 85: The balanceable part of the MD step is 28%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.4%. 85: 85: 85: NOTE: 45 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.027 0.014 198.4 85: (ns/day) (hour/ns) 85: Performance: 106.091 0.226 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 5 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 4.2%. 85: The balanceable part of the MD step is 38%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.6%. 85: 85: 85: NOTE: 47 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.033 0.017 198.9 85: (ns/day) (hour/ns) 85: Performance: 88.467 0.271 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 85: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (6569 ms) 85: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 0.4%. 85: The balanceable part of the MD step is 54%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.2%. 85: 85: 85: NOTE: 43 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.019 0.010 197.7 85: (ns/day) (hour/ns) 85: Performance: 151.336 0.159 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 0.5%. 85: The balanceable part of the MD step is 50%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.3%. 85: 85: 85: NOTE: 44 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.017 0.008 197.1 85: (ns/day) (hour/ns) 85: Performance: 173.211 0.139 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 3.8%. 85: The balanceable part of the MD step is 42%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.6%. 85: 85: 85: NOTE: 46 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.022 0.011 197.6 85: (ns/day) (hour/ns) 85: Performance: 132.610 0.181 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB got disabled because it was unsuitable to use. 85: Average load imbalance: 5.6%. 85: The balanceable part of the MD step is 41%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 2.3%. 85: 85: 85: NOTE: 46 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.028 0.014 198.1 85: (ns/day) (hour/ns) 85: Performance: 102.197 0.235 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.2%. 85: The balanceable part of the MD step is 40%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.5%. 85: 85: 85: NOTE: 46 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.024 0.012 198.0 85: (ns/day) (hour/ns) 85: Performance: 122.216 0.196 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.1%. 85: The balanceable part of the MD step is 41%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.5%. 85: 85: 85: NOTE: 47 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.025 0.013 197.8 85: (ns/day) (hour/ns) 85: Performance: 116.442 0.206 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 85: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (3433 ms) 85: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 0.9%. 85: The balanceable part of the MD step is 48%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.5%. 85: 85: 85: NOTE: 49 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.214 0.107 199.7 85: (ns/day) (hour/ns) 85: Performance: 13.726 1.749 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.0%. 85: The balanceable part of the MD step is 48%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.5%. 85: 85: 85: NOTE: 50 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.611 0.306 199.9 85: (ns/day) (hour/ns) 85: Performance: 4.805 4.995 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.6%. 85: The balanceable part of the MD step is 42%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.7%. 85: 85: 85: NOTE: 50 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 1.280 0.640 200.0 85: (ns/day) (hour/ns) 85: Performance: 2.295 10.456 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 4.7%. 85: The balanceable part of the MD step is 41%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.9%. 85: 85: 85: NOTE: 50 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 3.612 1.806 200.0 85: (ns/day) (hour/ns) 85: Performance: 0.813 29.514 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 0.9%. 85: The balanceable part of the MD step is 47%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.4%. 85: 85: 85: NOTE: 49 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.144 0.072 199.8 85: (ns/day) (hour/ns) 85: Performance: 20.335 1.180 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.5%. 85: The balanceable part of the MD step is 46%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.7%. 85: 85: 85: NOTE: 49 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.155 0.078 199.6 85: (ns/day) (hour/ns) 85: Performance: 18.938 1.267 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 85: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (7152 ms) 85: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.077 0.039 199.2 85: (ns/day) (hour/ns) 85: Performance: 37.969 0.632 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.016 0.008 197.6 85: (ns/day) (hour/ns) 85: Performance: 178.786 0.134 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.022 0.011 197.9 85: (ns/day) (hour/ns) 85: Performance: 130.507 0.184 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.020 0.010 197.3 85: (ns/day) (hour/ns) 85: Performance: 144.747 0.166 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.028 0.014 197.2 85: (ns/day) (hour/ns) 85: Performance: 102.352 0.234 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.029 0.014 197.9 85: (ns/day) (hour/ns) 85: Performance: 101.838 0.236 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 85: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (3253 ms) 85: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.175 0.088 199.7 85: (ns/day) (hour/ns) 85: Performance: 16.727 1.435 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.040 0.020 198.8 85: (ns/day) (hour/ns) 85: Performance: 73.300 0.327 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.786 0.393 199.9 85: (ns/day) (hour/ns) 85: Performance: 3.735 6.426 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 1.382 0.691 200.0 85: (ns/day) (hour/ns) 85: Performance: 2.125 11.296 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 1.469 0.734 200.0 85: (ns/day) (hour/ns) 85: Performance: 2.000 12.000 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.023 0.012 197.9 85: (ns/day) (hour/ns) 85: Performance: 126.270 0.190 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 85: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (5693 ms) 85: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.019 0.010 197.4 85: (ns/day) (hour/ns) 85: Performance: 149.574 0.160 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.061 0.031 198.7 85: (ns/day) (hour/ns) 85: Performance: 47.555 0.505 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.045 0.023 198.8 85: (ns/day) (hour/ns) 85: Performance: 64.431 0.372 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.072 0.036 198.8 85: (ns/day) (hour/ns) 85: Performance: 40.418 0.594 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.107 0.054 199.6 85: (ns/day) (hour/ns) 85: Performance: 27.443 0.875 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.071 0.036 199.2 85: (ns/day) (hour/ns) 85: Performance: 41.209 0.582 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 85: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (4721 ms) 85: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.113 0.056 199.5 85: (ns/day) (hour/ns) 85: Performance: 26.032 0.922 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.069 0.035 198.8 85: (ns/day) (hour/ns) 85: Performance: 42.384 0.566 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 4. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 4. 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.077 0.038 199.4 85: (ns/day) (hour/ns) 85: Performance: 38.185 0.629 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.080 0.040 199.2 85: (ns/day) (hour/ns) 85: Performance: 36.510 0.657 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.090 0.046 195.4 85: (ns/day) (hour/ns) 85: Performance: 31.793 0.755 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.104 0.052 199.6 85: (ns/day) (hour/ns) 85: Performance: 28.189 0.851 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 85: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (4970 ms) 85: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.094 0.047 199.4 85: (ns/day) (hour/ns) 85: Performance: 31.149 0.770 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.035 0.019 178.6 85: (ns/day) (hour/ns) 85: Performance: 75.755 0.317 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.065 0.034 195.0 85: (ns/day) (hour/ns) 85: Performance: 43.743 0.549 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.055 0.028 199.1 85: (ns/day) (hour/ns) 85: Performance: 52.707 0.455 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.112 0.056 199.5 85: (ns/day) (hour/ns) 85: Performance: 26.178 0.917 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.041 0.021 198.8 85: (ns/day) (hour/ns) 85: Performance: 71.433 0.336 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 85: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (4664 ms) 85: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.067 0.034 199.2 85: (ns/day) (hour/ns) 85: Performance: 43.519 0.551 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.017 0.009 197.7 85: (ns/day) (hour/ns) 85: Performance: 168.684 0.142 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.030 0.015 198.7 85: (ns/day) (hour/ns) 85: Performance: 98.656 0.243 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.125 0.063 199.6 85: (ns/day) (hour/ns) 85: Performance: 23.483 1.022 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.032 0.016 198.3 85: (ns/day) (hour/ns) 85: Performance: 91.999 0.261 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.028 0.014 193.2 85: (ns/day) (hour/ns) 85: Performance: 102.253 0.235 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 85: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (3856 ms) 85: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 0.3%. 85: The balanceable part of the MD step is 55%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.2%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.048 0.024 198.5 85: (ns/day) (hour/ns) 85: Performance: 60.198 0.399 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB got disabled because it was unsuitable to use. 85: Average load imbalance: 65.9%. 85: The balanceable part of the MD step is 16%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 10.8%. 85: 85: NOTE: 10.8 % of the available CPU time was lost due to load imbalance 85: in the domain decomposition. 85: You can consider manually changing the decomposition (option -dd); 85: e.g. by using fewer domains along the box dimension in which there is 85: considerable inhomogeneity in the simulated system. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.105 0.053 199.2 85: (ns/day) (hour/ns) 85: Performance: 27.942 0.859 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 4. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 4. 85: 85: 85: There were 5 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 4.3%. 85: The balanceable part of the MD step is 43%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.8%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 1.941 0.971 199.9 85: (ns/day) (hour/ns) 85: Performance: 1.513 15.865 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 5 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 3.8%. 85: The balanceable part of the MD step is 46%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.8%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 1.970 0.986 199.9 85: (ns/day) (hour/ns) 85: Performance: 1.490 16.104 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 5 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.4%. 85: The balanceable part of the MD step is 40%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.0%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 3.713 1.931 192.3 85: (ns/day) (hour/ns) 85: Performance: 0.761 31.553 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 5 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB got disabled because it was unsuitable to use. 85: Average load imbalance: 6.3%. 85: The balanceable part of the MD step is 43%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 2.7%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 3.443 1.725 199.6 85: (ns/day) (hour/ns) 85: Performance: 0.851 28.187 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 85: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (11053 ms) 85: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 0.3%. 85: The balanceable part of the MD step is 2%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.0%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 1.506 0.753 199.9 85: (ns/day) (hour/ns) 85: Performance: 1.950 12.308 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.6%. 85: The balanceable part of the MD step is 58%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.9%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 2.418 1.209 200.0 85: (ns/day) (hour/ns) 85: Performance: 1.215 19.761 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.8%. 85: The balanceable part of the MD step is 55%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.0%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.066 0.034 196.8 85: (ns/day) (hour/ns) 85: Performance: 43.699 0.549 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.8%. 85: The balanceable part of the MD step is 49%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.9%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.081 0.041 198.9 85: (ns/day) (hour/ns) 85: Performance: 36.205 0.663 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.7%. 85: The balanceable part of the MD step is 51%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.9%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.053 0.027 198.6 85: (ns/day) (hour/ns) 85: Performance: 54.597 0.440 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: NVE simulation: will use the initial temperature of 398.997 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 1.9%. 85: The balanceable part of the MD step is 40%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 0.8%. 85: 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.109 0.055 199.1 85: (ns/day) (hour/ns) 85: Performance: 26.718 0.898 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 85: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (6520 ms) 85: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.095 0.048 199.1 85: (ns/day) (hour/ns) 85: Performance: 30.832 0.778 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.075 0.038 198.5 85: (ns/day) (hour/ns) 85: Performance: 38.916 0.617 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.056 0.028 198.1 85: (ns/day) (hour/ns) 85: Performance: 51.814 0.463 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.093 0.047 197.4 85: (ns/day) (hour/ns) 85: Performance: 31.270 0.768 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.044 0.022 198.1 85: (ns/day) (hour/ns) 85: Performance: 66.294 0.362 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.037 0.019 192.9 85: (ns/day) (hour/ns) 85: Performance: 75.878 0.316 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 85: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (4602 ms) 85: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.044 0.022 197.9 85: (ns/day) (hour/ns) 85: Performance: 66.622 0.360 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.047 0.025 192.4 85: (ns/day) (hour/ns) 85: Performance: 59.577 0.403 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.054 0.027 197.7 85: (ns/day) (hour/ns) 85: Performance: 53.905 0.445 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.047 0.024 198.0 85: (ns/day) (hour/ns) 85: Performance: 62.150 0.386 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.072 0.036 198.6 85: (ns/day) (hour/ns) 85: Performance: 40.396 0.594 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 27.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: You are using a plain Coulomb cut-off, which might produce artifacts. 85: You might want to consider using PME electrostatics. 85: 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 85: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 85: 85: Using 2 MPI threads 85: Using 1 OpenMP thread per tMPI thread 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'spc2' 85: 16 steps, 0.0 ps. 85: Generated 330891 of the 330891 non-bonded parameter combinations 85: 85: Generated 330891 of the 330891 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.220 0.110 199.6 85: (ns/day) (hour/ns) 85: Performance: 13.308 1.803 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 85: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (4092 ms) 85: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest (70586 ms total) 85: 85: [----------] Global test environment tear-down 85: [==========] 13 tests from 1 test suite ran. (70702 ms total) 85: [ PASSED ] 13 tests. 85/90 Test #85: MdrunCoordinationConstraintsTests2Ranks ... Passed 70.74 sec test 86 Start 86: MdrunFEPTests 86: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/mdrun-fep-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/MdrunFEPTests.xml" 86: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests 86: Test timeout computed to be: 600 86: [==========] Running 14 tests from 2 test suites. 86: [----------] Global test environment set-up. 86: [----------] 2 tests from ExpandedEnsembleTest 86: [ RUN ] ExpandedEnsembleTest.ContinuationPreservesExpandedEnsembleState 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 79.00 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 2 NOTEs 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun '30 atom system in water' 86: 16 steps, 0.0 ps. 86: Generated 2485 of the 2485 non-bonded parameter combinations 86: 86: Generated 2485 of the 2485 1-4 parameter combinations 86: 86: Excluding 3 bonded neighbours molecule type 'nonanol' 86: 86: turning H bonds into constraints... 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: turning H bonds into constraints... 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.046 0.023 199.3 86: (ns/day) (hour/ns) 86: Performance: 62.989 0.381 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 86: Overriding nsteps with value passed on the command line: 8 steps, 0.008 ps 86: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 86: 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun '30 atom system in water' 86: 24 steps, 0.0 ps (continuing from step 16, 0.0 ps). 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.046 0.023 198.7 86: (ns/day) (hour/ns) 86: Performance: 33.402 0.719 86: [ OK ] ExpandedEnsembleTest.ContinuationPreservesExpandedEnsembleState (105 ms) 86: [ RUN ] ExpandedEnsembleTest.WeightEquilibrationReported 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_WeightEquilibrationReported_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 79.00 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_WeightEquilibrationReported_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 2 NOTEs 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_WeightEquilibrationReported.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun '30 atom system in water' 86: 1 steps, 0.0 ps. 86: Generated 2485 of the 2485 non-bonded parameter combinations 86: 86: Generated 2485 of the 2485 1-4 parameter combinations 86: 86: Excluding 3 bonded neighbours molecule type 'nonanol' 86: 86: turning H bonds into constraints... 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: turning H bonds into constraints... 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.034 0.017 199.1 86: (ns/day) (hour/ns) 86: Performance: 10.109 2.374 86: [ OK ] ExpandedEnsembleTest.WeightEquilibrationReported (48 ms) 86: [----------] 2 tests from ExpandedEnsembleTest (154 ms total) 86: 86: [----------] 12 tests from EquivalentToReference/FreeEnergyReferenceTest 86: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_d 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp, line 149]: 86: For proper sampling of the (nearly) decoupled state, stochastic dynamics 86: should be used 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 355.00 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 86: The optimal PME mesh load for parallel simulations is below 0.5 86: and for highly parallel simulations between 0.25 and 0.33, 86: for higher performance, increase the cut-off and the PME grid spacing. 86: 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 86: For free energy simulations, the optimal load limit increases from 0.5 to 86: 0.667 86: 86: 86: 86: There were 3 NOTEs 86: 86: There was 1 WARNING 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_d_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 86: Changing nstlist from 10 to 100, rlist from 1 to 1 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'AA' 86: 20 steps, 0.0 ps. 86: Setting the LD random seed to -235016515 86: 86: Generated 153 of the 153 non-bonded parameter combinations 86: 86: Generated 153 of the 153 1-4 parameter combinations 86: 86: Excluding 3 bonded neighbours molecule type 'ASN' 86: 86: turning H bonds into constraints... 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: turning H bonds into constraints... 86: 86: Coupling 1 copies of molecule type 'ASN' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/conf.gro' 86: Analysing residue names: 86: There are: 1 Protein residues 86: There are: 56 Water residues 86: Analysing Protein... 86: 86: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 86: 86: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: Calculating fourier grid dimensions for X Y Z 86: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 86: 86: Estimate for the relative computational load of the PME mesh part: 0.92 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.219 0.110 199.8 86: (ns/day) (hour/ns) 86: Performance: 16.520 1.453 86: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_d_energy.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 trr version: GMX_trn_file (double precision) 86: 86: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_d (421 ms) 86: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_d 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp, line 148]: 86: For proper sampling of the (nearly) decoupled state, stochastic dynamics 86: should be used 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 355.00 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 86: The optimal PME mesh load for parallel simulations is below 0.5 86: and for highly parallel simulations between 0.25 and 0.33, 86: for higher performance, increase the cut-off and the PME grid spacing. 86: 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 86: For free energy simulations, the optimal load limit increases from 0.5 to 86: 0.667 86: 86: 86: 86: There were 3 NOTEs 86: 86: There was 1 WARNING 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_d_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 86: Changing nstlist from 10 to 100, rlist from 1 to 1 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'AA' 86: 20 steps, 0.0 ps. 86: Setting the LD random seed to -881868935 86: 86: Generated 153 of the 153 non-bonded parameter combinations 86: 86: Generated 153 of the 153 1-4 parameter combinations 86: 86: Excluding 3 bonded neighbours molecule type 'ASN' 86: 86: turning H bonds into constraints... 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: turning H bonds into constraints... 86: 86: Coupling 1 copies of molecule type 'ASN' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/conf.gro' 86: Analysing residue names: 86: There are: 1 Protein residues 86: There are: 56 Water residues 86: Analysing Protein... 86: 86: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 86: 86: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: Calculating fourier grid dimensions for X Y Z 86: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 86: 86: Estimate for the relative computational load of the PME mesh part: 0.92 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.213 0.107 199.8 86: (ns/day) (hour/ns) 86: Performance: 17.022 1.410 86: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_d_energy.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 86: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_d (284 ms) 86: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_d 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp, line 147]: 86: For proper sampling of the (nearly) decoupled state, stochastic dynamics 86: should be used 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 86: With PME there is a minor soft core effect present at the cut-off, 86: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 86: energy conservation, but usually other effects dominate. With a common 86: sigma value of 0.34 nm the fraction of the particle-particle potential at 86: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 355.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 86: The optimal PME mesh load for parallel simulations is below 0.5 86: and for highly parallel simulations between 0.25 and 0.33, 86: for higher performance, increase the cut-off and the PME grid spacing. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 86: For free energy simulations, the optimal load limit increases from 0.5 to 86: 0.667 86: 86: 86: 86: There were 4 NOTEs 86: 86: There was 1 WARNING 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_d_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 86: Changing nstlist from 10 to 100, rlist from 1 to 1 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'AA' 86: 20 steps, 0.0 ps. 86: Setting the LD random seed to -25296899 86: 86: Generated 153 of the 153 non-bonded parameter combinations 86: 86: Generated 153 of the 153 1-4 parameter combinations 86: 86: Excluding 3 bonded neighbours molecule type 'ASN' 86: 86: turning H bonds into constraints... 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: turning H bonds into constraints... 86: 86: Coupling 1 copies of molecule type 'ASN' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/conf.gro' 86: Analysing residue names: 86: There are: 1 Protein residues 86: There are: 56 Water residues 86: Analysing Protein... 86: 86: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 86: 86: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: Calculating fourier grid dimensions for X Y Z 86: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 86: 86: Estimate for the relative computational load of the PME mesh part: 0.92 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.164 0.082 199.4 86: (ns/day) (hour/ns) 86: Performance: 22.017 1.090 86: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_d_energy.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 86: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_d (287 ms) 86: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_net_charge_d 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp, line 147]: 86: For proper sampling of the (nearly) decoupled state, stochastic dynamics 86: should be used 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 86: With PME there is a minor soft core effect present at the cut-off, 86: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 86: energy conservation, but usually other effects dominate. With a common 86: sigma value of 0.34 nm the fraction of the particle-particle potential at 86: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: 86: NOTE 3 [file topol.top, line 155]: 86: System has non-zero total charge: 1.000000 86: Total charge should normally be an integer. See 86: https://manual.gromacs.org/current/user-guide/floating-point.html 86: for discussion on how close it should be to an integer. 86: 86: 86: 86: 86: WARNING 2 [file topol.top, line 155]: 86: You are using Ewald electrostatics in a system with net charge. This can 86: lead to severe artifacts, such as ions moving into regions with low 86: dielectric, due to the uniform background charge. We suggest to 86: neutralize your system with counter ions, possibly in combination with a 86: physiological salt concentration. 86: 86: Setting the LD random seed to -272105729 86: 86: Generated 171 of the 171 non-bonded parameter combinations 86: 86: Generated 171 of the 171 1-4 parameter combinations 86: 86: Excluding 3 bonded neighbours molecule type 'ASN' 86: 86: turning H bonds into constraints... 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: turning H bonds into constraints... 86: 86: Excluding 1 bonded neighbours molecule type 'NA' 86: 86: turning H bonds into constraints... 86: 86: Coupling 1 copies of molecule type 'ASN' 86: 86: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 86: J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof 86: Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net 86: Charge 86: J. Chem. Theory Comput. (2014) 86: DOI: 10.1021/ct400626b 86: -------- -------- --- Thank You --- -------- -------- 86: 86: Number of degrees of freedom in T-Coupling group System is 358.00 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 86: The optimal PME mesh load for parallel simulations is below 0.5 86: and for highly parallel simulations between 0.25 and 0.33, 86: for higher performance, increase the cut-off and the PME grid spacing. 86: 86: 86: 86: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 86: For free energy simulations, the optimal load limit increases from 0.5 to 86: 0.667 86: 86: 86: 86: There were 5 NOTEs 86: 86: There were 2 WARNINGs 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_net_charge_d_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 86: Changing nstlist from 10 to 50, rlist from 1.008 to 1.12 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'AA' 86: 20 steps, 0.0 ps. 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/conf.gro' 86: Analysing residue names: 86: There are: 1 Protein residues 86: There are: 56 Water residues 86: There are: 1 Ion residues 86: Analysing Protein... 86: 86: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 86: 86: Determining Verlet buffer for a tolerance of 5e-05 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 1.004 nm, buffer size 0.004 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: Calculating fourier grid dimensions for X Y Z 86: Using a fourier grid of 32x32x32, spacing 0.095 0.095 0.095 86: 86: Estimate for the relative computational load of the PME mesh part: 0.95 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.204 0.102 199.6 86: (ns/day) (hour/ns) 86: Performance: 17.735 1.353 86: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_net_charge_d_energy.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 86: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_net_charge_d (317 ms) 86: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_decouple_counter_charge_d 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp, line 147]: 86: For proper sampling of the (nearly) decoupled state, stochastic dynamics 86: should be used 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 86: With PME there is a minor soft core effect present at the cut-off, 86: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 86: energy conservation, but usually other effects dominate. With a common 86: sigma value of 0.34 nm the fraction of the particle-particle potential at 86: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: 86: NOTE 3 [file topol.top, line 165]: 86: System has non-zero total charge: 1.000000 86: Total charge should normally be an integer. See 86: https://manual.gromacs.org/current/user-guide/floating-point.html 86: for discussion on how close it should be to an integer. 86: 86: 86: 86: 86: WARNING 2 [file topol.top, line 165]: 86: You are using Ewald electrostatics in a system with net charge. This can 86: lead to severe artifacts, such as ions moving into regions with low 86: dielectric, due to the uniform background charge. We suggest to 86: neutralize your system with counter ions, possibly in combination with a 86: physiological salt concentration. 86: 86: Setting the LD random seed to -1906608706 86: 86: Generated 190 of the 190 non-bonded parameter combinations 86: 86: Generated 190 of the 190 1-4 parameter combinations 86: 86: Excluding 3 bonded neighbours molecule type 'ASN' 86: 86: turning H bonds into constraints... 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: turning H bonds into constraints... 86: 86: Excluding 1 bonded neighbours molecule type 'NA' 86: 86: turning H bonds into constraints... 86: 86: Excluding 1 bonded neighbours molecule type 'CL' 86: 86: turning H bonds into constraints... 86: 86: Coupling 1 copies of molecule type 'CL' 86: 86: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 86: J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof 86: Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net 86: Charge 86: J. Chem. Theory Comput. (2014) 86: DOI: 10.1021/ct400626b 86: -------- -------- --- Thank You --- -------- -------- 86: 86: Number of degrees of freedom in T-Coupling group System is 361.00 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 86: The optimal PME mesh load for parallel simulations is below 0.5 86: and for highly parallel simulations between 0.25 and 0.33, 86: for higher performance, increase the cut-off and the PME grid spacing. 86: 86: 86: 86: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 86: For free energy simulations, the optimal load limit increases from 0.5 to 86: 0.667 86: 86: 86: 86: There were 5 NOTEs 86: 86: There were 2 WARNINGs 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_decouple_counter_charge_d_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 86: Changing nstlist from 10 to 50, rlist from 1.008 to 1.121 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'AA' 86: 20 steps, 0.0 ps. 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/conf.gro' 86: Analysing residue names: 86: There are: 1 Protein residues 86: There are: 56 Water residues 86: There are: 2 Ion residues 86: Analysing Protein... 86: 86: The largest distance between non-perturbed excluded atoms is 0.331 nm between atom 1 and 9 86: 86: Determining Verlet buffer for a tolerance of 5e-05 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 1.004 nm, buffer size 0.004 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: Calculating fourier grid dimensions for X Y Z 86: Using a fourier grid of 32x32x32, spacing 0.095 0.095 0.095 86: 86: Estimate for the relative computational load of the PME mesh part: 0.95 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.235 0.118 199.7 86: (ns/day) (hour/ns) 86: Performance: 15.432 1.555 86: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_decouple_counter_charge_d_energy.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 86: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_decouple_counter_charge_d (176 ms) 86: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_d 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp, line 171]: 86: For proper sampling of the (nearly) decoupled state, stochastic dynamics 86: should be used 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 86: Replacing vdwtype=Shift by the equivalent combination of vdwtype=Cut-off 86: and vdw_modifier=Force-switch 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 355.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 86: The optimal PME mesh load for parallel simulations is below 0.5 86: and for highly parallel simulations between 0.25 and 0.33, 86: for higher performance, increase the cut-off and the PME grid spacing. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 86: For free energy simulations, the optimal load limit increases from 0.5 to 86: 0.667 86: 86: 86: 86: There were 4 NOTEs 86: 86: There was 1 WARNING 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_d_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 86: Changing nstlist from 10 to 100, rlist from 1 to 1 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'AA' 86: 100 steps, 0.1 ps. 86: Setting the LD random seed to -1375895767 86: 86: Generated 153 of the 153 non-bonded parameter combinations 86: 86: Generated 153 of the 153 1-4 parameter combinations 86: 86: Excluding 3 bonded neighbours molecule type 'ASN' 86: 86: turning H bonds into constraints... 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: turning H bonds into constraints... 86: 86: Coupling 1 copies of molecule type 'ASN' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/expanded/conf.gro' 86: Analysing residue names: 86: There are: 1 Protein residues 86: There are: 56 Water residues 86: Analysing Protein... 86: 86: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 86: 86: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: Calculating fourier grid dimensions for X Y Z 86: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 86: 86: Estimate for the relative computational load of the PME mesh part: 0.92 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 1.011 0.506 199.9 86: (ns/day) (hour/ns) 86: Performance: 17.248 1.391 86: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_d_energy.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Reading energy frame 30 time 0.030 Reading energy frame 40 time 0.040 Reading energy frame 50 time 0.050 Reading energy frame 60 time 0.060 Reading energy frame 70 time 0.070 Reading energy frame 80 time 0.080 Reading energy frame 90 time 0.090 Reading energy frame 100 time 0.100 Last energy frame read 100 time 0.100 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_d (726 ms) 86: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_d 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: 86: WARNING 2 [file topol.top, line 72]: 86: No default Bond types for perturbed atoms in interaction, using normal 86: values. The interaction was 86: '7 8 1'. 86: 86: 86: WARNING 3 [file topol.top, line 73]: 86: No default Bond types for perturbed atoms in interaction, using normal 86: values. The interaction was 86: '7 9 1'. 86: 86: 86: WARNING 4 [file topol.top, line 98]: 86: No default Angle types for perturbed atoms in interaction, using normal 86: values. The interaction was 86: '6 5 7 1'. 86: 86: 86: WARNING 5 [file topol.top, line 99]: 86: No default Angle types for perturbed atoms in interaction, using normal 86: values. The interaction was 86: '5 7 8 1'. 86: 86: 86: WARNING 6 [file topol.top, line 100]: 86: No default Angle types for perturbed atoms in interaction, using normal 86: values. The interaction was 86: '5 7 9 1'. 86: 86: 86: WARNING 7 [file topol.top, line 101]: 86: No default Angle types for perturbed atoms in interaction, using normal 86: values. The interaction was 86: '8 7 9 1'. 86: 86: 86: WARNING 8 [file topol.top, line 111]: 86: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 86: normal values. The interaction was 86: '1 5 7 8 3'. 86: 86: 86: WARNING 9 [file topol.top, line 112]: 86: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 86: normal values. The interaction was 86: '1 5 7 9 3'. 86: 86: 86: WARNING 10 [file topol.top, line 113]: 86: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 86: normal values. The interaction was 86: '6 5 7 8 3'. 86: 86: 86: WARNING 11 [file topol.top, line 114]: 86: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 86: normal values. The interaction was 86: '6 5 7 9 3'. 86: 86: Number of degrees of freedom in T-Coupling group System is 355.00 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 86: The optimal PME mesh load for parallel simulations is below 0.5 86: and for highly parallel simulations between 0.25 and 0.33, 86: for higher performance, increase the cut-off and the PME grid spacing. 86: 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 86: For free energy simulations, the optimal load limit increases from 0.5 to 86: 0.667 86: 86: 86: 86: There were 2 NOTEs 86: 86: There were 11 WARNINGs 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_d_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 86: Changing nstlist from 10 to 100, rlist from 1 to 1 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'AA' 86: 20 steps, 0.0 ps. 86: Setting the LD random seed to -688062721 86: 86: Generated 136 of the 136 non-bonded parameter combinations 86: 86: Generated 136 of the 136 1-4 parameter combinations 86: 86: Excluding 3 bonded neighbours molecule type 'ASN' 86: 86: turning H bonds into constraints... 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: turning H bonds into constraints... 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/relative/conf.gro' 86: Analysing residue names: 86: There are: 1 Protein residues 86: There are: 56 Water residues 86: Analysing Protein... 86: 86: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 86: 86: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: Calculating fourier grid dimensions for X Y Z 86: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 86: 86: Estimate for the relative computational load of the PME mesh part: 0.92 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.701 0.351 199.9 86: (ns/day) (hour/ns) 86: Performance: 5.171 4.641 86: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_d_energy.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 86: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_d (558 ms) 86: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_d 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: 86: WARNING 2 [file topol.top, line 72]: 86: No default Bond types for perturbed atoms in interaction, using normal 86: values. The interaction was 86: '7 8 1'. 86: 86: 86: WARNING 3 [file topol.top, line 73]: 86: No default Bond types for perturbed atoms in interaction, using normal 86: values. The interaction was 86: '7 9 1'. 86: 86: 86: WARNING 4 [file topol.top, line 98]: 86: No default Angle types for perturbed atoms in interaction, using normal 86: values. The interaction was 86: '6 5 7 1'. 86: 86: 86: WARNING 5 [file topol.top, line 99]: 86: No default Angle types for perturbed atoms in interaction, using normal 86: values. The interaction was 86: '5 7 8 1'. 86: 86: 86: WARNING 6 [file topol.top, line 100]: 86: No default Angle types for perturbed atoms in interaction, using normal 86: values. The interaction was 86: '5 7 9 1'. 86: 86: 86: WARNING 7 [file topol.top, line 101]: 86: No default Angle types for perturbed atoms in interaction, using normal 86: values. The interaction was 86: '8 7 9 1'. 86: 86: 86: WARNING 8 [file topol.top, line 111]: 86: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 86: normal values. The interaction was 86: '1 5 7 8 3'. 86: 86: 86: WARNING 9 [file topol.top, line 112]: 86: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 86: normal values. The interaction was 86: '1 5 7 9 3'. 86: 86: 86: WARNING 10 [file topol.top, line 113]: 86: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 86: normal values. The interaction was 86: '6 5 7 8 3'. 86: 86: 86: WARNING 11 [file topol.top, line 114]: 86: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 86: normal values. The interaction was 86: '6 5 7 9 3'. 86: 86: Number of degrees of freedom in T-Coupling group System is 355.00 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 86: Removing center of mass motion in the presence of position restraints 86: might cause artifacts. When you are using position restraints to 86: equilibrate a macro-molecule, the artifacts are usually negligible. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 86: The optimal PME mesh load for parallel simulations is below 0.5 86: and for highly parallel simulations between 0.25 and 0.33, 86: for higher performance, increase the cut-off and the PME grid spacing. 86: 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 86: For free energy simulations, the optimal load limit increases from 0.5 to 86: 0.667 86: 86: 86: 86: There were 3 NOTEs 86: 86: There were 11 WARNINGs 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_d_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 86: Changing nstlist from 10 to 100, rlist from 1 to 1 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'AA' 86: 20 steps, 0.0 ps. 86: Setting the LD random seed to -100794945 86: 86: Generated 136 of the 136 non-bonded parameter combinations 86: 86: Generated 136 of the 136 1-4 parameter combinations 86: 86: Excluding 3 bonded neighbours molecule type 'ASN' 86: 86: turning H bonds into constraints... 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: turning H bonds into constraints... 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/conf.gro' 86: Analysing residue names: 86: There are: 1 Protein residues 86: There are: 56 Water residues 86: Analysing Protein... 86: 86: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 86: 86: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: Calculating fourier grid dimensions for X Y Z 86: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 86: 86: Estimate for the relative computational load of the PME mesh part: 0.92 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.388 0.194 199.8 86: (ns/day) (hour/ns) 86: Performance: 9.333 2.572 86: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_d_energy.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 86: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_d (423 ms) 86: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/restraints_d 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 355.00 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 86: The optimal PME mesh load for parallel simulations is below 0.5 86: and for highly parallel simulations between 0.25 and 0.33, 86: for higher performance, increase the cut-off and the PME grid spacing. 86: 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 86: For free energy simulations, the optimal load limit increases from 0.5 to 86: 0.667 86: 86: 86: 86: There were 2 NOTEs 86: 86: There was 1 WARNING 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_d_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 86: Changing nstlist from 10 to 100, rlist from 1 to 1 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'AA' 86: 20 steps, 0.0 ps. 86: Setting the LD random seed to -847790083 86: 86: Generated 136 of the 136 non-bonded parameter combinations 86: 86: Generated 136 of the 136 1-4 parameter combinations 86: 86: Excluding 3 bonded neighbours molecule type 'ASN' 86: 86: turning H bonds into constraints... 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: turning H bonds into constraints... 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/restraints/conf.gro' 86: Analysing residue names: 86: There are: 1 Protein residues 86: There are: 56 Water residues 86: Analysing Protein... 86: 86: The largest distance between non-perturbed excluded atoms is 0.331 nm between atom 1 and 9 86: 86: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: Calculating fourier grid dimensions for X Y Z 86: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 86: 86: Estimate for the relative computational load of the PME mesh part: 0.86 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.138 0.069 199.6 86: (ns/day) (hour/ns) 86: Performance: 26.303 0.912 86: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_d_energy.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 86: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/restraints_d (265 ms) 86: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_d 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/simtemp/grompp.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 355.00 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/simtemp/grompp.mdp]: 86: The optimal PME mesh load for parallel simulations is below 0.5 86: and for highly parallel simulations between 0.25 and 0.33, 86: for higher performance, increase the cut-off and the PME grid spacing. 86: 86: 86: 86: There was 1 NOTE 86: 86: There was 1 WARNING 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_d_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 86: Changing nstlist from 10 to 100, rlist from 1 to 1 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'AA' 86: 20 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.056 0.028 199.0 86: (ns/day) (hour/ns) 86: Performance: 64.424 0.373 86: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_d_energy.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 86: Setting the LD random seed to -385948699 86: 86: Generated 136 of the 136 non-bonded parameter combinations 86: 86: Generated 136 of the 136 1-4 parameter combinations 86: 86: Excluding 3 bonded neighbours molecule type 'ASN' 86: 86: turning H bonds into constraints... 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: turning H bonds into constraints... 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/simtemp/conf.gro' 86: Analysing residue names: 86: There are: 1 Protein residues 86: There are: 56 Water residues 86: Analysing Protein... 86: 86: The largest distance between excluded atoms is 0.331 nm between atom 1 and 9 86: 86: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: Calculating fourier grid dimensions for X Y Z 86: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 86: 86: Estimate for the relative computational load of the PME mesh part: 0.86 86: 86: This run will generate roughly 0 Mb of data 86: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_d (217 ms) 86: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_d 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 86: With PME there is a minor soft core effect present at the cut-off, 86: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 86: energy conservation, but usually other effects dominate. With a common 86: sigma value of 0.34 nm the fraction of the particle-particle potential at 86: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 355.00 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 86: The optimal PME mesh load for parallel simulations is below 0.5 86: and for highly parallel simulations between 0.25 and 0.33, 86: for higher performance, increase the cut-off and the PME grid spacing. 86: 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 86: For free energy simulations, the optimal load limit increases from 0.5 to 86: 0.667 86: 86: 86: 86: There were 3 NOTEs 86: 86: There was 1 WARNING 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_d_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 86: Changing nstlist from 10 to 100, rlist from 1 to 1 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'AA' 86: 20 steps, 0.0 ps. 86: Setting the LD random seed to -1267269637 86: 86: Generated 136 of the 136 non-bonded parameter combinations 86: 86: Generated 136 of the 136 1-4 parameter combinations 86: 86: Excluding 3 bonded neighbours molecule type 'ASN' 86: 86: turning H bonds into constraints... 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: turning H bonds into constraints... 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/transformAtoB/conf.gro' 86: Analysing residue names: 86: There are: 1 Protein residues 86: There are: 56 Water residues 86: Analysing Protein... 86: 86: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 86: 86: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: Calculating fourier grid dimensions for X Y Z 86: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 86: 86: Estimate for the relative computational load of the PME mesh part: 0.92 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.193 0.097 199.7 86: (ns/day) (hour/ns) 86: Performance: 18.791 1.277 86: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_d_energy.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 86: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_d (293 ms) 86: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/vdwalone_d 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 86: With PME there is a minor soft core effect present at the cut-off, 86: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 86: energy conservation, but usually other effects dominate. With a common 86: sigma value of 0.34 nm the fraction of the particle-particle potential at 86: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 355.00 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 86: The optimal PME mesh load for parallel simulations is below 0.5 86: and for highly parallel simulations between 0.25 and 0.33, 86: for higher performance, increase the cut-off and the PME grid spacing. 86: 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 86: For free energy simulations, the optimal load limit increases from 0.5 to 86: 0.667 86: 86: 86: 86: There were 3 NOTEs 86: 86: There was 1 WARNING 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_d_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 86: Changing nstlist from 10 to 100, rlist from 1 to 1 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'AA' 86: 20 steps, 0.0 ps. 86: Setting the LD random seed to -1510081569 86: 86: Generated 136 of the 136 non-bonded parameter combinations 86: 86: Generated 136 of the 136 1-4 parameter combinations 86: 86: Excluding 3 bonded neighbours molecule type 'ASN' 86: 86: turning H bonds into constraints... 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: turning H bonds into constraints... 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/vdwalone/conf.gro' 86: Analysing residue names: 86: There are: 1 Protein residues 86: There are: 56 Water residues 86: Analysing Protein... 86: 86: The largest distance between non-perturbed excluded atoms is 0.172 nm between atom 8 and 9 86: 86: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: Calculating fourier grid dimensions for X Y Z 86: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 86: 86: Estimate for the relative computational load of the PME mesh part: 0.86 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.124 0.062 199.6 86: (ns/day) (hour/ns) 86: Performance: 29.281 0.820 86: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_d_energy.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 86: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/vdwalone_d (249 ms) 86: [----------] 12 tests from EquivalentToReference/FreeEnergyReferenceTest (4236 ms total) 86: 86: [----------] Global test environment tear-down 86: [==========] 14 tests from 2 test suites ran. (4606 ms total) 86: [ PASSED ] 14 tests. 86/90 Test #86: MdrunFEPTests ............................. Passed 4.64 sec test 87 Start 87: MdrunPullTests 87: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/mdrun-pull-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/MdrunPullTests.xml" 87: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests 87: Test timeout computed to be: 600 87: [==========] Running 4 tests from 1 test suite. 87: [----------] Global test environment set-up. 87: [----------] 4 tests from PullTest/PullIntegrationTest 87: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/0 87: Generating 1-4 interactions: fudge = 0.5 87: Pull group 1 'r_1' has 3 atoms 87: Pull group 2 'r_2' has 3 atoms 87: Number of degrees of freedom in T-Coupling group System is 1293.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0_input.mdp]: 87: NVE simulation: will use the initial temperature of 303.122 K for 87: determining the Verlet buffer size 87: 87: Pull group natoms pbc atom distance at start reference at t=0 87: 1 3 2 87: 2 3 5 0.575 nm 0.600 nm 87: 87: There was 1 NOTE 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 1 MPI thread 87: Using 2 OpenMP threads 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 20 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc216.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.353 0.177 199.8 87: (ns/day) (hour/ns) 87: Performance: 10.278 2.335 87: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/0 (729 ms) 87: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/1 87: Generating 1-4 interactions: fudge = 0.5 87: Pull group 1 'r_1' has 3 atoms 87: Pull group 2 'r_2' has 3 atoms 87: Number of degrees of freedom in T-Coupling group System is 1293.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1_input.mdp]: 87: NVE simulation: will use the initial temperature of 303.122 K for 87: determining the Verlet buffer size 87: 87: Pull group natoms pbc atom distance at start reference at t=0 87: 1 3 2 87: 2 3 5 0.301 nm 0.400 nm 87: 87: There was 1 NOTE 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 1 MPI thread 87: Using 2 OpenMP threads 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 20 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc216.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.097 0.049 199.6 87: (ns/day) (hour/ns) 87: Performance: 37.273 0.644 87: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/1 (671 ms) 87: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/2 87: Generating 1-4 interactions: fudge = 0.5 87: Pull group 1 'r_1' has 3 atoms 87: Pull group 2 'r_2' has 3 atoms 87: Pull group 3 'r_3' has 3 atoms 87: Number of degrees of freedom in T-Coupling group System is 1292.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2_input.mdp]: 87: NVE simulation: will use the initial temperature of 303.357 K for 87: determining the Verlet buffer size 87: 87: Pull group natoms pbc atom distance at start reference at t=0 87: 1 3 2 87: 2 3 5 0.575 nm 0.500 nm 87: 1 3 2 87: 3 3 8 0.331 nm 0.400 nm 87: 87: There was 1 NOTE 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 1 MPI thread 87: Using 2 OpenMP threads 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 20 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc216.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.357 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.084 0.042 199.5 87: (ns/day) (hour/ns) 87: Performance: 43.053 0.557 87: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/2 (602 ms) 87: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/3 87: Generating 1-4 interactions: fudge = 0.5 87: Pull group 1 'r_1' has 3 atoms 87: Pull group 2 'r_2' has 3 atoms 87: Number of degrees of freedom in T-Coupling group System is 1293.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3_input.mdp]: 87: NVE simulation: will use the initial temperature of 303.122 K for 87: determining the Verlet buffer size 87: 87: Pull group natoms pbc atom distance at start reference at t=0 87: 1 3 2 87: 2 3 5 0.575 nm 0.000 nm 87: 1 3 2 87: 2 3 5 0.050 nm 0.000 nm 87: 87: There was 1 NOTE 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 1 MPI thread 87: Using 2 OpenMP threads 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 20 steps, 0.0 ps. 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc216.gro' 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.090 0.045 199.4 87: (ns/day) (hour/ns) 87: Performance: 40.007 0.600 87: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3.edr as double precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/3 (636 ms) 87: [----------] 4 tests from PullTest/PullIntegrationTest (2640 ms total) 87: 87: [----------] Global test environment tear-down 87: [==========] 4 tests from 1 test suite ran. (2722 ms total) 87: [ PASSED ] 4 tests. 87/90 Test #87: MdrunPullTests ............................ Passed 2.75 sec test 88 Start 88: MdrunRotationTests 88: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/mdrun-rotation-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/MdrunRotationTests.xml" 88: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests 88: Test timeout computed to be: 600 88: [==========] Running 12 tests from 1 test suite. 88: [----------] Global test environment set-up. 88: [----------] 12 tests from RotationWorks/RotationTest 88: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/0 88: Enforced rotation: Group 0 (iso) normalized rot. vector: 0.267261 0.534522 0.801784 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: Rotation group 0 'system' has 4 atoms 88: Number of degrees of freedom in T-Coupling group rest is 9.00 88: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0_input.mdp]: 88: NVE simulation with an initial temperature of zero: will use a Verlet 88: buffer of 10%. Check your energy drift! 88: 88: Enforced rotation: group 0 has 4 reference positions. 88: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 88: trr version: GMX_trn_file (single precision) 88: 88: There were 2 NOTEs 88: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 88: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 88: 25 steps, 0.1 ps. 88: Setting the LD random seed to -268730641 88: 88: Generated 1 of the 1 non-bonded parameter combinations 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonA' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonB' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonC' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonD' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.908 0.454 200.0 88: (ns/day) (hour/ns) 88: Performance: 9.894 2.426 88: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.edr as double precision energy file 88: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.edr as double precision energy file 88: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 88: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/0 (471 ms) 88: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/1 88: Enforced rotation: Group 0 (iso-pf) normalized rot. vector: 0.267261 0.534522 0.801784 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: Rotation group 0 'system' has 4 atoms 88: Number of degrees of freedom in T-Coupling group rest is 9.00 88: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1_input.mdp]: 88: NVE simulation with an initial temperature of zero: will use a Verlet 88: buffer of 10%. Check your energy drift! 88: 88: Enforced rotation: group 0 has 4 reference positions. 88: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 88: 88: There were 2 NOTEs 88: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 88: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 88: 25 steps, 0.1 ps. 88: Setting the LD random seed to -536936453 88: 88: Generated 1 of the 1 non-bonded parameter combinations 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonA' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonB' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonC' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonD' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.028 0.014 198.9 88: (ns/day) (hour/ns) 88: Performance: 322.233 0.074 88: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.edr as double precision energy file 88: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.edr as double precision energy file 88: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 88: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/1 (27 ms) 88: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/2 88: Enforced rotation: Group 0 (pm) normalized rot. vector: 0.267261 0.534522 0.801784 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: Rotation group 0 'system' has 4 atoms 88: Number of degrees of freedom in T-Coupling group rest is 9.00 88: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2_input.mdp]: 88: NVE simulation with an initial temperature of zero: will use a Verlet 88: buffer of 10%. Check your energy drift! 88: 88: Enforced rotation: group 0 has 4 reference positions. 88: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 88: 88: There were 2 NOTEs 88: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 88: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 88: 25 steps, 0.1 ps. 88: Setting the LD random seed to 1340537751 88: 88: Generated 1 of the 1 non-bonded parameter combinations 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonA' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonB' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonC' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonD' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.042 0.021 199.2 88: (ns/day) (hour/ns) 88: Performance: 211.291 0.114 88: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.edr as double precision energy file 88: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.edr as double precision energy file 88: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 88: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/2 (33 ms) 88: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/3 88: Enforced rotation: Group 0 (pm-pf) normalized rot. vector: 0.267261 0.534522 0.801784 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: Rotation group 0 'system' has 4 atoms 88: Number of degrees of freedom in T-Coupling group rest is 9.00 88: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3_input.mdp]: 88: NVE simulation with an initial temperature of zero: will use a Verlet 88: buffer of 10%. Check your energy drift! 88: 88: Enforced rotation: group 0 has 4 reference positions. 88: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 88: 88: There were 2 NOTEs 88: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 88: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 88: 25 steps, 0.1 ps. 88: Setting the LD random seed to -1343366273 88: 88: Generated 1 of the 1 non-bonded parameter combinations 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonA' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonB' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonC' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonD' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.038 0.019 199.2 88: (ns/day) (hour/ns) 88: Performance: 235.152 0.102 88: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.edr as double precision energy file 88: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.edr as double precision energy file 88: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 88: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/3 (30 ms) 88: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/4 88: Enforced rotation: Group 0 (rm) normalized rot. vector: 0.267261 0.534522 0.801784 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: Rotation group 0 'system' has 4 atoms 88: Number of degrees of freedom in T-Coupling group rest is 9.00 88: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4_input.mdp]: 88: NVE simulation with an initial temperature of zero: will use a Verlet 88: buffer of 10%. Check your energy drift! 88: 88: Enforced rotation: group 0 has 4 reference positions. 88: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 88: 88: There were 2 NOTEs 88: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 88: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 88: 25 steps, 0.1 ps. 88: Setting the LD random seed to -1629512578 88: 88: Generated 1 of the 1 non-bonded parameter combinations 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonA' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonB' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonC' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonD' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.033 0.016 199.0 88: (ns/day) (hour/ns) 88: Performance: 272.551 0.088 88: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.edr as double precision energy file 88: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.edr as double precision energy file 88: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 88: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/4 (29 ms) 88: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/5 88: Enforced rotation: Group 0 (rm-pf) normalized rot. vector: 0.267261 0.534522 0.801784 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: Rotation group 0 'system' has 4 atoms 88: Number of degrees of freedom in T-Coupling group rest is 9.00 88: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5_input.mdp]: 88: NVE simulation with an initial temperature of zero: will use a Verlet 88: buffer of 10%. Check your energy drift! 88: 88: Enforced rotation: group 0 has 4 reference positions. 88: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 88: 88: There were 2 NOTEs 88: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 88: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 88: 25 steps, 0.1 ps. 88: Setting the LD random seed to -27590787 88: 88: Generated 1 of the 1 non-bonded parameter combinations 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonA' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonB' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonC' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonD' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.026 0.014 191.5 88: (ns/day) (hour/ns) 88: Performance: 326.402 0.074 88: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.edr as double precision energy file 88: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.edr as double precision energy file 88: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 88: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/5 (23 ms) 88: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/6 88: Enforced rotation: Group 0 (rm2) normalized rot. vector: 0.267261 0.534522 0.801784 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: Rotation group 0 'system' has 4 atoms 88: Number of degrees of freedom in T-Coupling group rest is 9.00 88: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6_input.mdp]: 88: NVE simulation with an initial temperature of zero: will use a Verlet 88: buffer of 10%. Check your energy drift! 88: 88: Enforced rotation: group 0 has 4 reference positions. 88: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 88: 88: There were 2 NOTEs 88: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 88: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 88: 25 steps, 0.1 ps. 88: Setting the LD random seed to -605164050 88: 88: Generated 1 of the 1 non-bonded parameter combinations 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonA' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonB' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonC' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonD' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.027 0.014 198.7 88: (ns/day) (hour/ns) 88: Performance: 331.717 0.072 88: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.edr as double precision energy file 88: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.edr as double precision energy file 88: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 88: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/6 (23 ms) 88: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/7 88: Enforced rotation: Group 0 (rm2-pf) normalized rot. vector: 0.267261 0.534522 0.801784 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: Rotation group 0 'system' has 4 atoms 88: Number of degrees of freedom in T-Coupling group rest is 9.00 88: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7_input.mdp]: 88: NVE simulation with an initial temperature of zero: will use a Verlet 88: buffer of 10%. Check your energy drift! 88: 88: Enforced rotation: group 0 has 4 reference positions. 88: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 88: 88: There were 2 NOTEs 88: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 88: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 88: 25 steps, 0.1 ps. 88: Setting the LD random seed to -5785620 88: 88: Generated 1 of the 1 non-bonded parameter combinations 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonA' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonB' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonC' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonD' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.036 0.018 199.0 88: (ns/day) (hour/ns) 88: Performance: 251.594 0.095 88: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.edr as double precision energy file 88: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.edr as double precision energy file 88: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 88: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/7 (26 ms) 88: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/8 88: Enforced rotation: Group 0 (flex) normalized rot. vector: 0.267261 0.534522 0.801784 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: Rotation group 0 'system' has 4 atoms 88: Number of degrees of freedom in T-Coupling group rest is 9.00 88: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8_input.mdp]: 88: NVE simulation with an initial temperature of zero: will use a Verlet 88: buffer of 10%. Check your energy drift! 88: 88: Enforced rotation: group 0 has 4 reference positions. 88: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 88: 88: There were 2 NOTEs 88: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 88: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 88: 25 steps, 0.1 ps. 88: Setting the LD random seed to -134787683 88: 88: Generated 1 of the 1 non-bonded parameter combinations 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonA' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonB' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonC' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonD' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.031 0.015 198.9 88: (ns/day) (hour/ns) 88: Performance: 291.237 0.082 88: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.edr as double precision energy file 88: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.edr as double precision energy file 88: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 88: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/8 (25 ms) 88: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/9 88: Enforced rotation: Group 0 (flex-t) normalized rot. vector: 0.267261 0.534522 0.801784 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: Rotation group 0 'system' has 4 atoms 88: Number of degrees of freedom in T-Coupling group rest is 9.00 88: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9_input.mdp]: 88: NVE simulation with an initial temperature of zero: will use a Verlet 88: buffer of 10%. Check your energy drift! 88: 88: Enforced rotation: group 0 has 4 reference positions. 88: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 88: 88: There were 2 NOTEs 88: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 88: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 88: 25 steps, 0.1 ps. 88: Setting the LD random seed to -245452433 88: 88: Generated 1 of the 1 non-bonded parameter combinations 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonA' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonB' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonC' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonD' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.031 0.015 198.8 88: (ns/day) (hour/ns) 88: Performance: 289.915 0.083 88: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.edr as double precision energy file 88: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.edr as double precision energy file 88: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 88: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/9 (24 ms) 88: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/10 88: Enforced rotation: Group 0 (flex2) normalized rot. vector: 0.267261 0.534522 0.801784 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: Rotation group 0 'system' has 4 atoms 88: Number of degrees of freedom in T-Coupling group rest is 9.00 88: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10_input.mdp]: 88: NVE simulation with an initial temperature of zero: will use a Verlet 88: buffer of 10%. Check your energy drift! 88: 88: Enforced rotation: group 0 has 4 reference positions. 88: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 88: 88: There were 2 NOTEs 88: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 88: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 88: 25 steps, 0.1 ps. 88: Setting the LD random seed to -1619285027 88: 88: Generated 1 of the 1 non-bonded parameter combinations 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonA' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonB' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonC' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonD' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.030 0.015 198.7 88: (ns/day) (hour/ns) 88: Performance: 296.941 0.081 88: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.edr as double precision energy file 88: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.edr as double precision energy file 88: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 88: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/10 (24 ms) 88: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/11 88: Enforced rotation: Group 0 (flex2-t) normalized rot. vector: 0.267261 0.534522 0.801784 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: Rotation group 0 'system' has 4 atoms 88: Number of degrees of freedom in T-Coupling group rest is 9.00 88: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11_input.mdp]: 88: NVE simulation with an initial temperature of zero: will use a Verlet 88: buffer of 10%. Check your energy drift! 88: 88: Enforced rotation: group 0 has 4 reference positions. 88: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 88: 88: There were 2 NOTEs 88: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 88: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 88: Can not increase nstlist because an NVE ensemble is used 88: Using 1 MPI thread 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 88: 25 steps, 0.1 ps. 88: Setting the LD random seed to -335821314 88: 88: Generated 1 of the 1 non-bonded parameter combinations 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonA' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonB' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonC' 88: 88: Excluding 1 bonded neighbours molecule type 'ArgonD' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.031 0.015 198.9 88: (ns/day) (hour/ns) 88: Performance: 290.958 0.082 88: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.edr as double precision energy file 88: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.edr as double precision energy file 88: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 88: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/11 (24 ms) 88: [----------] 12 tests from RotationWorks/RotationTest (765 ms total) 88: 88: [----------] Global test environment tear-down 88: [==========] 12 tests from 1 test suite ran. (874 ms total) 88: [ PASSED ] 12 tests. 88/90 Test #88: MdrunRotationTests ........................ Passed 0.90 sec test 89 Start 89: MdrunSimulatorComparison 89: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/mdrun-simulator-comparison-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/MdrunSimulatorComparison.xml" 89: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests 89: Test timeout computed to be: 600 89: [==========] Running 94 tests from 4 test suites. 89: [----------] Global test environment set-up. 89: [----------] 60 tests from SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/0 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/0 (0 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/1 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: 89: NVE simulation: will use the initial temperature of 68.810 K for 89: determining the Verlet buffer size 89: 89: 89: There were 3 NOTEs 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.032 0.016 199.3 89: (ns/day) (hour/ns) 89: Performance: 90.440 0.265 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.021 0.011 198.7 89: (ns/day) (hour/ns) 89: Performance: 139.750 0.172 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 trr version: GMX_trn_file (double precision) 89: 89: 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/1 (41 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/2 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 89: The Berendsen barostat does not generate any strictly correct ensemble, 89: and should not be used for new production simulations (in our opinion). 89: We recommend using the C-rescale barostat instead. 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 89: NVE simulation: will use the initial temperature of 68.810 K for 89: determining the Verlet buffer size 89: 89: 89: There were 3 NOTEs 89: 89: There was 1 WARNING 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.028 0.014 199.1 89: (ns/day) (hour/ns) 89: Performance: 103.111 0.233 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.028 0.014 198.8 89: (ns/day) (hour/ns) 89: Performance: 102.912 0.233 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim2.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/2 (41 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/3 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/3 (0 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/4 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/4 (0 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/5 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/5 (0 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/6 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_6_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_6_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: There were 2 NOTEs 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_6_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.041 0.021 199.2 89: (ns/day) (hour/ns) 89: Performance: 71.112 0.337 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_6_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.021 0.011 198.8 89: (ns/day) (hour/ns) 89: Performance: 138.090 0.174 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_6_sim2.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_6_sim1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/6 (49 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/7 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_input.mdp]: 89: The Berendsen barostat does not generate any strictly correct ensemble, 89: and should not be used for new production simulations (in our opinion). 89: We recommend using the C-rescale barostat instead. 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: There were 2 NOTEs 89: 89: There was 1 WARNING 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.035 0.018 199.3 89: (ns/day) (hour/ns) 89: Performance: 83.630 0.287 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.022 0.011 198.3 89: (ns/day) (hour/ns) 89: Performance: 134.455 0.178 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_sim2.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_sim1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/7 (39 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/8 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_8_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_8_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: There were 2 NOTEs 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_8_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.036 0.018 199.3 89: (ns/day) (hour/ns) 89: Performance: 80.733 0.297 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_8_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.023 0.012 198.6 89: (ns/day) (hour/ns) 89: Performance: 127.435 0.188 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_8_sim2.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_8_sim1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/8 (41 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/9 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/9 (0 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/10 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/10 (0 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/11 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_input.mdp]: 89: The Berendsen thermostat does not generate the correct kinetic energy 89: distribution, and should not be used for new production simulations (in 89: our opinion). We would recommend the V-rescale thermostat. 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: There were 2 NOTEs 89: 89: There was 1 WARNING 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.032 0.016 199.2 89: (ns/day) (hour/ns) 89: Performance: 90.103 0.266 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.020 0.010 198.0 89: (ns/day) (hour/ns) 89: Performance: 147.559 0.163 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_sim2.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_sim1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/11 (37 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/12 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: 89: The Berendsen thermostat does not generate the correct kinetic energy 89: distribution, and should not be used for new production simulations (in 89: our opinion). We would recommend the V-rescale thermostat. 89: 89: 89: WARNING 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: 89: The Berendsen barostat does not generate any strictly correct ensemble, 89: and should not be used for new production simulations (in our opinion). 89: We recommend using the C-rescale barostat instead. 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: There were 2 NOTEs 89: 89: There were 2 WARNINGs 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.027 0.014 198.8 89: (ns/day) (hour/ns) 89: Performance: 107.124 0.224 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.021 0.010 198.5 89: (ns/day) (hour/ns) 89: Performance: 139.893 0.172 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_sim2.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_sim1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/12 (34 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/13 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_input.mdp]: 89: The Berendsen thermostat does not generate the correct kinetic energy 89: distribution, and should not be used for new production simulations (in 89: our opinion). We would recommend the V-rescale thermostat. 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: There were 2 NOTEs 89: 89: There was 1 WARNING 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.034 0.017 199.3 89: (ns/day) (hour/ns) 89: Performance: 87.019 0.276 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.025 0.013 198.8 89: (ns/day) (hour/ns) 89: Performance: 116.506 0.206 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_sim2.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_sim1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/13 (39 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/14 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/14 (0 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/15 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_input.mdp]: 89: MTTK coupling is deprecated and will soon be removed 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: There were 3 NOTEs 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.030 0.015 198.7 89: (ns/day) (hour/ns) 89: Performance: 98.236 0.244 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.020 0.010 198.4 89: (ns/day) (hour/ns) 89: Performance: 144.775 0.166 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_sim2.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_sim1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/15 (37 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/16 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_16_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_16_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: There were 2 NOTEs 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_16_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.046 0.023 199.3 89: (ns/day) (hour/ns) 89: Performance: 63.922 0.375 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_16_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.051 0.026 199.1 89: (ns/day) (hour/ns) 89: Performance: 57.360 0.418 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_16_sim2.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_16_sim1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/16 (60 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/17 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/17 (0 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/18 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: There were 2 NOTEs 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_18_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.061 0.031 199.4 89: (ns/day) (hour/ns) 89: Performance: 47.945 0.501 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_18_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.028 0.014 198.9 89: (ns/day) (hour/ns) 89: Performance: 104.465 0.230 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_18_sim2.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_18_sim1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/18 (69 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/19 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_input.mdp]: 89: MTTK coupling is deprecated and will soon be removed 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: There were 3 NOTEs 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.033 0.017 199.1 89: (ns/day) (hour/ns) 89: Performance: 88.100 0.272 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.938 0.469 199.9 89: (ns/day) (hour/ns) 89: Performance: 3.130 7.668 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_sim2.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_sim1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/19 (577 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/20 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/20 (0 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/21 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_input.mdp]: 89: Andersen temperature control methods assume nsttcouple = 1; there is no 89: need for larger nsttcouple > 1, since no global parameters are computed. 89: nsttcouple has been reset to 1 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: There were 3 NOTEs 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 2.343 1.172 200.0 89: (ns/day) (hour/ns) 89: Performance: 1.254 19.146 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 2.106 1.053 200.0 89: (ns/day) (hour/ns) 89: Performance: 1.395 17.208 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_sim2.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_sim1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/21 (2465 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/22 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 89: The Berendsen barostat does not generate any strictly correct ensemble, 89: and should not be used for new production simulations (in our opinion). 89: We recommend using the C-rescale barostat instead. 89: 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 89: Andersen temperature control methods assume nsttcouple = 1; there is no 89: need for larger nsttcouple > 1, since no global parameters are computed. 89: nsttcouple has been reset to 1 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: There were 3 NOTEs 89: 89: There was 1 WARNING 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.573 0.287 199.9 89: (ns/day) (hour/ns) 89: Performance: 5.125 4.683 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 3.008 1.504 200.0 89: (ns/day) (hour/ns) 89: Performance: 0.977 24.575 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_sim2.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_sim1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/22 (1973 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/23 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_input.mdp]: 89: Andersen temperature control methods assume nsttcouple = 1; there is no 89: need for larger nsttcouple > 1, since no global parameters are computed. 89: nsttcouple has been reset to 1 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: There were 3 NOTEs 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 1.273 0.636 200.0 89: (ns/day) (hour/ns) 89: Performance: 2.308 10.398 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.094 0.047 199.6 89: (ns/day) (hour/ns) 89: Performance: 31.271 0.767 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_sim2.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_sim1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/23 (722 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/24 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/24 (0 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/25 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/25 (0 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/26 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 89: Center of mass removal not necessary for Andersen. All velocities of 89: coupled groups are rerandomized periodically, so flying ice cube errors 89: will not occur. 89: 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 89: Andersen temperature control methods assume nsttcouple = 1; there is no 89: need for larger nsttcouple > 1, since no global parameters are computed. 89: nsttcouple has been reset to 1 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: There were 3 NOTEs 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.046 0.023 199.3 89: (ns/day) (hour/ns) 89: Performance: 63.221 0.380 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.027 0.013 198.8 89: (ns/day) (hour/ns) 89: Performance: 109.500 0.219 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_sim2.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_sim1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/26 (62 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/27 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 89: Center of mass removal not necessary for Andersen. All velocities of 89: coupled groups are rerandomized periodically, so flying ice cube errors 89: will not occur. 89: 89: 89: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 89: The Berendsen barostat does not generate any strictly correct ensemble, 89: and should not be used for new production simulations (in our opinion). 89: We recommend using the C-rescale barostat instead. 89: 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 89: Andersen temperature control methods assume nsttcouple = 1; there is no 89: need for larger nsttcouple > 1, since no global parameters are computed. 89: nsttcouple has been reset to 1 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: There were 3 NOTEs 89: 89: There was 1 WARNING 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.036 0.018 199.1 89: (ns/day) (hour/ns) 89: Performance: 80.722 0.297 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.029 0.015 198.8 89: (ns/day) (hour/ns) 89: Performance: 99.153 0.242 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_sim2.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_sim1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/27 (58 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/28 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: 89: Center of mass removal not necessary for Andersen. All velocities of 89: coupled groups are rerandomized periodically, so flying ice cube errors 89: will not occur. 89: 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: 89: Andersen temperature control methods assume nsttcouple = 1; there is no 89: need for larger nsttcouple > 1, since no global parameters are computed. 89: nsttcouple has been reset to 1 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: There were 3 NOTEs 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.055 0.027 199.3 89: (ns/day) (hour/ns) 89: Performance: 53.544 0.448 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.037 0.019 198.6 89: (ns/day) (hour/ns) 89: Performance: 78.140 0.307 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_sim2.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_sim1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/28 (60 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/29 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/29 (0 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/30 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/30 (0 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/31 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Generating 1-4 interactions: fudge = 0.5 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 89: NVE simulation: will use the initial temperature of 398.997 K for 89: determining the Verlet buffer size 89: 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 4 NOTEs 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.678 0.339 200.0 89: (ns/day) (hour/ns) 89: Performance: 4.332 5.540 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.959 0.480 200.0 89: (ns/day) (hour/ns) 89: Performance: 3.063 7.835 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_sim2.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_sim1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/31 (1662 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/32 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_input.mdp]: 89: The Berendsen barostat does not generate any strictly correct ensemble, 89: and should not be used for new production simulations (in our opinion). 89: We recommend using the C-rescale barostat instead. 89: 89: Generating 1-4 interactions: fudge = 0.5 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_input.mdp]: 89: NVE simulation: will use the initial temperature of 398.997 K for 89: determining the Verlet buffer size 89: 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 4 NOTEs 89: 89: There was 1 WARNING 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 1.556 0.778 200.0 89: (ns/day) (hour/ns) 89: Performance: 1.887 12.715 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 2.355 1.178 200.0 89: (ns/day) (hour/ns) 89: Performance: 1.247 19.243 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_sim2.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_sim1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/32 (3336 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/33 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/33 (0 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/34 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/34 (0 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/35 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/35 (0 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/36 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Generating 1-4 interactions: fudge = 0.5 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 3 NOTEs 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 1.339 0.670 200.0 89: (ns/day) (hour/ns) 89: Performance: 2.193 10.942 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 2.251 1.125 200.0 89: (ns/day) (hour/ns) 89: Performance: 1.305 18.389 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_sim2.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_sim1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/36 (2854 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/37 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_input.mdp]: 89: The Berendsen barostat does not generate any strictly correct ensemble, 89: and should not be used for new production simulations (in our opinion). 89: We recommend using the C-rescale barostat instead. 89: 89: Generating 1-4 interactions: fudge = 0.5 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 3 NOTEs 89: 89: There was 1 WARNING 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.727 0.364 199.9 89: (ns/day) (hour/ns) 89: Performance: 4.040 5.941 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.142 0.071 199.3 89: (ns/day) (hour/ns) 89: Performance: 20.671 1.161 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_sim2.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_sim1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/37 (1104 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/38 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Generating 1-4 interactions: fudge = 0.5 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 3 NOTEs 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.117 0.059 199.6 89: (ns/day) (hour/ns) 89: Performance: 25.076 0.957 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.095 0.048 199.1 89: (ns/day) (hour/ns) 89: Performance: 30.811 0.779 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_sim2.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_sim1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/38 (1215 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/39 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/39 (0 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/40 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/40 (0 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/41 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_input.mdp]: 89: The Berendsen thermostat does not generate the correct kinetic energy 89: distribution, and should not be used for new production simulations (in 89: our opinion). We would recommend the V-rescale thermostat. 89: 89: Generating 1-4 interactions: fudge = 0.5 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 3 NOTEs 89: 89: There was 1 WARNING 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: NOTE: 26 % of the run time was spent in pair search, 89: you might want to increase nstlist (this has no effect on accuracy) 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.617 0.309 199.9 89: (ns/day) (hour/ns) 89: Performance: 4.759 5.043 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.089 0.045 199.5 89: (ns/day) (hour/ns) 89: Performance: 32.790 0.732 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_sim2.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_sim1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/41 (1600 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/42 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_input.mdp]: 89: The Berendsen thermostat does not generate the correct kinetic energy 89: distribution, and should not be used for new production simulations (in 89: our opinion). We would recommend the V-rescale thermostat. 89: 89: 89: WARNING 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_input.mdp]: 89: The Berendsen barostat does not generate any strictly correct ensemble, 89: and should not be used for new production simulations (in our opinion). 89: We recommend using the C-rescale barostat instead. 89: 89: Generating 1-4 interactions: fudge = 0.5 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 3 NOTEs 89: 89: There were 2 WARNINGs 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 1.411 0.706 200.0 89: (ns/day) (hour/ns) 89: Performance: 2.082 11.530 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 2.436 1.218 199.9 89: (ns/day) (hour/ns) 89: Performance: 1.205 19.910 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_sim2.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_sim1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/42 (2730 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/43 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_input.mdp]: 89: The Berendsen thermostat does not generate the correct kinetic energy 89: distribution, and should not be used for new production simulations (in 89: our opinion). We would recommend the V-rescale thermostat. 89: 89: Generating 1-4 interactions: fudge = 0.5 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 3 NOTEs 89: 89: There was 1 WARNING 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.131 0.066 199.7 89: (ns/day) (hour/ns) 89: Performance: 22.320 1.075 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.131 0.066 199.7 89: (ns/day) (hour/ns) 89: Performance: 22.352 1.074 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_sim2.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_sim1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/43 (990 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/44 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/44 (0 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/45 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/45 (0 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/46 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Generating 1-4 interactions: fudge = 0.5 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 3 NOTEs 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.479 0.240 199.9 89: (ns/day) (hour/ns) 89: Performance: 6.128 3.916 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.156 0.078 199.6 89: (ns/day) (hour/ns) 89: Performance: 18.741 1.281 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_sim2.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_sim1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/46 (1461 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/47 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/47 (0 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/48 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Generating 1-4 interactions: fudge = 0.5 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 3 NOTEs 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.087 0.043 199.6 89: (ns/day) (hour/ns) 89: Performance: 33.823 0.710 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.078 0.039 199.3 89: (ns/day) (hour/ns) 89: Performance: 37.617 0.638 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_sim2.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_sim1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/48 (978 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/49 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/49 (0 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/50 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/50 (0 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/51 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Generating 1-4 interactions: fudge = 0.5 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_input.mdp]: 89: Andersen temperature control methods assume nsttcouple = 1; there is no 89: need for larger nsttcouple > 1, since no global parameters are computed. 89: nsttcouple has been reset to 1 89: 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 4 NOTEs 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.234 0.117 199.8 89: (ns/day) (hour/ns) 89: Performance: 12.547 1.913 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.119 0.059 199.7 89: (ns/day) (hour/ns) 89: Performance: 24.689 0.972 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_sim2.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_sim1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/51 (973 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/52 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_input.mdp]: 89: The Berendsen barostat does not generate any strictly correct ensemble, 89: and should not be used for new production simulations (in our opinion). 89: We recommend using the C-rescale barostat instead. 89: 89: Generating 1-4 interactions: fudge = 0.5 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_input.mdp]: 89: Andersen temperature control methods assume nsttcouple = 1; there is no 89: need for larger nsttcouple > 1, since no global parameters are computed. 89: nsttcouple has been reset to 1 89: 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 4 NOTEs 89: 89: There was 1 WARNING 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.059 0.029 199.3 89: (ns/day) (hour/ns) 89: Performance: 50.045 0.480 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.065 0.032 199.4 89: (ns/day) (hour/ns) 89: Performance: 45.262 0.530 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_sim2.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_sim1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/52 (1007 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/53 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Generating 1-4 interactions: fudge = 0.5 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_input.mdp]: 89: Andersen temperature control methods assume nsttcouple = 1; there is no 89: need for larger nsttcouple > 1, since no global parameters are computed. 89: nsttcouple has been reset to 1 89: 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 4 NOTEs 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.033 0.017 198.9 89: (ns/day) (hour/ns) 89: Performance: 88.262 0.272 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.049 0.025 199.1 89: (ns/day) (hour/ns) 89: Performance: 59.110 0.406 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_sim2.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_sim1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/53 (688 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/54 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/54 (0 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/55 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/55 (0 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/56 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/56 (0 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/57 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/57 (0 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/58 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/58 (0 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/59 89: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/59 (0 ms) 89: [----------] 60 tests from SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest (27025 ms total) 89: 89: [----------] 32 tests from SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/0 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 89: NVE simulation: will use the initial temperature of 68.810 K for 89: determining the Verlet buffer size 89: 89: 89: There were 3 NOTEs 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.032 0.016 199.0 89: (ns/day) (hour/ns) 89: Performance: 90.218 0.266 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.037 0.019 199.4 89: (ns/day) (hour/ns) 89: Performance: 78.873 0.304 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/0 (51 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/1 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: 89: NVE simulation: will use the initial temperature of 68.810 K for 89: determining the Verlet buffer size 89: 89: 89: There were 3 NOTEs 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.019 0.010 198.4 89: (ns/day) (hour/ns) 89: Performance: 154.061 0.156 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.029 0.014 199.2 89: (ns/day) (hour/ns) 89: Performance: 101.595 0.236 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/1 (39 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/2 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 89: The Berendsen barostat does not generate any strictly correct ensemble, 89: and should not be used for new production simulations (in our opinion). 89: We recommend using the C-rescale barostat instead. 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 89: NVE simulation: will use the initial temperature of 68.810 K for 89: determining the Verlet buffer size 89: 89: 89: There were 3 NOTEs 89: 89: There was 1 WARNING 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.022 0.011 198.5 89: (ns/day) (hour/ns) 89: Performance: 133.543 0.180 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.025 0.013 199.1 89: (ns/day) (hour/ns) 89: Performance: 115.408 0.208 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim2.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/2 (41 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/3 89: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/3 (0 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/4 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: There were 2 NOTEs 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.023 0.012 198.8 89: (ns/day) (hour/ns) 89: Performance: 125.757 0.191 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.039 0.019 199.3 89: (ns/day) (hour/ns) 89: Performance: 75.557 0.318 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim2.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/4 (44 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/5 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: There were 2 NOTEs 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.037 0.019 199.2 89: (ns/day) (hour/ns) 89: Performance: 79.344 0.302 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.045 0.023 199.3 89: (ns/day) (hour/ns) 89: Performance: 65.090 0.369 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim2.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/5 (59 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/6 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_input.mdp]: 89: The Berendsen barostat does not generate any strictly correct ensemble, 89: and should not be used for new production simulations (in our opinion). 89: We recommend using the C-rescale barostat instead. 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: There were 2 NOTEs 89: 89: There was 1 WARNING 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.025 0.012 198.8 89: (ns/day) (hour/ns) 89: Performance: 117.535 0.204 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.037 0.019 199.2 89: (ns/day) (hour/ns) 89: Performance: 79.221 0.303 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim2.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/6 (47 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/7 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: There were 2 NOTEs 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.033 0.017 199.0 89: (ns/day) (hour/ns) 89: Performance: 88.658 0.271 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.035 0.018 198.7 89: (ns/day) (hour/ns) 89: Performance: 83.150 0.289 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim2.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/7 (52 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/8 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_input.mdp]: 89: The Berendsen thermostat does not generate the correct kinetic energy 89: distribution, and should not be used for new production simulations (in 89: our opinion). We would recommend the V-rescale thermostat. 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: There were 2 NOTEs 89: 89: There was 1 WARNING 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.028 0.014 199.0 89: (ns/day) (hour/ns) 89: Performance: 104.136 0.230 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.032 0.016 199.2 89: (ns/day) (hour/ns) 89: Performance: 90.307 0.266 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_sim2.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_sim1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/8 (53 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/9 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_input.mdp]: 89: The Berendsen thermostat does not generate the correct kinetic energy 89: distribution, and should not be used for new production simulations (in 89: our opinion). We would recommend the V-rescale thermostat. 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: There were 2 NOTEs 89: 89: There was 1 WARNING 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.034 0.017 199.2 89: (ns/day) (hour/ns) 89: Performance: 84.841 0.283 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.073 0.036 199.6 89: (ns/day) (hour/ns) 89: Performance: 40.341 0.595 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_sim2.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_sim1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/9 (85 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/10 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_input.mdp]: 89: The Berendsen thermostat does not generate the correct kinetic energy 89: distribution, and should not be used for new production simulations (in 89: our opinion). We would recommend the V-rescale thermostat. 89: 89: 89: WARNING 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_input.mdp]: 89: The Berendsen barostat does not generate any strictly correct ensemble, 89: and should not be used for new production simulations (in our opinion). 89: We recommend using the C-rescale barostat instead. 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: There were 2 NOTEs 89: 89: There were 2 WARNINGs 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.026 0.013 198.9 89: (ns/day) (hour/ns) 89: Performance: 114.326 0.210 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.050 0.025 199.2 89: (ns/day) (hour/ns) 89: Performance: 58.803 0.408 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_sim2.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_sim1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/10 (48 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/11 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_input.mdp]: 89: The Berendsen thermostat does not generate the correct kinetic energy 89: distribution, and should not be used for new production simulations (in 89: our opinion). We would recommend the V-rescale thermostat. 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: There were 2 NOTEs 89: 89: There was 1 WARNING 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.048 0.024 199.3 89: (ns/day) (hour/ns) 89: Performance: 60.663 0.396 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.063 0.032 199.4 89: (ns/day) (hour/ns) 89: Performance: 46.249 0.519 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_sim2.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_sim1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/11 (70 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/12 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: 89: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 89: 1 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: There were 3 NOTEs 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.029 0.014 198.9 89: (ns/day) (hour/ns) 89: Performance: 101.573 0.236 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.062 0.031 199.5 89: (ns/day) (hour/ns) 89: Performance: 47.242 0.508 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_sim2.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_sim1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/12 (65 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/13 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_input.mdp]: 89: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 89: 1 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: There were 3 NOTEs 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.018 0.009 198.2 89: (ns/day) (hour/ns) 89: Performance: 161.636 0.148 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.032 0.016 199.0 89: (ns/day) (hour/ns) 89: Performance: 91.372 0.263 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_sim2.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_sim1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/13 (35 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/14 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_input.mdp]: 89: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 89: 1 89: 89: 89: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_input.mdp]: 89: The Berendsen barostat does not generate any strictly correct ensemble, 89: and should not be used for new production simulations (in our opinion). 89: We recommend using the C-rescale barostat instead. 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: There were 3 NOTEs 89: 89: There was 1 WARNING 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.025 0.012 198.5 89: (ns/day) (hour/ns) 89: Performance: 118.715 0.202 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.030 0.015 198.9 89: (ns/day) (hour/ns) 89: Performance: 97.829 0.245 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_sim2.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_sim1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/14 (41 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/15 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_input.mdp]: 89: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 89: 1 89: 89: Number of degrees of freedom in T-Coupling group System is 33.00 89: 89: There were 3 NOTEs 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: Generated 1 of the 1 non-bonded parameter combinations 89: 89: Excluding 1 bonded neighbours molecule type 'Argon' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.025 0.013 198.6 89: (ns/day) (hour/ns) 89: Performance: 116.530 0.206 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Argon' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.030 0.015 198.9 89: (ns/day) (hour/ns) 89: Performance: 98.063 0.245 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_sim2.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_sim1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/15 (40 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/16 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Generating 1-4 interactions: fudge = 0.5 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_input.mdp]: 89: NVE simulation: will use the initial temperature of 398.997 K for 89: determining the Verlet buffer size 89: 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 4 NOTEs 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 1.066 0.533 199.9 89: (ns/day) (hour/ns) 89: Performance: 2.756 8.708 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.227 0.114 199.7 89: (ns/day) (hour/ns) 89: Performance: 12.897 1.861 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_sim2.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_sim1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/16 (1323 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/17 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Generating 1-4 interactions: fudge = 0.5 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_input.mdp]: 89: NVE simulation: will use the initial temperature of 398.997 K for 89: determining the Verlet buffer size 89: 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 4 NOTEs 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.372 0.186 199.9 89: (ns/day) (hour/ns) 89: Performance: 7.897 3.039 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.050 0.025 199.4 89: (ns/day) (hour/ns) 89: Performance: 58.983 0.407 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_sim2.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_sim1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/17 (970 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/18 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: 89: The Berendsen barostat does not generate any strictly correct ensemble, 89: and should not be used for new production simulations (in our opinion). 89: We recommend using the C-rescale barostat instead. 89: 89: Generating 1-4 interactions: fudge = 0.5 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: 89: NVE simulation: will use the initial temperature of 398.997 K for 89: determining the Verlet buffer size 89: 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 4 NOTEs 89: 89: There was 1 WARNING 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.068 0.034 199.3 89: (ns/day) (hour/ns) 89: Performance: 42.983 0.558 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 26 % of the run time was spent in pair search, 89: you might want to increase nstlist (this has no effect on accuracy) 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.152 0.076 199.7 89: (ns/day) (hour/ns) 89: Performance: 19.352 1.240 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_sim2.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_sim1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/18 (749 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/19 89: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/19 (0 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/20 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Generating 1-4 interactions: fudge = 0.5 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 3 NOTEs 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 3.036 1.518 200.0 89: (ns/day) (hour/ns) 89: Performance: 0.968 24.805 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.137 0.068 199.7 89: (ns/day) (hour/ns) 89: Performance: 21.479 1.117 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_sim2.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_sim1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/20 (2342 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/21 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Generating 1-4 interactions: fudge = 0.5 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 3 NOTEs 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.157 0.078 199.7 89: (ns/day) (hour/ns) 89: Performance: 18.715 1.282 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.104 0.052 199.5 89: (ns/day) (hour/ns) 89: Performance: 28.086 0.855 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_sim2.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_sim1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/21 (840 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/22 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 89: The Berendsen barostat does not generate any strictly correct ensemble, 89: and should not be used for new production simulations (in our opinion). 89: We recommend using the C-rescale barostat instead. 89: 89: Generating 1-4 interactions: fudge = 0.5 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 3 NOTEs 89: 89: There was 1 WARNING 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.087 0.044 199.1 89: (ns/day) (hour/ns) 89: Performance: 33.693 0.712 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.106 0.053 199.0 89: (ns/day) (hour/ns) 89: Performance: 27.687 0.867 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_sim2.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_sim1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/22 (845 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/23 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Generating 1-4 interactions: fudge = 0.5 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 3 NOTEs 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 2.826 1.413 200.0 89: (ns/day) (hour/ns) 89: Performance: 1.039 23.092 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 2.579 1.290 200.0 89: (ns/day) (hour/ns) 89: Performance: 1.139 21.071 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_sim2.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_sim1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/23 (4160 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/24 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_input.mdp]: 89: The Berendsen thermostat does not generate the correct kinetic energy 89: distribution, and should not be used for new production simulations (in 89: our opinion). We would recommend the V-rescale thermostat. 89: 89: Generating 1-4 interactions: fudge = 0.5 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 3 NOTEs 89: 89: There was 1 WARNING 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.529 0.265 199.9 89: (ns/day) (hour/ns) 89: Performance: 5.548 4.326 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 3.399 1.700 200.0 89: (ns/day) (hour/ns) 89: Performance: 0.864 27.771 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_sim2.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_sim1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/24 (3057 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/25 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_input.mdp]: 89: The Berendsen thermostat does not generate the correct kinetic energy 89: distribution, and should not be used for new production simulations (in 89: our opinion). We would recommend the V-rescale thermostat. 89: 89: Generating 1-4 interactions: fudge = 0.5 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 3 NOTEs 89: 89: There was 1 WARNING 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 2.187 1.093 200.0 89: (ns/day) (hour/ns) 89: Performance: 1.343 17.866 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 1.994 0.997 200.0 89: (ns/day) (hour/ns) 89: Performance: 1.473 16.296 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_sim2.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_sim1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/25 (2822 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/26 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 89: The Berendsen thermostat does not generate the correct kinetic energy 89: distribution, and should not be used for new production simulations (in 89: our opinion). We would recommend the V-rescale thermostat. 89: 89: 89: WARNING 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 89: The Berendsen barostat does not generate any strictly correct ensemble, 89: and should not be used for new production simulations (in our opinion). 89: We recommend using the C-rescale barostat instead. 89: 89: Generating 1-4 interactions: fudge = 0.5 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 3 NOTEs 89: 89: There were 2 WARNINGs 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 2.464 1.235 199.4 89: (ns/day) (hour/ns) 89: Performance: 1.189 20.184 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 3.579 1.790 200.0 89: (ns/day) (hour/ns) 89: Performance: 0.821 29.245 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_sim2.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_sim1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/26 (3830 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/27 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 89: The Berendsen thermostat does not generate the correct kinetic energy 89: distribution, and should not be used for new production simulations (in 89: our opinion). We would recommend the V-rescale thermostat. 89: 89: Generating 1-4 interactions: fudge = 0.5 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 3 NOTEs 89: 89: There was 1 WARNING 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 1.435 0.717 200.0 89: (ns/day) (hour/ns) 89: Performance: 2.047 11.724 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 4.209 2.105 200.0 89: (ns/day) (hour/ns) 89: Performance: 0.698 34.387 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_sim2.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_sim1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/27 (3860 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/28 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: 89: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 89: 1 89: 89: Generating 1-4 interactions: fudge = 0.5 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 4 NOTEs 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 3.450 1.725 200.0 89: (ns/day) (hour/ns) 89: Performance: 0.851 28.187 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 3.342 1.671 200.0 89: (ns/day) (hour/ns) 89: Performance: 0.879 27.303 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_sim2.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_sim1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/28 (4104 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/29 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_input.mdp]: 89: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 89: 1 89: 89: Generating 1-4 interactions: fudge = 0.5 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 4 NOTEs 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 1.257 0.629 200.0 89: (ns/day) (hour/ns) 89: Performance: 2.337 10.270 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.060 0.030 198.9 89: (ns/day) (hour/ns) 89: Performance: 48.677 0.493 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_sim2.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_sim1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/29 (1500 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/30 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_input.mdp]: 89: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 89: 1 89: 89: 89: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_input.mdp]: 89: The Berendsen barostat does not generate any strictly correct ensemble, 89: and should not be used for new production simulations (in our opinion). 89: We recommend using the C-rescale barostat instead. 89: 89: Generating 1-4 interactions: fudge = 0.5 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 4 NOTEs 89: 89: There was 1 WARNING 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.104 0.052 199.5 89: (ns/day) (hour/ns) 89: Performance: 28.121 0.853 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.087 0.043 199.6 89: (ns/day) (hour/ns) 89: Performance: 33.826 0.710 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_sim2.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_sim1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/30 (951 ms) 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/31 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 89: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 89: 1 89: 89: Generating 1-4 interactions: fudge = 0.5 89: Number of degrees of freedom in T-Coupling group System is 27.00 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 4 NOTEs 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.880 0.440 200.0 89: (ns/day) (hour/ns) 89: Performance: 3.338 7.190 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 89: 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.108 0.054 199.3 89: (ns/day) (hour/ns) 89: Performance: 27.131 0.885 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_sim2.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_sim1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/31 (1219 ms) 89: [----------] 32 tests from SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest (33357 ms total) 89: 89: [----------] 1 test from SimulatorsAreEquivalentDefaultModularPull/SimulatorComparisonTest 89: [ RUN ] SimulatorsAreEquivalentDefaultModularPull/SimulatorComparisonTest.WithinTolerances/0 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Generating 1-4 interactions: fudge = 0.5 89: Pull group 1 'FirstWaterMolecule' has 3 atoms 89: Pull group 2 'SecondWaterMolecule' has 3 atoms 89: Number of degrees of freedom in T-Coupling group System is 9.00 89: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 89: NVE simulation: will use the initial temperature of 2573.591 K for 89: determining the Verlet buffer size 89: 89: Pull group natoms pbc atom distance at start reference at t=0 89: 1 3 2 89: 2 3 5 1.112 nm 1.000 nm 89: 89: There were 3 NOTEs 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: Generated 3 of the 3 non-bonded parameter combinations 89: 89: Generated 3 of the 3 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.271 0.135 199.8 89: (ns/day) (hour/ns) 89: Performance: 10.841 2.214 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.147 0.074 199.7 89: (ns/day) (hour/ns) 89: Performance: 19.920 1.205 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultModularPull/SimulatorComparisonTest.WithinTolerances/0 (253 ms) 89: [----------] 1 test from SimulatorsAreEquivalentDefaultModularPull/SimulatorComparisonTest (253 ms total) 89: 89: [----------] 1 test from SimulatorsAreEquivalentDefaultLegacyPull/SimulatorComparisonTest 89: [ RUN ] SimulatorsAreEquivalentDefaultLegacyPull/SimulatorComparisonTest.WithinTolerances/0 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Generating 1-4 interactions: fudge = 0.5 89: Pull group 1 'FirstWaterMolecule' has 3 atoms 89: Pull group 2 'SecondWaterMolecule' has 3 atoms 89: Number of degrees of freedom in T-Coupling group System is 9.00 89: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 89: NVE simulation: will use the initial temperature of 2573.591 K for 89: determining the Verlet buffer size 89: 89: Pull group natoms pbc atom distance at start reference at t=0 89: 1 3 2 89: 2 3 5 1.112 nm 1.000 nm 89: 89: There were 3 NOTEs 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: Generated 3 of the 3 non-bonded parameter combinations 89: 89: Generated 3 of the 3 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.064 0.032 199.2 89: (ns/day) (hour/ns) 89: Performance: 45.512 0.527 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI thread 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 16 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.111 0.056 198.9 89: (ns/day) (hour/ns) 89: Performance: 26.343 0.911 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 89: Opened /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 89: 89: [ OK ] SimulatorsAreEquivalentDefaultLegacyPull/SimulatorComparisonTest.WithinTolerances/0 (121 ms) 89: [----------] 1 test from SimulatorsAreEquivalentDefaultLegacyPull/SimulatorComparisonTest (121 ms total) 89: 89: [----------] Global test environment tear-down 89: [==========] 94 tests from 4 test suites ran. (61138 ms total) 89: [ PASSED ] 94 tests. 89/90 Test #89: MdrunSimulatorComparison .................. Passed 61.18 sec test 90 Start 90: MdrunVirtualSiteTests 90: Test command: /build/reproducible-path/gromacs-2025.0/build/basic-dp/bin/mdrun-vsites-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/basic-dp/Testing/Temporary/MdrunVirtualSiteTests.xml" 90: Working Directory: /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests 90: Test timeout computed to be: 600 90: [==========] Running 37 tests from 2 test suites. 90: [----------] Global test environment set-up. 90: [----------] 1 test from VirtualSiteVelocityTest 90: [ RUN ] VirtualSiteVelocityTest.ReferenceIsCorrect 90: [ OK ] VirtualSiteVelocityTest.ReferenceIsCorrect (0 ms) 90: [----------] 1 test from VirtualSiteVelocityTest (0 ms total) 90: 90: [----------] 36 tests from VelocitiesConformToExpectations/VirtualSiteTest 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/0 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: 90: Dynamic load balancing report: 90: DLB was off during the run due to low measured imbalance. 90: Average load imbalance: 1.0%. 90: The balanceable part of the MD step is 38%, load imbalance is computed from this. 90: Part of the total run time spent waiting due to load imbalance: 0.4%. 90: 90: 90: NOTE: 47 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.049 0.025 195.6 90: (ns/day) (hour/ns) 90: Performance: 31.110 0.771 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: trr version: GMX_trn_file (double precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/0 (50 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/1 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: 90: Dynamic load balancing report: 90: DLB was off during the run due to low measured imbalance. 90: Average load imbalance: 2.5%. 90: The balanceable part of the MD step is 45%, load imbalance is computed from this. 90: Part of the total run time spent waiting due to load imbalance: 1.1%. 90: 90: 90: NOTE: 46 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.070 0.035 199.5 90: (ns/day) (hour/ns) 90: Performance: 22.314 1.076 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/1 (84 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/2 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: 90: Dynamic load balancing report: 90: DLB was off during the run due to low measured imbalance. 90: Average load imbalance: 0.1%. 90: The balanceable part of the MD step is 39%, load imbalance is computed from this. 90: Part of the total run time spent waiting due to load imbalance: 0.0%. 90: 90: 90: NOTE: 48 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.053 0.027 199.1 90: (ns/day) (hour/ns) 90: Performance: 28.940 0.829 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/2 (50 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/3 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 90: There are 6 non-linear virtual site constructions. Their contribution to 90: the energy error is approximated. In most cases this does not affect the 90: error significantly. 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 90: 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 48 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.056 0.028 199.1 90: (ns/day) (hour/ns) 90: Performance: 27.696 0.867 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/3 (63 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/4 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 90: There are 6 non-linear virtual site constructions. Their contribution to 90: the energy error is approximated. In most cases this does not affect the 90: error significantly. 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 90: 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 48 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.043 0.022 199.0 90: (ns/day) (hour/ns) 90: Performance: 35.670 0.673 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/4 (66 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/5 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 90: There are 6 non-linear virtual site constructions. Their contribution to 90: the energy error is approximated. In most cases this does not affect the 90: error significantly. 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 90: 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 43 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.041 0.021 198.7 90: (ns/day) (hour/ns) 90: Performance: 37.451 0.641 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/5 (61 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/6 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 90: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 90: 1 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 90: There are 6 non-linear virtual site constructions. Their contribution to 90: the energy error is approximated. In most cases this does not affect the 90: error significantly. 90: 90: 90: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 5 NOTEs 90: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 90: 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 46 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.037 0.019 198.9 90: (ns/day) (hour/ns) 90: Performance: 41.586 0.577 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/6 (54 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/7 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 90: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 90: 1 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 90: There are 6 non-linear virtual site constructions. Their contribution to 90: the energy error is approximated. In most cases this does not affect the 90: error significantly. 90: 90: 90: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 5 NOTEs 90: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 90: 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 45 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.044 0.022 198.6 90: (ns/day) (hour/ns) 90: Performance: 35.109 0.684 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/7 (54 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/8 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 90: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 90: 1 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 90: There are 6 non-linear virtual site constructions. Their contribution to 90: the energy error is approximated. In most cases this does not affect the 90: error significantly. 90: 90: 90: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 5 NOTEs 90: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 90: 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 48 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.053 0.026 199.1 90: (ns/day) (hour/ns) 90: Performance: 29.385 0.817 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/8 (76 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/9 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: 90: Dynamic load balancing report: 90: DLB was off during the run due to low measured imbalance. 90: Average load imbalance: 2.4%. 90: The balanceable part of the MD step is 9%, load imbalance is computed from this. 90: Part of the total run time spent waiting due to load imbalance: 0.2%. 90: 90: 90: NOTE: 39 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.050 0.025 198.8 90: (ns/day) (hour/ns) 90: Performance: 30.707 0.782 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/9 (57 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/10 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: 90: Dynamic load balancing report: 90: DLB was off during the run due to low measured imbalance. 90: Average load imbalance: 0.9%. 90: The balanceable part of the MD step is 40%, load imbalance is computed from this. 90: Part of the total run time spent waiting due to load imbalance: 0.4%. 90: 90: 90: NOTE: 47 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.063 0.032 198.8 90: (ns/day) (hour/ns) 90: Performance: 24.625 0.975 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/10 (52 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/11 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/11 (0 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/12 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 90: There are 6 non-linear virtual site constructions. Their contribution to 90: the energy error is approximated. In most cases this does not affect the 90: error significantly. 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 90: 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 48 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.052 0.026 199.1 90: (ns/day) (hour/ns) 90: Performance: 29.696 0.808 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/12 (60 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/13 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 90: There are 6 non-linear virtual site constructions. Their contribution to 90: the energy error is approximated. In most cases this does not affect the 90: error significantly. 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 90: 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 48 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.076 0.038 199.3 90: (ns/day) (hour/ns) 90: Performance: 20.444 1.174 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/13 (77 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/14 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/14 (0 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/15 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 90: There are 6 non-linear virtual site constructions. Their contribution to 90: the energy error is approximated. In most cases this does not affect the 90: error significantly. 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 90: 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 48 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.062 0.031 199.0 90: (ns/day) (hour/ns) 90: Performance: 24.772 0.969 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/15 (82 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/16 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 90: There are 6 non-linear virtual site constructions. Their contribution to 90: the energy error is approximated. In most cases this does not affect the 90: error significantly. 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 90: 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 47 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.045 0.022 199.1 90: (ns/day) (hour/ns) 90: Performance: 34.584 0.694 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/16 (57 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/17 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/17 (0 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/18 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 90: There are 6 non-linear virtual site constructions. Their contribution to 90: the energy error is approximated. In most cases this does not affect the 90: error significantly. 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 90: 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 47 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.034 0.017 198.7 90: (ns/day) (hour/ns) 90: Performance: 46.098 0.521 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/18 (60 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/19 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 90: There are 6 non-linear virtual site constructions. Their contribution to 90: the energy error is approximated. In most cases this does not affect the 90: error significantly. 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 90: 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 48 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.053 0.027 198.9 90: (ns/day) (hour/ns) 90: Performance: 29.043 0.826 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/19 (63 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/20 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 90: There are 6 non-linear virtual site constructions. Their contribution to 90: the energy error is approximated. In most cases this does not affect the 90: error significantly. 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 90: 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 49 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.078 0.039 199.4 90: (ns/day) (hour/ns) 90: Performance: 19.852 1.209 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/20 (210 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/21 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/21 (0 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/22 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/22 (0 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/23 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/23 (0 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/24 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/24 (0 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/25 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/25 (0 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/26 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/26 (0 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/27 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 90: There are 6 non-linear virtual site constructions. Their contribution to 90: the energy error is approximated. In most cases this does not affect the 90: error significantly. 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Changing nstlist from 8 to 100, rlist from 0.729 to 0.81 90: 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 46 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.039 0.020 198.7 90: (ns/day) (hour/ns) 90: Performance: 39.825 0.603 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/27 (195 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/28 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 90: There are 6 non-linear virtual site constructions. Their contribution to 90: the energy error is approximated. In most cases this does not affect the 90: error significantly. 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Changing nstlist from 8 to 100, rlist from 0.729 to 0.81 90: 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 49 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.112 0.056 199.5 90: (ns/day) (hour/ns) 90: Performance: 13.797 1.740 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/28 (109 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/29 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 90: Setting nstcalcenergy (100) equal to nstenergy (4) 90: 90: Number of degrees of freedom in T-Coupling group System is 45.00 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 90: There are 6 non-linear virtual site constructions. Their contribution to 90: the energy error is approximated. In most cases this does not affect the 90: error significantly. 90: 90: 90: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 90: You are using a plain Coulomb cut-off, which might produce artifacts. 90: You might want to consider using PME electrostatics. 90: 90: 90: 90: There were 4 NOTEs 90: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Changing nstlist from 8 to 100, rlist from 0.729 to 0.81 90: 90: Update groups can not be used for this system because an incompatible virtual site type is used 90: 90: Using 2 MPI threads 90: Using 1 OpenMP thread per tMPI thread 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Virtual sites test system in vacuo' 90: 8 steps, 0.0 ps. 90: Generated 3 of the 6 non-bonded parameter combinations 90: 90: Excluding 3 bonded neighbours molecule type 'VSTEST' 90: 90: Cleaning up constraints and constant bonded interactions with virtual sites 90: 90: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 90: 90: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: NOTE: 46 % of the run time was spent communicating energies, 90: you might want to increase some nst* mdp options 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.032 0.016 197.3 90: (ns/day) (hour/ns) 90: Performance: 47.313 0.507 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: Reading file /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2025.0-Debian_2025.0_2 (double precision) 90: 90: Reading virtual site types... 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/29 (53 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/30 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/30 (0 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/31 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/31 (0 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/32 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/32 (0 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/33 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/33 (0 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/34 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/34 (0 ms) 90: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/35 90: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/35 (0 ms) 90: [----------] 36 tests from VelocitiesConformToExpectations/VirtualSiteTest (1647 ms total) 90: 90: [----------] Global test environment tear-down 90: [==========] 37 tests from 2 test suites ran. (1724 ms total) 90: [ PASSED ] 37 tests. 90/90 Test #90: MdrunVirtualSiteTests ..................... Passed 1.76 sec 100% tests passed, 0 tests failed out of 90 Label Time Summary: GTest = 784.29 sec*proc (88 tests) IntegrationTest = 414.98 sec*proc (28 tests) MpiTest = 484.69 sec*proc (21 tests) QuickGpuTest = 110.51 sec*proc (22 tests) SlowGpuTest = 611.43 sec*proc (14 tests) SlowTest = 359.36 sec*proc (14 tests) UnitTest = 9.95 sec*proc (46 tests) Total Test time (real) = 439.99 sec touch build-basic dh_testdir LD_LIBRARY_PATH=/build/reproducible-path/gromacs-2025.0/build/mpi/lib /usr/bin/make -j20 -C build/mpi make[1]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/cmake -P /build/reproducible-path/gromacs-2025.0/build/mpi/CMakeFiles/VerifyGlobs.cmake /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.0 -B/build/reproducible-path/gromacs-2025.0/build/mpi --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.0/build/mpi/CMakeFiles 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'/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.0/build/mpi/src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 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src/programs/CMakeFiles/gmx_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs 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'/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/external/rpc_xdr && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_float.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_float.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_float.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/rpc_xdr/xdr_float.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/external/rpc_xdr && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT 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VERSION_STRING_OF_FORK=Debian-2025.0-2 -P /build/reproducible-path/gromacs-2025.0/cmake/gmxGenerateVersionInfoWithoutGit.cmake /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT 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/build/reproducible-path/gromacs-2025.0/src/programs/gmx.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/linearalgebra && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/matrix.cpp.o -MF CMakeFiles/linearalgebra.dir/matrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/matrix.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/linearalgebra && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -MF CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/sparsematrix.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvar_neuralnetworkcompute.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/selection && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/scanner.cpp.o -MF CMakeFiles/scanner.dir/scanner.cpp.o.d -o CMakeFiles/scanner.dir/scanner.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/scanner.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/abstractsection.cpp.o -MF CMakeFiles/options.dir/abstractsection.cpp.o.d -o CMakeFiles/options.dir/abstractsection.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/abstractsection.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/basicoptions.cpp.o -MF CMakeFiles/options.dir/basicoptions.cpp.o.d -o CMakeFiles/options.dir/basicoptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/basicoptions.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/behaviorcollection.cpp.o -MF CMakeFiles/options.dir/behaviorcollection.cpp.o.d -o CMakeFiles/options.dir/behaviorcollection.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/behaviorcollection.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/coder.c [ 0%] Built target internal_rpc_xdr cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/filenameoption.cpp.o -MF CMakeFiles/options.dir/filenameoption.cpp.o.d -o CMakeFiles/options.dir/filenameoption.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/filenameoption.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 0%] Built target thread_mpi cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -MF CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o.d -o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/legacymodules.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/nonbonded_bench.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/dict.c cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/fixpoint.c cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/filenameoptionmanager.cpp.o -MF CMakeFiles/options.dir/filenameoptionmanager.cpp.o.d -o CMakeFiles/options.dir/filenameoptionmanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/filenameoptionmanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/huffman.c cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/huffmem.c cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/options.cpp.o -MF CMakeFiles/options.dir/options.cpp.o.d -o CMakeFiles/options.dir/options.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/options.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsassigner.cpp.o -MF CMakeFiles/options.dir/optionsassigner.cpp.o.d -o CMakeFiles/options.dir/optionsassigner.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/optionsassigner.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/lz77.c cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/merge_sort.c cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsection.cpp.o -MF CMakeFiles/options.dir/optionsection.cpp.o.d -o CMakeFiles/options.dir/optionsection.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/optionsection.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/mtf.c cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/rle.c cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsvisitor.cpp.o -MF CMakeFiles/options.dir/optionsvisitor.cpp.o.d -o CMakeFiles/options.dir/optionsvisitor.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/optionsvisitor.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/tng_compress.c cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/vals16.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 0%] Built target lmfit_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/warnmalloc.c cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/widemuldiv.c [ 2%] Built target gmx_objlib cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/xtc2.c cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/timeunitmanager.cpp.o -MF CMakeFiles/options.dir/timeunitmanager.cpp.o.d -o CMakeFiles/options.dir/timeunitmanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/timeunitmanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/treesupport.cpp.o -MF CMakeFiles/options.dir/treesupport.cpp.o.d -o CMakeFiles/options.dir/treesupport.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/treesupport.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 2%] Built target energyanalysis cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/xtc3.c cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/lib/tng_io.c cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/lib/md5.c cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvaratoms.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias_abf.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias_abmd.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 2%] Built target mdrun_objlib cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong 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/usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias_meta.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias_opes.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias_restraint.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat 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CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_angles.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_apath.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_combination.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_coordnums.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_coordnums.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_coordnums.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_coordnums.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_distances.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_distances.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_distances.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_distances.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_gpath.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 4%] Built target linearalgebra /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make 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-Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/output.cpp.o -MF CMakeFiles/pulling.dir/output.cpp.o.d -o CMakeFiles/pulling.dir/output.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/output.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_neuralnetwork.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_neuralnetwork.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_neuralnetwork.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_neuralnetwork.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 4%] Built target scanner cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pull.cpp.o -MF CMakeFiles/pulling.dir/pull.cpp.o.d -o CMakeFiles/pulling.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/pull.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_protein.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_rotations.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_rotations.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_rotations.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_rotations.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_torchann.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_torchann.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_torchann.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_torchann.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_volmaps.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvardeps.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvardeps.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvardeps.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvardeps.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvargrid.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarmodule.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarmodule.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarmodule.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarmodule.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparams.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparams.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparams.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarparams.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparse.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparse.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparse.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarparse.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarproxy.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_io.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_io.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_io.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarproxy_io.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pull_rotation.cpp.o -MF CMakeFiles/pulling.dir/pull_rotation.cpp.o.d -o CMakeFiles/pulling.dir/pull_rotation.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/pull_rotation.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o -MF CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o.d -o CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/pullcoordexpressionparser.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_replicas.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_replicas.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_replicas.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarproxy_replicas.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 6%] Built target tng_io_obj cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_system.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_system.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_system.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarproxy_system.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_tcl.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_tcl.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_tcl.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarproxy_tcl.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_volmaps.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_volmaps.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_volmaps.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarproxy_volmaps.cpp [ 8%] Built target options cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvars_memstream.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvars_memstream.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvars_memstream.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvars_memstream.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pullutil.cpp.o -MF CMakeFiles/pulling.dir/pullutil.cpp.o.d -o CMakeFiles/pulling.dir/pullutil.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/pullutil.cpp cd 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-fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -MF CMakeFiles/pulling.dir/transformationcoordinate.cpp.o.d -o CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/transformationcoordinate.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarscript.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarscript_commands.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_bias.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_bias.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_bias.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarscript_commands_bias.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_colvar.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_colvar.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_colvar.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarscript_commands_colvar.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvartypes.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvartypes.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvartypes.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvartypes.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarvalue.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarvalue.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarvalue.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarvalue.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/nr_jacobi.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 10%] Built target pulling /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/taskassignment && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o -MF CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o.d -o CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/decidegpuusage.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/taskassignment && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o -MF CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o.d -o CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/decidesimulationworkload.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/taskassignment && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/findallgputasks.cpp.o -MF CMakeFiles/taskassignment.dir/findallgputasks.cpp.o.d -o CMakeFiles/taskassignment.dir/findallgputasks.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/findallgputasks.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/andersentemperaturecoupling.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/taskassignment && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o -MF CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o.d -o CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/reportgpuusage.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H 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src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/referencetemperaturemanager.cpp.o -MF CMakeFiles/modularsimulator.dir/referencetemperaturemanager.cpp.o.d -o CMakeFiles/modularsimulator.dir/referencetemperaturemanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/referencetemperaturemanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/velocityscalingtemperaturecoupling.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 14%] Built target colvars_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 18%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/reproducible-path/gromacs-2025.0/build/mpi/VersionInfo.cmake -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /build/reproducible-path/gromacs-2025.0/cmake/gmxConfigureVersionInfo.cmake cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' 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-I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include 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-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include 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-I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops 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-I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS 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-I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include 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-isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c 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-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include 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-isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c 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-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include 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-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include 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/build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include 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-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include 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-isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit 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/build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include 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-I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override 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-I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include 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-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include 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-isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include 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-isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include 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-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H 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-I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit 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-I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include 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-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include 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-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. 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-I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit 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/build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include 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-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops 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-I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/benchmark/bench_setup.cpp cd 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/benchmark/bench_system.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/exclusionchecker.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/exclusionchecker.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/exclusionchecker.cpp.o -c 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 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-I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops 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-I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops 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-I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_4x4.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_4x4.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_4x4.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_permute.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include 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-isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_position.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include 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-Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_same.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_simple.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -MF CMakeFiles/libgromacs.dir/selection/symrec.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/symrec.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/cmake -E cmake_link_script CMakeFiles/libgromacs.dir/link.txt --verbose=1 /usr/bin/mpicxx -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file=CMakeFiles/libgromacs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgromacs_mpi.so.10 -o ../../lib/libgromacs_mpi.so.10.0.0 @CMakeFiles/libgromacs.dir/objects1.rsp /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so -lm /usr/lib/x86_64-linux-gnu/liblapack.so -lm -lm /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 -lmuparser -ldl cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgromacs_mpi.so.10.0.0 ../../lib/libgromacs_mpi.so.10 ../../lib/libgromacs_mpi.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 94%] Built target libgromacs /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/depend /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/gmxapi /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/CMakeFiles/nblib.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmx.dir/link.txt --verbose=1 make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/system.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/system.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/system.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/system.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include 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/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/workflow.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tpr.cpp /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include 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-msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/box.cpp.o -MF CMakeFiles/nblib.dir/box.cpp.o.d -o CMakeFiles/nblib.dir/box.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/box.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include 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api/nblib/CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o -MF CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o.d -o CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/gmxcalculatorcpu.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/integrator.cpp.o -MF CMakeFiles/nblib.dir/integrator.cpp.o.d -o CMakeFiles/nblib.dir/integrator.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/integrator.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/interactions.cpp.o -MF CMakeFiles/nblib.dir/interactions.cpp.o.d -o CMakeFiles/nblib.dir/interactions.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/interactions.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib 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-std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/molecules.cpp.o -MF CMakeFiles/nblib.dir/molecules.cpp.o.d -o CMakeFiles/nblib.dir/molecules.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/molecules.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include 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/build/reproducible-path/gromacs-2025.0/api/nblib/particlesequencer.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/simulationstate.cpp.o -MF CMakeFiles/nblib.dir/simulationstate.cpp.o.d -o CMakeFiles/nblib.dir/simulationstate.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/simulationstate.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include 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make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 94%] Built target gmx cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/transformations.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/conversions.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/convertGmxToNblib.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/util/setup.cpp.o -MF CMakeFiles/nblib.dir/util/setup.cpp.o.d -o CMakeFiles/nblib.dir/util/setup.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/util/setup.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi.dir/link.txt --verbose=1 /usr/bin/mpicxx -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file=CMakeFiles/gmxapi.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgmxapi_mpi.so.0 -o ../../lib/libgmxapi_mpi.so.0.4.0 CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o CMakeFiles/gmxapi.dir/cpp/context.cpp.o CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o CMakeFiles/gmxapi.dir/cpp/md.cpp.o CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o CMakeFiles/gmxapi.dir/cpp/session.cpp.o CMakeFiles/gmxapi.dir/cpp/status.cpp.o CMakeFiles/gmxapi.dir/cpp/system.cpp.o CMakeFiles/gmxapi.dir/cpp/version.cpp.o CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o ../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgmxapi_mpi.so.0.4.0 ../../lib/libgmxapi_mpi.so.0 ../../lib/libgmxapi_mpi.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 96%] Built target gmxapi /usr/bin/make -f python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build.make python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/depend /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/gmxapi /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build.make python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/src/cpp && /usr/bin/mpicxx -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/python_packaging/sample_restraint/src/cpp -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -MD -MT python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/sessionresources.cpp.o -MF CMakeFiles/gmxapi_extension_resources.dir/sessionresources.cpp.o.d -o CMakeFiles/gmxapi_extension_resources.dir/sessionresources.cpp.o -c /build/reproducible-path/gromacs-2025.0/python_packaging/sample_restraint/src/cpp/sessionresources.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -isystem /usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -Wno-old-style-cast -Wno-cast-qual 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-isystem /usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/export_context.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/export_context.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/export_context.cpp.o -c /build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi/src/cpp/export_context.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -isystem /usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/export_system.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/export_system.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/export_system.cpp.o -c /build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi/src/cpp/export_system.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -isystem /usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/export_tprfile.cpp.o -MF 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/pycontext.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/pycontext.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/pycontext.cpp.o -c /build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi/src/cpp/pycontext.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -isystem /usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/pysystem.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/pysystem.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/pysystem.cpp.o -c /build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi/src/cpp/pysystem.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -isystem /usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/wrapped_exceptions_0_3_1.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/wrapped_exceptions_0_3_1.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/wrapped_exceptions_0_3_1.cpp.o -c 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-MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/mpi_bindings.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/mpi_bindings.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/mpi_bindings.cpp.o -c /build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi/src/cpp/mpi_bindings.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -isystem /usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/pycontext_create.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/pycontext_create.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/pycontext_create.cpp.o -c /build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi/src/cpp/pycontext_create.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -isystem /usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/mpi_gromacs_support.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/mpi_gromacs_support.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/mpi_gromacs_support.cpp.o -c /build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi/src/cpp/mpi_gromacs_support.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/src/cpp && /usr/bin/cmake -P CMakeFiles/gmxapi_extension_resources.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/src/cpp && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi_extension_resources.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libgmxapi_extension_resources.a CMakeFiles/gmxapi_extension_resources.dir/sessionresources.cpp.o /usr/bin/ranlib ../../../../lib/libgmxapi_extension_resources.a make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 96%] Built target gmxapi_extension_resources /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/depend /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/src/cpp && /usr/bin/mpicxx -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/python_packaging/sample_restraint/src/cpp -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -MD -MT python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/nullpotential.cpp.o -MF CMakeFiles/gmxapi_extension_test.dir/nullpotential.cpp.o.d -o CMakeFiles/gmxapi_extension_test.dir/nullpotential.cpp.o -c /build/reproducible-path/gromacs-2025.0/python_packaging/sample_restraint/src/cpp/nullpotential.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/src/cpp && /usr/bin/mpicxx -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/python_packaging/sample_restraint/src/cpp -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -MD -MT python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/ensemblepotential.cpp.o -MF CMakeFiles/gmxapi_extension_ensemblepotential.dir/ensemblepotential.cpp.o.d -o CMakeFiles/gmxapi_extension_ensemblepotential.dir/ensemblepotential.cpp.o -c /build/reproducible-path/gromacs-2025.0/python_packaging/sample_restraint/src/cpp/ensemblepotential.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/src/cpp && /usr/bin/cmake -P CMakeFiles/gmxapi_extension_test.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/src/cpp && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi_extension_test.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libgmxapi_extension_test.a CMakeFiles/gmxapi_extension_test.dir/nullpotential.cpp.o /usr/bin/ranlib ../../../../lib/libgmxapi_extension_test.a make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 96%] Built target gmxapi_extension_test cd /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/src/cpp && /usr/bin/cmake -P CMakeFiles/gmxapi_extension_ensemblepotential.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/src/cpp && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi_extension_ensemblepotential.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libgmxapi_extension_ensemblepotential.a CMakeFiles/gmxapi_extension_ensemblepotential.dir/ensemblepotential.cpp.o /usr/bin/ranlib ../../../../lib/libgmxapi_extension_ensemblepotential.a make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 96%] Built target gmxapi_extension_ensemblepotential /usr/bin/make -f python_packaging/sample_restraint/src/pythonmodule/CMakeFiles/gmxapi_extension.dir/build.make python_packaging/sample_restraint/src/pythonmodule/CMakeFiles/gmxapi_extension.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/python_packaging/sample_restraint/src/pythonmodule /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/src/pythonmodule /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/src/pythonmodule/CMakeFiles/gmxapi_extension.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f python_packaging/sample_restraint/src/pythonmodule/CMakeFiles/gmxapi_extension.dir/build.make python_packaging/sample_restraint/src/pythonmodule/CMakeFiles/gmxapi_extension.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/src/pythonmodule && /usr/bin/mpicxx -DGMX_DOUBLE=0 -Dgmxapi_extension_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/python_packaging/sample_restraint/src/cpp -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -isystem /usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -MD -MT python_packaging/sample_restraint/src/pythonmodule/CMakeFiles/gmxapi_extension.dir/export_plugin.cpp.o -MF CMakeFiles/gmxapi_extension.dir/export_plugin.cpp.o.d -o CMakeFiles/gmxapi_extension.dir/export_plugin.cpp.o -c /build/reproducible-path/gromacs-2025.0/python_packaging/sample_restraint/src/pythonmodule/export_plugin.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/gmxapi && /usr/bin/cmake -E cmake_link_script CMakeFiles/_gmxapi.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/src/pythonmodule && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi_extension.dir/link.txt --verbose=1 /usr/bin/mpicxx -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -Wl,--dependency-file=CMakeFiles/_gmxapi.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o gmxapi_staging/gmxapi/_gmxapi.cpython-313-x86_64-linux-gnu.so CMakeFiles/_gmxapi.dir/src/cpp/launch_0_2_1.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/module.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/export_context.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/export_system.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/export_tprfile.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/gmxpy_exceptions.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/pycontext.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/pysystem.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/wrapped_exceptions_0_3_1.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/mpi_bindings.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/pycontext_create.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/mpi_gromacs_support.cpp.o ../../lib/libgmxapi_mpi.so.0.4.0 -Wl,-rpath-link,/build/reproducible-path/gromacs-2025.0/build/mpi/lib cd /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/gmxapi && /usr/bin/strip /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/gmxapi/gmxapi_staging/gmxapi/_gmxapi.cpython-313-x86_64-linux-gnu.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 96%] Built target _gmxapi /usr/bin/mpicxx -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection 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/usr/bin/mpicxx -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file=CMakeFiles/nblib.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libnblib_gmx.so.0 -o ../../lib/libnblib_gmx.so.0.1.0 CMakeFiles/nblib.dir/box.cpp.o CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o CMakeFiles/nblib.dir/integrator.cpp.o CMakeFiles/nblib.dir/interactions.cpp.o CMakeFiles/nblib.dir/molecules.cpp.o CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o CMakeFiles/nblib.dir/particlesequencer.cpp.o CMakeFiles/nblib.dir/particletype.cpp.o CMakeFiles/nblib.dir/simulationstate.cpp.o CMakeFiles/nblib.dir/topologyhelpers.cpp.o CMakeFiles/nblib.dir/topology.cpp.o CMakeFiles/nblib.dir/tpr.cpp.o CMakeFiles/nblib.dir/virials.cpp.o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o CMakeFiles/nblib.dir/util/setup.cpp.o -lm ../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -lmuparser /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib && /usr/bin/cmake -E cmake_symlink_library ../../lib/libnblib_gmx.so.0.1.0 ../../lib/libnblib_gmx.so.0 ../../lib/libnblib_gmx.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [100%] Built target nblib /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/samples/CMakeFiles/argon-forces-integration.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/samples 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-I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fopenmp -MD -MT api/nblib/samples/CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o -MF CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o.d -o CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/samples/argon-forces-integration.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/samples && /usr/bin/cmake -E cmake_link_script CMakeFiles/argon-forces-integration.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection 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-Wl,--dependency-file=CMakeFiles/methane-water-integration.dir/link.d "CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o" -o ../../../bin/methane-water-integration ../../../lib/libnblib_gmx.so.0.1.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -Wl,-rpath-link,/build/reproducible-path/gromacs-2025.0/build/mpi/lib make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [100%] Built target methane-water-integration make[2]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.0/build/mpi/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -j20 -C build/mpi-dp make[1]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.0 -B/build/reproducible-path/gromacs-2025.0/build/mpi-dp 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make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/linearalgebra 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/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/errhandler.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/external/rpc_xdr && /usr/bin/mpicxx -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time 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src/gromacs/CMakeFiles/tng_io_obj.dir/build cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c 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/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/atomic.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/lock.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/pthreads.cpp /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers 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-O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -MF CMakeFiles/linearalgebra.dir/eigensolver.cpp.o.d -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/eigensolver.cpp /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 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/build/reproducible-path/gromacs-2025.0/src/gromacs/options/abstractoption.cpp /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/energyanalysis && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-cast-function-type-strict -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/energyterm.cpp.o -MF CMakeFiles/energyanalysis.dir/energyterm.cpp.o.d -o CMakeFiles/energyanalysis.dir/energyterm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/energyterm.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/programs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/mdrun.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/programs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/gmx.cpp.o -MF CMakeFiles/gmx_objlib.dir/gmx.cpp.o.d -o CMakeFiles/gmx_objlib.dir/gmx.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/gmx.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvar.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' [ 0%] Built target release-version-info cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/abstractsection.cpp.o -MF CMakeFiles/options.dir/abstractsection.cpp.o.d -o CMakeFiles/options.dir/abstractsection.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/abstractsection.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvar_neuralnetworkcompute.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/programs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -MF CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o.d -o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/legacymodules.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/basicoptions.cpp.o -MF CMakeFiles/options.dir/basicoptions.cpp.o.d -o CMakeFiles/options.dir/basicoptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/basicoptions.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvaratoms.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/programs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/nonbonded_bench.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/bwt.c cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/coder.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' [ 0%] Built target internal_rpc_xdr cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/behaviorcollection.cpp.o -MF CMakeFiles/options.dir/behaviorcollection.cpp.o.d -o CMakeFiles/options.dir/behaviorcollection.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/behaviorcollection.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' [ 0%] Built target thread_mpi cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/dict.c cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/fixpoint.c cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/huffman.c cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/huffmem.c cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias_abf.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/lz77.c cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -MF CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o.d -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/gmx_arpack.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/merge_sort.c cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/mtf.c cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/rle.c cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/tng_compress.c cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/vals16.c cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/warnmalloc.c cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/widemuldiv.c cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/filenameoption.cpp.o -MF CMakeFiles/options.dir/filenameoption.cpp.o.d -o CMakeFiles/options.dir/filenameoption.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/filenameoption.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/matrix.cpp.o -MF CMakeFiles/linearalgebra.dir/matrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/matrix.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/xtc2.c cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/xtc3.c cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/lib/tng_io.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' [ 0%] Built target gmx_objlib cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/filenameoptionmanager.cpp.o -MF CMakeFiles/options.dir/filenameoptionmanager.cpp.o.d -o CMakeFiles/options.dir/filenameoptionmanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/filenameoptionmanager.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' [ 0%] Built target lmfit_objlib cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/lib/md5.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -MF CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/sparsematrix.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/options.cpp.o -MF CMakeFiles/options.dir/options.cpp.o.d -o CMakeFiles/options.dir/options.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/options.cpp [ 0%] Built target energyanalysis cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsassigner.cpp.o -MF CMakeFiles/options.dir/optionsassigner.cpp.o.d -o CMakeFiles/options.dir/optionsassigner.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/optionsassigner.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsection.cpp.o -MF CMakeFiles/options.dir/optionsection.cpp.o.d -o CMakeFiles/options.dir/optionsection.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/optionsection.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsvisitor.cpp.o -MF CMakeFiles/options.dir/optionsvisitor.cpp.o.d -o CMakeFiles/options.dir/optionsvisitor.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/optionsvisitor.cpp [ 0%] Built target mdrun_objlib cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/timeunitmanager.cpp.o -MF CMakeFiles/options.dir/timeunitmanager.cpp.o.d -o CMakeFiles/options.dir/timeunitmanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/timeunitmanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/treesupport.cpp.o -MF CMakeFiles/options.dir/treesupport.cpp.o.d -o CMakeFiles/options.dir/treesupport.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/treesupport.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias_alb.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT 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/build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias_histogram_reweight_amd.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias_meta.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarbias_opes.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o -MF 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-DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_alchlambda.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_angles.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_apath.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_combination.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong 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CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_distances.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_distances.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_distances.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_gpath.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_neuralnetwork.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_neuralnetwork.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_neuralnetwork.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_neuralnetwork.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' [ 0%] Built target linearalgebra /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/pulling /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_protein.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/output.cpp.o -MF CMakeFiles/pulling.dir/output.cpp.o.d -o CMakeFiles/pulling.dir/output.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/output.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' [ 0%] Built target scanner cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pull.cpp.o -MF CMakeFiles/pulling.dir/pull.cpp.o.d -o CMakeFiles/pulling.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/pull.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_rotations.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_rotations.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_rotations.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_rotations.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_torchann.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_torchann.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_torchann.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_torchann.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarcomp_volmaps.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvardeps.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvardeps.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvardeps.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvardeps.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvargrid.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarmodule.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarmodule.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarmodule.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarmodule.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparams.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparams.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparams.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarparams.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparse.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparse.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarparse.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarparse.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarproxy.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pull_rotation.cpp.o -MF CMakeFiles/pulling.dir/pull_rotation.cpp.o.d -o CMakeFiles/pulling.dir/pull_rotation.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/pull_rotation.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_io.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_io.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_io.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarproxy_io.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_replicas.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_replicas.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_replicas.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarproxy_replicas.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' [ 0%] Built target tng_io_obj cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_system.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_system.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_system.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarproxy_system.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_tcl.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_tcl.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_tcl.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarproxy_tcl.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' [ 0%] Built target options cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o -MF CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o.d -o CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/pullcoordexpressionparser.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_volmaps.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_volmaps.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarproxy_volmaps.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarproxy_volmaps.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvars_memstream.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvars_memstream.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvars_memstream.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvars_memstream.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 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/build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarscript_commands.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_bias.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_bias.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_bias.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarscript_commands_bias.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_colvar.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_colvar.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_colvar.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvarscript_commands_colvar.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvartypes.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pullutil.cpp.o -MF CMakeFiles/pulling.dir/pullutil.cpp.o.d -o CMakeFiles/pulling.dir/pullutil.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/pullutil.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat 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CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/nr_jacobi.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -MF CMakeFiles/pulling.dir/transformationcoordinate.cpp.o.d -o CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/transformationcoordinate.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' [ 0%] Built target pulling /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/andersentemperaturecoupling.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/taskassignment && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o -MF CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o.d -o CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/decidegpuusage.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/taskassignment && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o -MF CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o.d -o CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/decidesimulationworkload.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/taskassignment && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/findallgputasks.cpp.o -MF CMakeFiles/taskassignment.dir/findallgputasks.cpp.o.d -o CMakeFiles/taskassignment.dir/findallgputasks.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/findallgputasks.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/taskassignment && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include 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-I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external 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-Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/velocityscalingtemperaturecoupling.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' [ 4%] Built target colvars_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' [ 6%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/reproducible-path/gromacs-2025.0/build/mpi-dp/VersionInfo.cmake -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /build/reproducible-path/gromacs-2025.0/cmake/gmxConfigureVersionInfo.cmake cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include 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-g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/alignedallocator.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include 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src/gromacs/CMakeFiles/libgromacs.dir/utility/any.cpp.o -MF CMakeFiles/libgromacs.dir/utility/any.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/any.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/any.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include 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-g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -MF CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/basenetwork.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include 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src/gromacs/CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -MF CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/baseversion.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include 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-I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include 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-I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include 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-I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include 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-I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem 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-I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops 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-I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr 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-I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. 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-I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem 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-I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override 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-I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override 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-I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem 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/build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. 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-I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops 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-I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/benchmark/bench_setup.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops 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-I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops 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-I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual 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-I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars 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-I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include 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-I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include 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-I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 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-I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/box.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/box.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/box.cpp.o -c 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 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-I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/collect.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/collect.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/collect.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/collect.cpp 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops 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-I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 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-I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 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-I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops 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-I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual 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-I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual 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-I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual 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-I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops 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-I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops 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-I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr 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-I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops 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-I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr 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-I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem 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-I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem 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-I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual 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-I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual 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-I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops 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-I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops 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-I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops 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-I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops 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-I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o -c 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual 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-I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops 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-I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr 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-I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr 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-I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops 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-I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops 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-I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual 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-I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops 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-I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. 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-I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops 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-I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual 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-I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops 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-I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed 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-I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual 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-I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem 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-I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem 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-g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_permute.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include 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src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_position.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include 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-g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_same.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include 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src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_simple.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -MF CMakeFiles/libgromacs.dir/selection/symrec.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/symrec.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/cmake -E cmake_link_script CMakeFiles/libgromacs.dir/link.txt --verbose=1 /usr/bin/mpicxx -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file=CMakeFiles/libgromacs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgromacs_mpi_d.so.10 -o ../../lib/libgromacs_mpi_d.so.10.0.0 @CMakeFiles/libgromacs.dir/objects1.rsp /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so -lm /usr/lib/x86_64-linux-gnu/liblapack.so -lm -lm /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 -lmuparser -ldl cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgromacs_mpi_d.so.10.0.0 ../../lib/libgromacs_mpi_d.so.10 ../../lib/libgromacs_mpi_d.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' [ 95%] Built target libgromacs /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/depend /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/depend /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/gmxapi /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/gmxapi /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/programs /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib/CMakeFiles/nblib.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/resourceassignment.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/gmxapi && 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-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/context.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/context.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/context.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/context.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include 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api/gmxapi/CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/exceptions.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/gmxapi.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/md.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/md.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/md.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/md.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src 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CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/mdmodule.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/mdsignals.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/session.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/session.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/session.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/session.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/status.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/status.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/status.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/status.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/system.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/system.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/system.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/system.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/version.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/version.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/version.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/version.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/workflow.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tpr.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/programs && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmx.dir/link.txt --verbose=1 /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/box.cpp.o -MF CMakeFiles/nblib.dir/box.cpp.o.d -o CMakeFiles/nblib.dir/box.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/box.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o -MF CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o.d -o CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/gmxcalculatorcpu.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/integrator.cpp.o -MF CMakeFiles/nblib.dir/integrator.cpp.o.d -o CMakeFiles/nblib.dir/integrator.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/integrator.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/interactions.cpp.o -MF CMakeFiles/nblib.dir/interactions.cpp.o.d -o CMakeFiles/nblib.dir/interactions.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/interactions.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/molecules.cpp.o -MF CMakeFiles/nblib.dir/molecules.cpp.o.d -o CMakeFiles/nblib.dir/molecules.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/molecules.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o -MF CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o.d -o CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/nbnxmsetuphelpers.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/particlesequencer.cpp.o -MF CMakeFiles/nblib.dir/particlesequencer.cpp.o.d -o CMakeFiles/nblib.dir/particlesequencer.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/particlesequencer.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib 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-std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/particletype.cpp.o -MF CMakeFiles/nblib.dir/particletype.cpp.o.d -o CMakeFiles/nblib.dir/particletype.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/particletype.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include 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-Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/simulationstate.cpp.o -MF CMakeFiles/nblib.dir/simulationstate.cpp.o.d -o CMakeFiles/nblib.dir/simulationstate.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/simulationstate.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/topologyhelpers.cpp.o -MF CMakeFiles/nblib.dir/topologyhelpers.cpp.o.d -o CMakeFiles/nblib.dir/topologyhelpers.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/topologyhelpers.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmx.dir/link.d CMakeFiles/gmx_objlib.dir/gmx.cpp.o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../bin/gmx_mpi_d ../../lib/libgromacs_mpi_d.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/topology.cpp.o -MF CMakeFiles/nblib.dir/topology.cpp.o.d -o CMakeFiles/nblib.dir/topology.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/topology.cpp [ 95%] Built target gmx cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include 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-Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/tpr.cpp.o -MF CMakeFiles/nblib.dir/tpr.cpp.o.d -o CMakeFiles/nblib.dir/tpr.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tpr.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/virials.cpp.o -MF CMakeFiles/nblib.dir/virials.cpp.o.d -o CMakeFiles/nblib.dir/virials.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/virials.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/calculator.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/transformations.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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-I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/convertGmxToNblib.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp 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CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o CMakeFiles/gmxapi.dir/cpp/session.cpp.o CMakeFiles/gmxapi.dir/cpp/status.cpp.o CMakeFiles/gmxapi.dir/cpp/system.cpp.o CMakeFiles/gmxapi.dir/cpp/version.cpp.o CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o ../../lib/libgromacs_mpi_d.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/gmxapi && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgmxapi_mpi_d.so.0.4.0 ../../lib/libgmxapi_mpi_d.so.0 ../../lib/libgmxapi_mpi_d.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' [ 97%] Built target gmxapi cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib.dir/link.txt --verbose=1 /usr/bin/mpicxx -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file=CMakeFiles/nblib.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libnblib_gmx.so.0 -o ../../lib/libnblib_gmx.so.0.1.0 CMakeFiles/nblib.dir/box.cpp.o CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o CMakeFiles/nblib.dir/integrator.cpp.o CMakeFiles/nblib.dir/interactions.cpp.o CMakeFiles/nblib.dir/molecules.cpp.o CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o CMakeFiles/nblib.dir/particlesequencer.cpp.o CMakeFiles/nblib.dir/particletype.cpp.o CMakeFiles/nblib.dir/simulationstate.cpp.o CMakeFiles/nblib.dir/topologyhelpers.cpp.o CMakeFiles/nblib.dir/topology.cpp.o CMakeFiles/nblib.dir/tpr.cpp.o CMakeFiles/nblib.dir/virials.cpp.o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o CMakeFiles/nblib.dir/util/setup.cpp.o -lm ../../lib/libgromacs_mpi_d.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -lmuparser /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib && /usr/bin/cmake -E cmake_symlink_library ../../lib/libnblib_gmx.so.0.1.0 ../../lib/libnblib_gmx.so.0 ../../lib/libnblib_gmx.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' [100%] Built target nblib /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib/samples/CMakeFiles/argon-forces-integration.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib/samples 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fopenmp -MD -MT api/nblib/samples/CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o -MF CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o.d -o CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/samples/argon-forces-integration.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib/samples && /usr/bin/mpicxx -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/legacy/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fopenmp -MD -MT api/nblib/samples/CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o -MF CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o.d -o CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/samples/methane-water-integration.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib/samples && /usr/bin/cmake -E cmake_link_script CMakeFiles/argon-forces-integration.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/argon-forces-integration.dir/link.d "CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o" -o ../../../bin/argon-forces-integration ../../../lib/libnblib_gmx.so.0.1.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -Wl,-rpath-link,/build/reproducible-path/gromacs-2025.0/build/mpi-dp/lib make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' [100%] Built target argon-forces-integration cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib/samples && /usr/bin/cmake -E cmake_link_script CMakeFiles/methane-water-integration.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/methane-water-integration.dir/link.d "CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o" -o ../../../bin/methane-water-integration ../../../lib/libnblib_gmx.so.0.1.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -Wl,-rpath-link,/build/reproducible-path/gromacs-2025.0/build/mpi-dp/lib make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' [100%] Built target methane-water-integration make[2]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.0/build/mpi-dp/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' LD_LIBRARY_PATH=/build/reproducible-path/gromacs-2025.0/build/mpi/lib /usr/bin/make -j20 -C build/mpi tests make[1]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/cmake -P /build/reproducible-path/gromacs-2025.0/build/mpi/CMakeFiles/VerifyGlobs.cmake /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.0 -B/build/reproducible-path/gromacs-2025.0/build/mpi --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/make -f CMakeFiles/Makefile2 tests make[2]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/cmake -P /build/reproducible-path/gromacs-2025.0/build/mpi/CMakeFiles/VerifyGlobs.cmake /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.0 -B/build/reproducible-path/gromacs-2025.0/build/mpi --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.0/build/mpi/CMakeFiles 76 /usr/bin/make -f CMakeFiles/Makefile2 CMakeFiles/tests.dir/all make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend 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/build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs 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/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/options /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/options /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/external/googletest/googletest/CMakeFiles/gtest.dir/build.make src/external/googletest/googletest/CMakeFiles/gtest.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/external/googletest/googletest /build/reproducible-path/gromacs-2025.0/build/mpi/src/external/googletest/googletest/CMakeFiles/gtest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2025.0-Debian_2025.0_2 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2025.0 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.0/build/mpi/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2025.0/build/mpi/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2025.0-2 -P /build/reproducible-path/gromacs-2025.0/cmake/gmxGenerateVersionInfoWithoutGit.cmake /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Nothing to be done for 'src/gromacs/selection/CMakeFiles/scanner.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Nothing to be done for 'src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Nothing to be done for 'src/programs/CMakeFiles/gmx_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Nothing to be done for 'src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/external/googletest/googletest/CMakeFiles/gtest.dir/build.make src/external/googletest/googletest/CMakeFiles/gtest.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/external/googletest/googletest && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_CREATE_SHARED_LIBRARY=1 -DGTEST_LANG_CXX11 -Dgtest_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -I/build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -Wall -Wshadow -Wno-error=dangling-else -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -MD -MT src/external/googletest/googletest/CMakeFiles/gtest.dir/src/gtest-all.cc.o -MF CMakeFiles/gtest.dir/src/gtest-all.cc.o.d -o CMakeFiles/gtest.dir/src/gtest-all.cc.o -c /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/src/gtest-all.cc make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 0%] Built target scanner [ 0%] Built target internal_rpc_xdr [ 0%] Built target lmfit_objlib [ 0%] Built target thread_mpi make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build [ 1%] Built target linearalgebra make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Nothing to be done for 'src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 2%] Built target gmx_objlib make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 2%] Built target release-version-info make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/pulling /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" [ 2%] Built target energyanalysis [ 3%] Built target tng_io_obj make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build [ 3%] Built target mdrun_objlib make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Nothing to be done for 'src/gromacs/options/CMakeFiles/options.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 5%] Built target options make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Nothing to be done for 'src/gromacs/pulling/CMakeFiles/pulling.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/colvars_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 6%] Built target pulling /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" [ 9%] Built target colvars_objlib make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Nothing to be done for 'src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 9%] Built target taskassignment make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 11%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 61%] Built target libgromacs /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake "--color=" /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/gmxapi /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/CMakeFiles/nblib.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Nothing to be done for 'src/programs/CMakeFiles/gmx.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Nothing to be done for 'api/gmxapi/CMakeFiles/gmxapi.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Nothing to be done for 'api/nblib/CMakeFiles/nblib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 61%] Built target gmx /usr/bin/make -f python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_spc2_water_box.dir/build.make python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_spc2_water_box.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/python_packaging/sample_restraint/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/tests /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_spc2_water_box.dir/DependInfo.cmake "--color=" [ 63%] Built target gmxapi /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/DependInfo.cmake "--color=" [ 64%] Built target nblib /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/samples/CMakeFiles/argon-forces-integration.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/samples/CMakeFiles/methane-water-integration.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_spc2_water_box.dir/build.make python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_spc2_water_box.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/tests && /build/reproducible-path/gromacs-2025.0/build/mpi/bin/gmx_mpi -quiet grompp -f /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/tests/grompp.mdp -c /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro -p /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.top make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Nothing to be done for 'python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 64%] Built target gmxapi_extension_resources /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Nothing to be done for 'python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Nothing to be done for 'api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Nothing to be done for 'api/nblib/samples/CMakeFiles/methane-water-integration.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 64%] Built target gmxapi_extension_ensemblepotential [ 64%] Built target methane-water-integration [ 64%] Built target argon-forces-integration Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group rest is 9.00 The integrator does not provide a ensemble temperature, there is no system ensemble temperature NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/tests/grompp.mdp]: NVE simulation: will use the initial temperature of 2573.591 K for determining the Verlet buffer size NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/tests/grompp.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 2 NOTEs Setting the LD random seed to -168296714 Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' Analysing residue names: There are: 2 Water residues Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 64%] Built target gmxapi_extension_spc2_water_box cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/external/googletest/googletest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest.dir/link.txt --verbose=1 /usr/bin/mpicxx -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file=CMakeFiles/gtest.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgtest.so.1.13.0 -o ../../../../lib/libgtest.so.1.13.0 "CMakeFiles/gtest.dir/src/gtest-all.cc.o" cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/external/googletest/googletest && /usr/bin/cmake -E cmake_symlink_library ../../../../lib/libgtest.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 ../../../../lib/libgtest.so make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 64%] Built target gtest /usr/bin/make -f src/external/googletest/googletest/CMakeFiles/gtest_main.dir/build.make src/external/googletest/googletest/CMakeFiles/gtest_main.dir/depend /usr/bin/make -f src/external/googletest/googlemock/CMakeFiles/gmock.dir/build.make src/external/googletest/googlemock/CMakeFiles/gmock.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/external/googletest/googletest /build/reproducible-path/gromacs-2025.0/build/mpi/src/external/googletest/googletest/CMakeFiles/gtest_main.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/external/googletest/googlemock /build/reproducible-path/gromacs-2025.0/build/mpi/src/external/googletest/googlemock/CMakeFiles/gmock.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/external/googletest/googletest/CMakeFiles/gtest_main.dir/build.make src/external/googletest/googletest/CMakeFiles/gtest_main.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/external/googletest/googlemock/CMakeFiles/gmock.dir/build.make src/external/googletest/googlemock/CMakeFiles/gmock.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/external/googletest/googletest && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_CREATE_SHARED_LIBRARY=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -Dgtest_main_EXPORTS -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -Wall -Wshadow -Wno-error=dangling-else -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -MD -MT src/external/googletest/googletest/CMakeFiles/gtest_main.dir/src/gtest_main.cc.o -MF CMakeFiles/gtest_main.dir/src/gtest_main.cc.o.d -o CMakeFiles/gtest_main.dir/src/gtest_main.cc.o -c /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/src/gtest_main.cc make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/external/googletest/googlemock && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_CAN_STREAM_RESULTS=0 -DGTEST_CREATE_SHARED_LIBRARY=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -D_GNU_SOURCE=1 -Dgmock_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -I/build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -Wall -Wshadow -Wno-error=dangling-else -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -Wno-deprecated-copy -MD -MT src/external/googletest/googlemock/CMakeFiles/gmock.dir/src/gmock-all.cc.o -MF CMakeFiles/gmock.dir/src/gmock-all.cc.o.d -o CMakeFiles/gmock.dir/src/gmock-all.cc.o -c /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/src/gmock-all.cc cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/external/googletest/googletest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest_main.dir/link.txt --verbose=1 /usr/bin/mpicxx -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file=CMakeFiles/gtest_main.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgtest_main.so.1.13.0 -o ../../../../lib/libgtest_main.so.1.13.0 CMakeFiles/gtest_main.dir/src/gtest_main.cc.o ../../../../lib/libgtest.so.1.13.0 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/external/googletest/googletest && /usr/bin/cmake -E cmake_symlink_library ../../../../lib/libgtest_main.so.1.13.0 ../../../../lib/libgtest_main.so.1.13.0 ../../../../lib/libgtest_main.so make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 65%] Built target gtest_main /usr/bin/make -f python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_bounding-test.dir/build.make python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_bounding-test.dir/depend /usr/bin/make -f python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_histogram-test.dir/build.make python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_histogram-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/python_packaging/sample_restraint/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/tests /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_histogram-test.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/python_packaging/sample_restraint/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/tests /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_bounding-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_histogram-test.dir/build.make python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_histogram-test.dir/build /usr/bin/make -f python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_bounding-test.dir/build.make python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_bounding-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -I/build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/tests -I/build/reproducible-path/gromacs-2025.0/python_packaging/sample_restraint/src/cpp -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fvisibility=hidden -MD -MT python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_histogram-test.dir/test_histogram.cpp.o -MF CMakeFiles/gmxapi_extension_histogram-test.dir/test_histogram.cpp.o.d -o CMakeFiles/gmxapi_extension_histogram-test.dir/test_histogram.cpp.o -c /build/reproducible-path/gromacs-2025.0/python_packaging/sample_restraint/tests/test_histogram.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -I/build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/tests -I/build/reproducible-path/gromacs-2025.0/python_packaging/sample_restraint/src/cpp -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fvisibility=hidden -MD -MT python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_bounding-test.dir/test_bounding_restraint.cpp.o -MF CMakeFiles/gmxapi_extension_bounding-test.dir/test_bounding_restraint.cpp.o.d -o CMakeFiles/gmxapi_extension_bounding-test.dir/test_bounding_restraint.cpp.o -c /build/reproducible-path/gromacs-2025.0/python_packaging/sample_restraint/tests/test_bounding_restraint.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi_extension_histogram-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. 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/usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/nnpot/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include 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/build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -MF CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o.d -o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/onlinehelp/tests/mock_helptopic.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/domdec/tests && /usr/bin/mpicxx 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override 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-I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o -MF CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o.d -o CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/tests/haloexchange_mpi.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY 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/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem 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src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/energycomparison.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/nbnxm/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nbnxm-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nbnxm-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-mpi-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/testutils/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -MF CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o.d -o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include 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-Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/qmmm/tests/qmmmtopologypreprocessor.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/testutils/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/naming.cpp.o -MF CMakeFiles/testutils-test.dir/naming.cpp.o.d -o CMakeFiles/testutils-test.dir/naming.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/tests/naming.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/utility-mpi-test.dir/link.d "CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o" "CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/utility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 68%] Built target utility-mpi-test /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/ewald/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/ewald/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -MF CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -c 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem 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-MT src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT 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-fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/moduletest.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/domdec-mpi-test.dir/link.d "CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o" "CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/domdec-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -lmuparser /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 69%] Built target domdec-mpi-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2025.0/build/mpi 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-I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/simulatorcomparison.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" 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cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem 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src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -MF CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/tests/devicetransfers.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src 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-fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/gmxlib/nonbonded/tests/CMakeFiles/nonbonded-fep-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nonbonded-fep-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nonbonded-fep-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/fft/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fft-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdrunutility/tests && /usr/bin/cmake -P CMakeFiles/mdrunutility-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdtypes/tests && /usr/bin/mpicxx 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-fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/complex.cpp.o -MF CMakeFiles/math-test.dir/complex.cpp.o.d -o CMakeFiles/math-test.dir/complex.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/complex.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -DGMX_CP2K=0 -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include 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-fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/trajectorycomparison.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/constrtestdata.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxlib/nonbonded/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nonbonded-fep-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/nbnxm/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o -MF CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o.d -o CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/tests/kernelsetup.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/nnpot/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem 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-I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/biasgrid.cpp.o -MF CMakeFiles/awh-test.dir/biasgrid.cpp.o.d -o CMakeFiles/awh-test.dir/biasgrid.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/biasgrid.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nonbonded-fep-test.dir/link.d "CMakeFiles/nonbonded-fep-test.dir/nb_free_energy.cpp.o" "CMakeFiles/nonbonded-fep-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/nonbonded-fep-test ../../../../../lib/libtestutils.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_mpi.so.10.0.0 -lm ../../../../../lib/libgmock.so.1.13.0 ../../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -lmuparser /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 71%] Built target nonbonded-fep-test /usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/pbcutil/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/pbcutil/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/com.cpp.o -MF CMakeFiles/pbcutil-test.dir/com.cpp.o.d -o CMakeFiles/pbcutil-test.dir/com.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/tests/com.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 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/build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -MF CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/onlinehelp/tests/helpmanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/testutils/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD 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-I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/qmmm/tests/qmmm.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF 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-Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/layouts.cpp.o -MF CMakeFiles/mdspan-test.dir/layouts.cpp.o.d -o CMakeFiles/mdspan-test.dir/layouts.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdspan/tests/layouts.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/nnpot/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nnpot_applied_forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem 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/build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/constrtestrunners.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/listed_forces/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o -MF CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o.d -o CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/tests/position_restraints.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nnpot_applied_forces-test.dir/link.d "CMakeFiles/nnpot_applied_forces-test.dir/nnpot.cpp.o" "CMakeFiles/nnpot_applied_forces-test.dir/nnpotoptions.cpp.o" "CMakeFiles/nnpot_applied_forces-test.dir/nnpottopologypreprocessor.cpp.o" "CMakeFiles/nnpot_applied_forces-test.dir/nnpotforceprovider.cpp.o" "CMakeFiles/nnpot_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/nnpot_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../../lib/libgmock.so.1.13.0 ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 71%] Built target nnpot_applied_forces-test /usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/random/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/random/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/random/tests/CMakeFiles/random-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/random/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -MF CMakeFiles/random-test.dir/exponentialdistribution.cpp.o.d -o CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/random/tests/exponentialdistribution.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/ewald/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD 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-I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/biassharing.cpp.o -MF CMakeFiles/awh-test.dir/biassharing.cpp.o.d -o CMakeFiles/awh-test.dir/biassharing.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/biassharing.cpp cd 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-I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/mdspan.cpp.o -MF CMakeFiles/mdspan-test.dir/mdspan.cpp.o.d -o CMakeFiles/mdspan-test.dir/mdspan.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdspan/tests/mdspan.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/density_fitting_applied_forces-test.dir/link.d "CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/density_fitting_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 72%] Built target density_fitting_applied_forces-test /usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/restraint/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/restraint/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/restraint/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/restraint/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/manager.cpp.o -MF CMakeFiles/restraintpotential-test.dir/manager.cpp.o.d -o CMakeFiles/restraintpotential-test.dir/manager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/restraint/tests/manager.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/onlinehelp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -MF CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/onlinehelp/tests/helpwritercontext.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src 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/build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/qmmm_applied_forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/hardware/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/onlinehelp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem 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/build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/testutils/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include 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src/testutils/tests/CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -MF CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o.d -o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/random/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/gammadistribution.cpp.o -MF CMakeFiles/random-test.dir/gammadistribution.cpp.o.d -o CMakeFiles/random-test.dir/gammadistribution.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/random/tests/gammadistribution.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/qmmm_applied_forces-test.dir/link.d "CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/qmmm_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 72%] Built target qmmm_applied_forces-test /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 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-I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem 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-MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/colvars_applied_forces-test.dir/link.d "CMakeFiles/colvars_applied_forces-test.dir/colvars.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/colvarsforceprovider.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/colvars_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../../lib/libgmock.so.1.13.0 -lm ../../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -lmuparser /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 73%] Built target colvars_applied_forces-test /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/taskassignment/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/taskassignment/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/taskassignment/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY 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/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/pbcutil/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include 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../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/restraintpotential-test.dir/link.d "CMakeFiles/restraintpotential-test.dir/manager.cpp.o" "CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/restraintpotential-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a 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-I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem 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mdrun_test_infrastructure /usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/depend cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdtypes/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include 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-Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o -MF CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o.d -o CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/checkpointdata.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/topology/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/topology/tests/CMakeFiles/topology-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/topology/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include 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-fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/atoms.cpp.o -MF CMakeFiles/topology-test.dir/atoms.cpp.o.d -o CMakeFiles/topology-test.dir/atoms.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/atoms.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/hardware/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testutils-test.dir/link.d "CMakeFiles/testutils-test.dir/interactivetest.cpp.o" "CMakeFiles/testutils-test.dir/naming.cpp.o" "CMakeFiles/testutils-test.dir/refdata_tests.cpp.o" "CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o" "CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o" "CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o" -o ../../../bin/testutils-test ../../../lib/libtestutils.a ../../../lib/libtestutils.a ../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 75%] Built target testutils-test /usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/pulling/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/nbnxm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nbnxm-test.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/pulling/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/pulling/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external 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Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 75%] Built target nbnxm-test /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/simd/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/simd/tests/CMakeFiles/simd-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build make[4]: Entering 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-MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/base.cpp.o -MF CMakeFiles/simd-test.dir/base.cpp.o.d -o CMakeFiles/simd-test.dir/base.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/base.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/hardware/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/hardware-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdspan/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/energyoutput.cpp.o -MF CMakeFiles/mdlib-test.dir/energyoutput.cpp.o.d -o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o -c 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'/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/listed_forces/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp [ 75%] Built target hardware-test cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/expanded.cpp.o -MF CMakeFiles/mdlib-test.dir/expanded.cpp.o.d -o CMakeFiles/mdlib-test.dir/expanded.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/expanded.cpp cd 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-fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -MF CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/tests/pmesplinespreadtest.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/random/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/seed.cpp.o -MF CMakeFiles/random-test.dir/seed.cpp.o.d -o CMakeFiles/random-test.dir/seed.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/random/tests/seed.cpp cd 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/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/timing/tests/CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/options/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/filenameoption.cpp.o -MF CMakeFiles/options-test.dir/filenameoption.cpp.o.d -o CMakeFiles/options-test.dir/filenameoption.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/tests/filenameoption.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/listed_forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/pbcutil/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o -MF CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o.d -o CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/tests/pbcenums.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdspan/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdspan-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/listed_forces-test.dir/link.d "CMakeFiles/listed_forces-test.dir/bonded.cpp.o" "CMakeFiles/listed_forces-test.dir/pairs.cpp.o" "CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o" "CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/listed_forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 75%] Built target listed_forces-test cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/pbcutil/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/timing/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/timing-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdspan-test.dir/link.d "CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o" "CMakeFiles/mdspan-test.dir/extents.cpp.o" "CMakeFiles/mdspan-test.dir/extensions.cpp.o" "CMakeFiles/mdspan-test.dir/layouts.cpp.o" "CMakeFiles/mdspan-test.dir/mdspan.cpp.o" "CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdspan-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/random/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -MF CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o.d -o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/random/tests/tabulatednormaldistribution.cpp [ 76%] Built target mdspan-test cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/ewald/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pme.cpp.o -MF CMakeFiles/ewald-test.dir/pme.cpp.o.d -o CMakeFiles/ewald-test.dir/pme.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/tests/pme.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/simd/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -MF CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o.d -o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/bootstrap_loadstore.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/timing-test.dir/link.d "CMakeFiles/timing-test.dir/timing.cpp.o" "CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/timing-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 77%] Built target timing-test /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/compat/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/compat/tests/CMakeFiles/compat-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/compat/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" 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/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/awh/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem 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src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o -MF CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o.d -o CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/compat/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/compat/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/compat/tests/CMakeFiles/compat-test.dir/pointers.cpp.o -MF CMakeFiles/compat-test.dir/pointers.cpp.o.d -o CMakeFiles/compat-test.dir/pointers.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/tests/pointers.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/taskassignment/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/taskassignment/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/pbcutil/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pbcutil-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pbcutil-test.dir/link.d "CMakeFiles/pbcutil-test.dir/com.cpp.o" "CMakeFiles/pbcutil-test.dir/mshift.cpp.o" "CMakeFiles/pbcutil-test.dir/pbc.cpp.o" "CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o" "CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pbcutil-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 78%] Built target pbcutil-test /usr/bin/make -f 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/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxana/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/random/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/threefry.cpp.o -MF CMakeFiles/random-test.dir/threefry.cpp.o.d -o CMakeFiles/random-test.dir/threefry.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/random/tests/threefry.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/math/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" 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/usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include 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../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -lmuparser /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 78%] Built target taskassignment-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests 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/build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/tests/typecasts.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem 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-MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/booltype.cpp.o -MF CMakeFiles/utility-test.dir/booltype.cpp.o.d -o CMakeFiles/utility-test.dir/booltype.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/booltype.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/pulling/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pull-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/compat/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/compat-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/options/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -MF CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o.d -o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/tests/filenameoptionmanager.cpp cd 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 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-I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 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src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd 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directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 80%] Built target compat-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include 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CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/tests/gmx_mindist.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/ewald/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat 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make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 80%] Built target gpu_utils-test cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include 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CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/tests/gmx_traj.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/math/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem 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-Wl,-z,now -Wl,--dependency-file=CMakeFiles/table-test.dir/link.d "CMakeFiles/table-test.dir/splinetable.cpp.o" "CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/table-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 80%] Built target table-test /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/depend cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/random/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" 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make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/analysisdata/tests && 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o -MF CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o.d -o CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/forcebuffers.cpp [ 80%] Built target awh-test /usr/bin/make -f src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build.make src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 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-MT src/gromacs/math/tests/CMakeFiles/math-test.dir/invertmatrix.cpp.o -MF CMakeFiles/math-test.dir/invertmatrix.cpp.o.d -o CMakeFiles/math-test.dir/invertmatrix.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/invertmatrix.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/analysisdata/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/analysisdata-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/analysisdata-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/cstringutil.cpp.o -MF CMakeFiles/utility-test.dir/cstringutil.cpp.o.d -o CMakeFiles/utility-test.dir/cstringutil.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/cstringutil.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/coordinateio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o -MF CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o.d -o CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/tests/outputadaptercontainer.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmxana-test.dir/link.d "CMakeFiles/gmxana-test.dir/entropy.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o" "CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gmxana-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 80%] Built target gmxana-test /usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/energyanalysis/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/energyanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/energyanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/energyterm.cpp.o -MF CMakeFiles/energyanalysis-test.dir/energyterm.cpp.o.d -o CMakeFiles/energyanalysis-test.dir/energyterm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/energyterm.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx1-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/topology/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 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/usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 80%] Built target pdb2gmx1-test cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/energyanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/energyanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 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-I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 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cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/energyanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/energyanalysis-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/math/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override 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/usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 80%] Built target energyanalysis-test cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/math/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include 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-I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 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/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD 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-I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -MF CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o.d -o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/keyvaluetreetransform.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/random-test.dir/link.d "CMakeFiles/random-test.dir/exponentialdistribution.cpp.o" "CMakeFiles/random-test.dir/gammadistribution.cpp.o" "CMakeFiles/random-test.dir/normaldistribution.cpp.o" "CMakeFiles/random-test.dir/seed.cpp.o" "CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o" "CMakeFiles/random-test.dir/threefry.cpp.o" "CMakeFiles/random-test.dir/uniformintdistribution.cpp.o" "CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o" "CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/random-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/simd/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include 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src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -MF CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o.d -o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/simd_floatingpoint.cpp [ 81%] Built target random-test /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/CMakeFiles/tool-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include 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-Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/dump.cpp.o -MF CMakeFiles/tool-test.dir/dump.cpp.o.d -o CMakeFiles/tool-test.dir/dump.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/tests/dump.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/correlationfunctions/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/correlations-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/simd/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem 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/build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/topology/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/topsort.cpp.o -MF CMakeFiles/topology-test.dir/topsort.cpp.o.d -o CMakeFiles/topology-test.dir/topsort.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/topsort.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/listoflists.cpp.o -MF CMakeFiles/utility-test.dir/listoflists.cpp.o.d -o CMakeFiles/utility-test.dir/listoflists.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/listoflists.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx3-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/correlations-test.dir/link.d "CMakeFiles/correlations-test.dir/autocorr.cpp.o" "CMakeFiles/correlations-test.dir/correlationdataset.cpp.o" "CMakeFiles/correlations-test.dir/expfit.cpp.o" "CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o" "CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/correlations-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 81%] Built target correlations-test cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem 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-MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/genion.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/math/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include 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-Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/optimization.cpp.o -MF CMakeFiles/math-test.dir/optimization.cpp.o.d -o CMakeFiles/math-test.dir/optimization.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/optimization.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pdb2gmx3-test.dir/link.d "CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o" "CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pdb2gmx3-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 81%] Built target pdb2gmx3-test /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include 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-fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/convert-tpr-with-leaks.cpp.o -MF CMakeFiles/tool-test-with-leaks.dir/convert-tpr-with-leaks.cpp.o.d -o CMakeFiles/tool-test-with-leaks.dir/convert-tpr-with-leaks.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/tests/convert-tpr-with-leaks.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include 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/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdtypes/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdtypes-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/math/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include 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-MT src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/tool-test-with-leaks.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/tool-test-with-leaks.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/gen_maxwell_velocities.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem 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-Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/confio.cpp.o -MF CMakeFiles/fileio-test.dir/confio.cpp.o.d -o CMakeFiles/fileio-test.dir/confio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/confio.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/topology/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/topology-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/simd/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_integer.cpp.o -MF CMakeFiles/simd-test.dir/simd_integer.cpp.o.d -o CMakeFiles/simd-test.dir/simd_integer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/simd_integer.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/analysisdata/tests && /usr/bin/cmake -P CMakeFiles/analysisdata-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test-shared.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libanalysisdata-test-shared.a "CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o" "CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o" "CMakeFiles/analysisdata-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o" /usr/bin/ranlib ../../../../lib/libanalysisdata-test-shared.a /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/topology-test.dir/link.d "CMakeFiles/topology-test.dir/atoms.cpp.o" "CMakeFiles/topology-test.dir/exclusionblocks.cpp.o" "CMakeFiles/topology-test.dir/idef.cpp.o" "CMakeFiles/topology-test.dir/index.cpp.o" "CMakeFiles/topology-test.dir/mtop.cpp.o" "CMakeFiles/topology-test.dir/symtab.cpp.o" "CMakeFiles/topology-test.dir/topsort.cpp.o" "CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/topology-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 82%] Built target analysisdata-test-shared /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/DependInfo.cmake "--color=" [ 82%] Built target topology-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o -MF CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/compressed_x_output.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem 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-MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/densityfittingmodule.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/simd/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_math.cpp.o -MF CMakeFiles/simd-test.dir/simd_math.cpp.o.d -o CMakeFiles/simd-test.dir/simd_math.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/simd_math.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/tool-test-with-leaks.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem 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-MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -MF CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o.d -o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/simulationsignal.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/path.cpp.o -MF CMakeFiles/utility-test.dir/path.cpp.o.d -o CMakeFiles/utility-test.dir/path.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/path.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -MF CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o.d -o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/physicalnodecommunicator.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/trjconv.cpp.o -MF CMakeFiles/tool-test.dir/trjconv.cpp.o.d -o CMakeFiles/tool-test.dir/trjconv.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/tests/trjconv.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tool-test-with-leaks.dir/link.d "CMakeFiles/tool-test-with-leaks.dir/convert-tpr-with-leaks.cpp.o" "CMakeFiles/tool-test-with-leaks.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/tool-test-with-leaks ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 82%] Built target tool-test-with-leaks cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY 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-I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/solvate.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/tool-test.dir/link.txt --verbose=1 cd 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/build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o -MF CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o.d -o CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/stringtoenumvalueconverter.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/coordinateio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/coordinateio-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tool-test.dir/link.d "CMakeFiles/tool-test.dir/dump.cpp.o" "CMakeFiles/tool-test.dir/helpwriting.cpp.o" "CMakeFiles/tool-test.dir/make_ndx.cpp.o" "CMakeFiles/tool-test.dir/report_methods.cpp.o" 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-I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/treesupport.cpp.o -MF CMakeFiles/options-test.dir/treesupport.cpp.o.d -o CMakeFiles/options-test.dir/treesupport.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/tests/treesupport.cpp [ 82%] Built target tool-test cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/options/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" 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/build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/stringutil.cpp.o -MF CMakeFiles/utility-test.dir/stringutil.cpp.o.d -o CMakeFiles/utility-test.dir/stringutil.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/stringutil.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/coordinateio-test.dir/link.d "CMakeFiles/coordinateio-test.dir/builder.cpp.o" "CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o" "CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o" "CMakeFiles/coordinateio-test.dir/register.cpp.o" "CMakeFiles/coordinateio-test.dir/requirements.cpp.o" "CMakeFiles/coordinateio-test.dir/setatoms.cpp.o" "CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o" "CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o" "CMakeFiles/coordinateio-test.dir/settimestep.cpp.o" "CMakeFiles/coordinateio-test.dir/testmodule.cpp.o" "CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/coordinateio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 82%] Built target coordinateio-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests 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src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -MF CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o.d -o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/tests/simd_vector_operations.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/simd/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection 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-I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/topdirs.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/simd/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem 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CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/simd/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 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-I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection 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make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 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-I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem 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/usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external 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CMakeFiles/selection-test.dir/selectionoption.cpp.o.d -o CMakeFiles/selection-test.dir/selectionoption.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/tests/selectionoption.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-output-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-modules-test.dir/link.d "CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o" "CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o" "CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o" "CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-modules-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 85%] Built target mdrun-modules-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests 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src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/minimize-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/minimize-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxpreprocess-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 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../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/selection/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include 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-Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/toputils.cpp.o -MF CMakeFiles/selection-test.dir/toputils.cpp.o.d -o CMakeFiles/selection-test.dir/toputils.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/tests/toputils.cpp [ 85%] Built target mdrun-output-test cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include 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/build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/nonbonded_bench.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmxpreprocess-test.dir/link.d "CMakeFiles/gmxpreprocess-test.dir/convparm.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/massrepartitioning.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gmxpreprocess-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 86%] Built target gmxpreprocess-test cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/fileio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" 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/build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/mrcserializer.cpp.o -MF CMakeFiles/fileio-test.dir/mrcserializer.cpp.o.d -o CMakeFiles/fileio-test.dir/mrcserializer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/mrcserializer.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem 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src/gromacs/utility/tests/CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/fileio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include 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-I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 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/build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/fileio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem 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-Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/normalmodes.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/selection/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem 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src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o -MF CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o.d -o 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"CMakeFiles/simd-test.dir/simd4.cpp.o" "CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o" "CMakeFiles/simd-test.dir/simd4_math.cpp.o" "CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o" "CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/simd-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 88%] Built target simd-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/domain_decomposition.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/options/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/options-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/options-test.dir/link.d "CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o" "CMakeFiles/options-test.dir/filenameoption.cpp.o" "CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o" "CMakeFiles/options-test.dir/option.cpp.o" "CMakeFiles/options-test.dir/optionsassigner.cpp.o" "CMakeFiles/options-test.dir/repeatingsection.cpp.o" "CMakeFiles/options-test.dir/timeunitmanager.cpp.o" "CMakeFiles/options-test.dir/treesupport.cpp.o" "CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/options-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 88%] Built target options-test cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/rerun.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -MF CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o.d -o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/tabulated_bonded_interactions.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-single-rank-algorithms-test.dir/link.d "CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/orires.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-single-rank-algorithms-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 88%] Built target mdrun-single-rank-algorithms-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override 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/build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o -MF CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o.d -o CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/fileioxdrserializer.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat 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src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd 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src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o -MF CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/multisimtest.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include 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-fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/multisimtest.cpp.o -MF CMakeFiles/mdrun-multisim-test.dir/multisimtest.cpp.o.d -o CMakeFiles/mdrun-multisim-test.dir/multisimtest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/multisimtest.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/fileio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/tngio.cpp.o -MF CMakeFiles/fileio-test.dir/tngio.cpp.o.d -o CMakeFiles/fileio-test.dir/tngio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/tngio.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" 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/build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem 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-MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/freezegroups.cpp.o -MF CMakeFiles/mdrun-test.dir/freezegroups.cpp.o.d -o CMakeFiles/mdrun-test.dir/freezegroups.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/freezegroups.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include 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-fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o -MF CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o.d -o CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/constantacceleration.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/fileio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-tpi-test.dir/link.d "CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o" "CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-tpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 88%] Built target mdrun-tpi-test cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/fileio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd 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-Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o -MF CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/replicaexchange_equivalence.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o -MF CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/replicaexchange.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem 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/build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem 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-fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/mimic.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem 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CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override 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/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include 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src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o -MF CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o.d -o CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/periodicactions_basic.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-non-integrator-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include 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Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser 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-fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/grompp.cpp.o -MF CMakeFiles/mdrun-io-test.dir/grompp.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/grompp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/grompp.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/math-test.dir/link.d "CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o" "CMakeFiles/math-test.dir/boxmatrix.cpp.o" "CMakeFiles/math-test.dir/complex.cpp.o" "CMakeFiles/math-test.dir/coordinatetransformation.cpp.o" "CMakeFiles/math-test.dir/densityfit.cpp.o" "CMakeFiles/math-test.dir/dofit.cpp.o" "CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o" "CMakeFiles/math-test.dir/functions.cpp.o" "CMakeFiles/math-test.dir/gausstransform.cpp.o" "CMakeFiles/math-test.dir/densityfittingforce.cpp.o" "CMakeFiles/math-test.dir/invertmatrix.cpp.o" "CMakeFiles/math-test.dir/matrix.cpp.o" "CMakeFiles/math-test.dir/multidimarray.cpp.o" "CMakeFiles/math-test.dir/neldermead.cpp.o" "CMakeFiles/math-test.dir/optimization.cpp.o" "CMakeFiles/math-test.dir/paddedvector.cpp.o" "CMakeFiles/math-test.dir/vectypes.cpp.o" "CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/math-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 89%] Built target math-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include 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src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/expandedensemble.cpp.o -MF CMakeFiles/mdrun-fep-test.dir/expandedensemble.cpp.o.d -o CMakeFiles/mdrun-fep-test.dir/expandedensemble.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/expandedensemble.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include 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-fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o -MF CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o.d -o CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/freeenergy.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/utility-test.dir/link.d 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"CMakeFiles/utility-test.dir/scope_guard.cpp.o" "CMakeFiles/utility-test.dir/strconvert.cpp.o" "CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o" "CMakeFiles/utility-test.dir/stringutil.cpp.o" "CMakeFiles/utility-test.dir/template_mp.cpp.o" "CMakeFiles/utility-test.dir/textreader.cpp.o" "CMakeFiles/utility-test.dir/textwriter.cpp.o" "CMakeFiles/utility-test.dir/typetraits.cpp.o" "CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/utility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 90%] Built target utility-test cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o -MF CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/initialconstraints.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-mpi-test.dir/link.d "CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o" "CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o" "CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 90%] Built target mdrun-mpi-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem 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'/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include 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../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 92%] Built target mdrun-multisim-test cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/termination.cpp.o -MF CMakeFiles/mdrun-io-test.dir/termination.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/termination.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/termination.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/fileio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileio-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-pme-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-replex-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser 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CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-multisim-replex-test.dir/link.d "CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o" "CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-replex-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-mpi-pme-test.dir/link.d "CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o" "CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-pme-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 92%] Built target mdrun-mpi-pme-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/depend [ 92%] Built target mdrun-multisim-replex-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests 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"CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o" "CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o" "CMakeFiles/fileio-test.dir/readinp.cpp.o" "CMakeFiles/fileio-test.dir/timecontrol.cpp.o" "CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o" "CMakeFiles/fileio-test.dir/tngio.cpp.o" "CMakeFiles/fileio-test.dir/xvgio.cpp.o" "CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/fileio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 92%] Built target fileio-test cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem 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/build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem 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/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/build.make api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include 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/build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/restraint.cpp.o -MF CMakeFiles/gmxapi-test.dir/restraint.cpp.o.d -o CMakeFiles/gmxapi-test.dir/restraint.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests/restraint.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 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/build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o -MF CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o.d -o CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/periodicactions_coupling.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/selection-test.dir/link.d "CMakeFiles/selection-test.dir/indexutil.cpp.o" "CMakeFiles/selection-test.dir/nbsearch.cpp.o" "CMakeFiles/selection-test.dir/poscalc.cpp.o" "CMakeFiles/selection-test.dir/selectioncollection.cpp.o" "CMakeFiles/selection-test.dir/selectionoption.cpp.o" "CMakeFiles/selection-test.dir/toputils.cpp.o" "CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/selection-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 92%] Built target selection-test cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-test.dir/link.d "CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o" "CMakeFiles/mdrun-test.dir/swapcoords.cpp.o" "CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o" "CMakeFiles/mdrun-test.dir/freezegroups.cpp.o" "CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o" "CMakeFiles/mdrun-test.dir/boxdeformation.cpp.o" "CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/runner.cpp.o -MF 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/status.cpp.o -MF CMakeFiles/gmxapi-test.dir/status.cpp.o.d -o CMakeFiles/gmxapi-test.dir/status.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests/status.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o -MF CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o.d -o CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests/stopsignaler.cpp /usr/bin/make -f api/gmxapi/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/build.make api/gmxapi/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/depend cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-coordination-basic-test.dir/link.txt --verbose=1 make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f api/gmxapi/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/build.make api/gmxapi/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/context.cpp.o -MF CMakeFiles/gmxapi-mpi-test.dir/context.cpp.o.d -o CMakeFiles/gmxapi-mpi-test.dir/context.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests/context.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests -I/build/reproducible-path/gromacs-2025.0/src/testutils/include 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-fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/version.cpp.o -MF CMakeFiles/gmxapi-test.dir/version.cpp.o.d -o CMakeFiles/gmxapi-test.dir/version.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests/version.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/workflow/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/workflow/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include 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-I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/tests -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include 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api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integration-test.dir/depend [ 93%] Built target mdrun-rotation-test /usr/bin/make -f api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build.make api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/listed_forces/tests /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd 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-I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o -MF CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tests/gmxcalculator.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/listed_forces/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/listed_forces/tests/Testing/Temporary\" 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/usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 94%] Built target mdrun-multisim-replex-equivalence-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include 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/build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/tests/gmxcalculator.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/util/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/util/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src 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/build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-simulator-comparison-test.dir/link.txt --verbose=1 cd 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/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -MF CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o.d -o CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/tests/threadaffinity_mpi.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-vsites-test.dir/link.txt --verbose=1 /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/analysisdata/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include 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-DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem 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CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/moduletest.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include 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-Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -MF CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/tests/threadaffinity.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-integrator-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-vsites-test.dir/link.d "CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o" "CMakeFiles/mdrun-vsites-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-vsites-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 96%] Built target mdrun-vsites-test cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/analysisdata/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -MF CMakeFiles/analysisdata-test.dir/arraydata.cpp.o.d -o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/tests/arraydata.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-fep-test.dir/link.d "CMakeFiles/mdrun-fep-test.dir/expandedensemble.cpp.o" "CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o" "CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-fep-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 96%] Built target mdrun-fep-test cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include 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-I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/average.cpp.o -MF CMakeFiles/analysisdata-test.dir/average.cpp.o.d -o CMakeFiles/analysisdata-test.dir/average.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/tests/average.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/angle.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-tpr-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/util/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-util-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-integrator-test.dir/link.d "CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o" "CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-integrator-test ../../../lib/libtestutils.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 ../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o -MF CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tests/nbkernelsystem.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/simstate.cpp.o -MF CMakeFiles/nblib-integration-test.dir/simstate.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/simstate.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/tests/simstate.cpp [ 96%] Built target nblib-integrator-test cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/analysisdata/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/histogram.cpp.o -MF CMakeFiles/analysisdata-test.dir/histogram.cpp.o.d -o CMakeFiles/analysisdata-test.dir/histogram.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/tests/histogram.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi-mpi-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-util-test.dir/link.d "CMakeFiles/nblib-util-test.dir/setup.cpp.o" "CMakeFiles/nblib-util-test.dir/traits.cpp.o" "CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../../bin/nblib-util-test ../../../../lib/libtestutils.a ../../../../lib/libnblib_test_infrastructure.a ../../../../lib/libnblib_gmx.so.0.1.0 ../../../../lib/libtestutils.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 96%] Built target nblib-util-test cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/analysisdata/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/lifetime.cpp.o -MF CMakeFiles/analysisdata-test.dir/lifetime.cpp.o.d -o CMakeFiles/analysisdata-test.dir/lifetime.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/analysisdata/tests/lifetime.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-tpr-test.dir/link.d "CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o" "CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-tpr-test ../../../lib/libtestutils.a ../../../lib/libmdrun_test_infrastructure.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 ../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 96%] Built target nblib-tpr-test cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/analysisdata/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-pull-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmxapi-mpi-test.dir/link.d "CMakeFiles/gmxapi-mpi-test.dir/context.cpp.o" "CMakeFiles/gmxapi-mpi-test.dir/restraint.cpp.o" "CMakeFiles/gmxapi-mpi-test.dir/runner.cpp.o" "CMakeFiles/gmxapi-mpi-test.dir/status.cpp.o" "CMakeFiles/gmxapi-mpi-test.dir/stopsignaler.cpp.o" "CMakeFiles/gmxapi-mpi-test.dir/system.cpp.o" "CMakeFiles/gmxapi-mpi-test.dir/version.cpp.o" "CMakeFiles/gmxapi-mpi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" ../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/gmxapi-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgmxapi_mpi.so.0.4.0 ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 96%] Built target gmxapi-mpi-test cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/listed_forces/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/tests/helpers.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/listed_forces/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/tests/listedtesthelpers.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/listed_forces/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/tests/kernels.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-pull-test.dir/link.d "CMakeFiles/mdrun-pull-test.dir/pull.cpp.o" "CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-pull-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 96%] Built target mdrun-pull-test cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 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-I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection 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-DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 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-I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/distance.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/dssp.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/dssp.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/dssp.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/dssp.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/extract_cluster.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrunutility-mpi-test.dir/link.d "CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o" "CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdrunutility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 96%] Built target mdrunutility-mpi-test cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/freevolume.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/listed_forces/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/tests/calculator.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/gyrate.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/gyrate.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/gyrate.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/gyrate.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrunutility-test.dir/link.d "CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o" "CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o" "CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdrunutility-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 96%] Built target mdrunutility-test cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/hbond.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/hbond.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/hbond.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/hbond.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include 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-I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem 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api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/tests/conversions.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/listed_forces/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem 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cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/listed_forces/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/nblib/tests -I/build/reproducible-path/gromacs-2025.0/api/nblib/include -I/build/reproducible-path/gromacs-2025.0/api/nblib -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o -c /build/reproducible-path/gromacs-2025.0/api/nblib/listed_forces/tests/transformations.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/commandline/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/tests/cmdlinemodulemanagertest.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-integration-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/pairdist.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-integration-test.dir/link.d "CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o" "CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o" "CMakeFiles/nblib-integration-test.dir/simstate.cpp.o" "CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-integration-test ../../../lib/libtestutils.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 ../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 96%] Built target nblib-integration-test cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/listed_forces/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/listed_forces/tests/Testing/Temporary\" 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src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection 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/build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trajectory.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/unionfind.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/commandline/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/pargs.cpp.o -MF CMakeFiles/commandline-test.dir/pargs.cpp.o.d -o CMakeFiles/commandline-test.dir/pargs.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/commandline/tests/pargs.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/analysisdata-test.dir/link.d "CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o" "CMakeFiles/analysisdata-test.dir/arraydata.cpp.o" "CMakeFiles/analysisdata-test.dir/average.cpp.o" "CMakeFiles/analysisdata-test.dir/histogram.cpp.o" "CMakeFiles/analysisdata-test.dir/lifetime.cpp.o" "CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/analysisdata-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 96%] Built target analysisdata-test cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/commandline/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/testutils/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -msse4.1 -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-setup-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-setup-test.dir/link.d "CMakeFiles/nblib-setup-test.dir/box.cpp.o" "CMakeFiles/nblib-setup-test.dir/interactions.cpp.o" "CMakeFiles/nblib-setup-test.dir/particletype.cpp.o" "CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o" "CMakeFiles/nblib-setup-test.dir/molecules.cpp.o" "CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o" "CMakeFiles/nblib-setup-test.dir/topology.cpp.o" "CMakeFiles/nblib-setup-test.dir/virials.cpp.o" "CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-setup-test ../../../lib/libtestutils.a ../../../lib/libmdrun_test_infrastructure.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 ../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 96%] Built target nblib-setup-test /usr/bin/make -f api/nblib/CMakeFiles/nblib-tests.dir/build.make api/nblib/CMakeFiles/nblib-tests.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/CMakeFiles/nblib-tests.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f api/nblib/CMakeFiles/nblib-tests.dir/build.make api/nblib/CMakeFiles/nblib-tests.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Nothing to be done for 'api/nblib/CMakeFiles/nblib-tests.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 96%] Built target nblib-tests cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/commandline/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/commandline-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/commandline-test.dir/link.d "CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o" "CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o" "CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o" "CMakeFiles/commandline-test.dir/filenm.cpp.o" "CMakeFiles/commandline-test.dir/pargs.cpp.o" "CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 96%] Built target commandline-test cd /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryanalysis-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/trajectoryanalysis-test.dir/link.d "CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/dssp.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/gyrate.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/hbond.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/msd.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/scattering.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/trajectoryanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 98%] Built target trajectoryanalysis-test cd /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-listed-forces-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-listed-forces-test.dir/link.d "CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../../bin/nblib-listed-forces-test ../../../../lib/libtestutils.a ../../../../lib/libnblib_test_infrastructure.a ../../../../lib/libnblib_gmx.so.0.1.0 ../../../../lib/libtestutils.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 ../../../../lib/libgromacs_mpi.so.10.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [100%] Built target nblib-listed-forces-test /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/CMakeFiles/tests.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [100%] Built target tests make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.0/build/mpi/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[1]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' (cd build/mpi ; LD_LIBRARY_PATH=/build/reproducible-path/gromacs-2025.0/build/mpi/lib \ OMPI_MCA_rmaps_base_oversubscribe=1 \ PRTE_MCA_rmaps_default_mapping_policy=:oversubscribe \ ctest -V) UpdateCTestConfiguration from :/build/reproducible-path/gromacs-2025.0/build/mpi/DartConfiguration.tcl Parse Config file:/build/reproducible-path/gromacs-2025.0/build/mpi/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/gromacs-2025.0/build/mpi/DartConfiguration.tcl Parse Config file:/build/reproducible-path/gromacs-2025.0/build/mpi/DartConfiguration.tcl Test project /build/reproducible-path/gromacs-2025.0/build/mpi Constructing a list of tests Done constructing a list of tests Updating test list for fixtures Added 0 tests to meet fixture requirements Checking test dependency graph... Checking test dependency graph end test 1 Start 1: GmxapiExternalInterfaceTests 1: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/gmxapi-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/GmxapiExternalInterfaceTests.xml" 1: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests 1: Test timeout computed to be: 600 1: [==========] Running 9 tests from 1 test suite. 1: [----------] Global test environment set-up. 1: [----------] 9 tests from GmxApiTest 1: [ RUN ] GmxApiTest.ApiRunnerRestrainedMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 1: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI process 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to -1626497 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.153 0.077 199.8 1: (ns/day) (hour/ns) 1: Performance: 6.598 3.638 1: [ OK ] GmxApiTest.ApiRunnerRestrainedMD (570 ms) 1: [ RUN ] GmxApiTest.RunnerBasicMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 1: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI process 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to -705381377 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.063 0.032 199.4 1: (ns/day) (hour/ns) 1: Performance: 15.983 1.502 1: [ OK ] GmxApiTest.RunnerBasicMD (554 ms) 1: [ RUN ] GmxApiTest.RunnerReinitialize 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 1: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI process 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 20 steps, 0.0 ps. 1: 1: 1: Received the remote INT/TERM signal, stopping within 200 steps 1: 1: Setting the LD random seed to -545670720 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.133 0.067 199.7 1: (ns/day) (hour/ns) 1: Performance: 53.183 0.451 1: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 1: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI process 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 20 steps, 0.0 ps. 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.034 0.017 199.0 1: (ns/day) (hour/ns) 1: Performance: 209.638 0.114 1: [ OK ] GmxApiTest.RunnerReinitialize (598 ms) 1: [ RUN ] GmxApiTest.RunnerChainedMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 1: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI process 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to -1084033298 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.148 0.074 199.7 1: (ns/day) (hour/ns) 1: Performance: 6.854 3.502 1: trr version: GMX_trn_file (single precision) 1: 1: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 1: Setting nsteps to 4 1: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 1: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI process 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 1: Input file: 1: Run start step 0 1: Run start time 0 ps 1: Step to be made during run 2 1: Runtime for the run 0.00390625 ps 1: Run end step 2 1: Run end time 0.00390625 ps 1: 1: 1: Output file: 1: Run start step 0 1: Run start time 0 ps 1: Step to be made during run 4 1: Runtime for the run 0.0078125 ps 1: Run end step 4 1: Run end time 0.0078125 ps 1: 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.038 0.019 199.3 1: (ns/day) (hour/ns) 1: Performance: 26.610 0.902 1: 1: [ OK ] GmxApiTest.RunnerChainedMD (636 ms) 1: [ RUN ] GmxApiTest.Status 1: [ OK ] GmxApiTest.Status (0 ms) 1: [ RUN ] GmxApiTest.ApiRunnerStopSignalClient 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 1: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 1: Changing nstlist from 10 to 1, rlist from 1.057 to 1 1: 1: Using 1 MPI process 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps. 1: Setting the LD random seed to 2063293911 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.039 0.020 199.0 1: (ns/day) (hour/ns) 1: Performance: 42.993 0.558 1: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 1: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 1: Overriding nsteps with value passed on the command line: 4 steps, 0.00781 ps 1: Changing nstlist from 10 to 1, rlist from 1.057 to 1 1: 1: 1: Using 1 MPI process 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.333 0.167 199.9 1: (ns/day) (hour/ns) 1: Performance: 2.027 11.840 1: [ OK ] GmxApiTest.ApiRunnerStopSignalClient (823 ms) 1: [ RUN ] GmxApiTest.SystemConstruction 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Setting the LD random seed to -543173209 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: [ OK ] GmxApiTest.SystemConstruction (417 ms) 1: [ RUN ] GmxApiTest.SaneVersionComparisons 1: [ OK ] GmxApiTest.SaneVersionComparisons (0 ms) 1: [ RUN ] GmxApiTest.VersionNamed0_1_Features 1: [ OK ] GmxApiTest.VersionNamed0_1_Features (0 ms) 1: [----------] 9 tests from GmxApiTest (3601 ms total) 1: 1: [----------] Global test environment tear-down 1: [==========] 9 tests from 1 test suite ran. (3651 ms total) 1: [ PASSED ] 9 tests. 1/94 Test #1: GmxapiExternalInterfaceTests ................. Passed 3.98 sec test 2 Start 2: GmxapiMpiTests 2: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2025.0/build/mpi/bin/gmxapi-mpi-test" "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/GmxapiMpiTests.xml" 2: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests 2: Test timeout computed to be: 600 2: [==========] Running 13 tests from 1 test suite. 2: [----------] Global test environment set-up. 2: [----------] 13 tests from GmxApiTest 2: [ RUN ] GmxApiTest.AllContext 2: [ OK ] GmxApiTest.AllContext (68 ms) 2: [ RUN ] GmxApiTest.NullContext 2: [ OK ] GmxApiTest.NullContext (0 ms) 2: [ RUN ] GmxApiTest.MpiWorldContext 2: [ OK ] GmxApiTest.MpiWorldContext (75 ms) 2: [ RUN ] GmxApiTest.MpiSplitContext 2: [ OK ] GmxApiTest.MpiSplitContext (71 ms) 2: [ RUN ] GmxApiTest.ApiRunnerRestrainedMD 2: Setting the LD random seed to -84492355 2: Setting the LD random seed to -379863559 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: Generating 1-4 interactions: fudge = 0.5 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: Generating 1-4 interactions: fudge = 0.5 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: 2: This run will generate roughly 0 Mb of data 2: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 2: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 2: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 2: 2: Using 2 MPI processes 2: Using 2 OpenMP threads per MPI process 2: 2: 2: NOTE: The number of threads is not equal to the number of (logical) cpus 2: and the -pin option is set to auto: will not pin threads to cpus. 2: This can lead to significant performance degradation. 2: Consider using -pin on (and -pinoffset in case you run multiple jobs). 2: starting mdrun 'Water and methane' 2: 2 steps, 0.0 ps. 2: 2: Writing final coordinates. 2: 2: NOTE: 50 % of the run time was spent communicating energies, 2: you might want to increase some nst* mdp options 2: 2: Core t (s) Wall t (s) (%) 2: Time: 1.402 0.351 399.9 2: (ns/day) (hour/ns) 2: Performance: 1.444 16.616 2: [ OK ] GmxApiTest.ApiRunnerRestrainedMD (930 ms) 2: [ RUN ] GmxApiTest.RunnerBasicMD 2: Setting the LD random seed to -34218049 2: Setting the LD random seed to -163791521 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: Generating 1-4 interactions: fudge = 0.5 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: Generating 1-4 interactions: fudge = 0.5 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 2: 2: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: 2: This run will generate roughly 0 Mb of data 2: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 2: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 2: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 2: 2: Using 2 MPI processes 2: Using 2 OpenMP threads per MPI process 2: 2: 2: NOTE: The number of threads is not equal to the number of (logical) cpus 2: and the -pin option is set to auto: will not pin threads to cpus. 2: This can lead to significant performance degradation. 2: Consider using -pin on (and -pinoffset in case you run multiple jobs). 2: starting mdrun 'Water and methane' 2: 2 steps, 0.0 ps. 2: 2: Writing final coordinates. 2: 2: NOTE: 48 % of the run time was spent communicating energies, 2: you might want to increase some nst* mdp options 2: 2: Core t (s) Wall t (s) (%) 2: Time: 0.069 0.017 396.2 2: (ns/day) (hour/ns) 2: Performance: 29.071 0.826 2: [ OK ] GmxApiTest.RunnerBasicMD (680 ms) 2: [ RUN ] GmxApiTest.RunnerReinitialize 2: Setting the LD random seed to -1493304482 2: Setting the LD random seed to -33702155 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: Generating 1-4 interactions: fudge = 0.5 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: Generating 1-4 interactions: fudge = 0.5 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 2: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 2: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 2: 2: Using 2 MPI processes 2: Using 2 OpenMP threads per MPI process 2: 2: 2: NOTE: The number of threads is not equal to the number of (logical) cpus 2: and the -pin option is set to auto: will not pin threads to cpus. 2: This can lead to significant performance degradation. 2: Consider using -pin on (and -pinoffset in case you run multiple jobs). 2: starting mdrun 'Water and methane' 2: 20 steps, 0.0 ps. 2: 2: 2: Received the remote INT/TERM signal, stopping within 200 steps 2: 2: 2: 2: Received the remote INT/TERM signal, stopping within 200 steps 2: 2: 2: Writing final coordinates. 2: 2: NOTE: 48 % of the run time was spent communicating energies, 2: you might want to increase some nst* mdp options 2: 2: Core t (s) Wall t (s) (%) 2: Time: 0.120 0.030 398.5 2: (ns/day) (hour/ns) 2: Performance: 117.565 0.204 2: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 2: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 2: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 2: 2: Using 2 MPI processes 2: Using 2 OpenMP threads per MPI process 2: 2: 2: NOTE: The number of threads is not equal to the number of (logical) cpus 2: and the -pin option is set to auto: will not pin threads to cpus. 2: This can lead to significant performance degradation. 2: Consider using -pin on (and -pinoffset in case you run multiple jobs). 2: starting mdrun 'Water and methane' 2: 20 steps, 0.0 ps. 2: 2: Writing final coordinates. 2: 2: NOTE: 48 % of the run time was spent communicating energies, 2: you might want to increase some nst* mdp options 2: 2: Core t (s) Wall t (s) (%) 2: Time: 0.161 0.040 398.9 2: (ns/day) (hour/ns) 2: Performance: 87.561 0.274 2: [ OK ] GmxApiTest.RunnerReinitialize (687 ms) 2: [ RUN ] GmxApiTest.RunnerChainedMD 2: Setting the LD random seed to -1078534217 2: Setting the LD random seed to -2115625 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: Generating 1-4 interactions: fudge = 0.5 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: Generating 1-4 interactions: fudge = 0.5 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 2: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 2: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 2: 2: Using 2 MPI processes 2: Using 2 OpenMP threads per MPI process 2: 2: 2: NOTE: The number of threads is not equal to the number of (logical) cpus 2: and the -pin option is set to auto: will not pin threads to cpus. 2: This can lead to significant performance degradation. 2: Consider using -pin on (and -pinoffset in case you run multiple jobs). 2: starting mdrun 'Water and methane' 2: 2 steps, 0.0 ps. 2: 2: Writing final coordinates. 2: 2: NOTE: 49 % of the run time was spent communicating energies, 2: you might want to increase some nst* mdp options 2: 2: Core t (s) Wall t (s) (%) 2: Time: 0.088 0.022 397.8 2: (ns/day) (hour/ns) 2: Performance: 22.927 1.047 2: trr version: GMX_trn_file (single precision) 2: 2: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 2: Setting nsteps to 4 2: Input file: 2: Run start step 0 2: Run start time 0 ps 2: Step to be made during run 2 2: Runtime for the run 0.00390625 ps 2: Run end step 2 2: Run end time 0.00390625 ps 2: 2: 2: Output file: 2: Run start step 0 2: Run start time 0 ps 2: Step to be made during run 4 2: Runtime for the run 0.0078125 ps 2: Run end step 4 2: Run end time 0.0078125 ps 2: 2: trr version: GMX_trn_file (single precision) 2: 2: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 2: Setting nsteps to 4 2: Input file: 2: Run start step 0 2: Run start time 0 ps 2: Step to be made during run 4 2: Runtime for the run 0.0078125 ps 2: Run end step 4 2: Run end time 0.0078125 ps 2: 2: 2: Output file: 2: Run start step 0 2: Run start time 0 ps 2: Step to be made during run 4 2: Runtime for the run 0.0078125 ps 2: Run end step 4 2: Run end time 0.0078125 ps 2: 2: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 2: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 2: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 2: 2: Using 2 MPI processes 2: Using 2 OpenMP threads per MPI process 2: 2: 2: NOTE: The number of threads is not equal to the number of (logical) cpus 2: and the -pin option is set to auto: will not pin threads to cpus. 2: This can lead to significant performance degradation. 2: Consider using -pin on (and -pinoffset in case you run multiple jobs). 2: starting mdrun 'Water and methane' 2: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 2: 2: Writing final coordinates. 2: 2: NOTE: 49 % of the run time was spent communicating energies, 2: you might want to increase some nst* mdp options 2: 2: Core t (s) Wall t (s) (%) 2: Time: 0.074 0.019 397.6 2: (ns/day) (hour/ns) 2: Performance: 27.293 0.879 2: 2: 2: [ OK ] GmxApiTest.RunnerChainedMD (665 ms) 2: [ RUN ] GmxApiTest.Status 2: [ OK ] GmxApiTest.Status (0 ms) 2: [ RUN ] GmxApiTest.ApiRunnerStopSignalClient 2: Setting the LD random seed to -47325221 2: Setting the LD random seed to -483923169 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: Generating 1-4 interactions: fudge = 0.5 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: Generating 1-4 interactions: fudge = 0.5 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 2: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 2: Changing nstlist from 10 to 1, rlist from 1.057 to 1 2: 2: Using 2 MPI processes 2: Using 2 OpenMP threads per MPI process 2: 2: 2: NOTE: The number of threads is not equal to the number of (logical) cpus 2: and the -pin option is set to auto: will not pin threads to cpus. 2: This can lead to significant performance degradation. 2: Consider using -pin on (and -pinoffset in case you run multiple jobs). 2: starting mdrun 'Water and methane' 2: 4 steps, 0.0 ps. 2: 2: Writing final coordinates. 2: 2: 2: Dynamic load balancing report: 2: DLB was off during the run due to low measured imbalance. 2: Average load imbalance: 15.8%. 2: The balanceable part of the MD step is 7%, load imbalance is computed from this. 2: Part of the total run time spent waiting due to load imbalance: 1.1%. 2: 2: 2: NOTE: 46 % of the run time was spent communicating energies, 2: you might want to increase some nst* mdp options 2: 2: Core t (s) Wall t (s) (%) 2: Time: 0.083 0.021 397.2 2: (ns/day) (hour/ns) 2: Performance: 40.145 0.598 2: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 2: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 2: Overriding nsteps with value passed on the command line: 4 steps, 0.00781 ps 2: Changing nstlist from 10 to 1, rlist from 1.057 to 1 2: 2: 2: Using 2 MPI processes 2: Using 2 OpenMP threads per MPI process 2: 2: 2: NOTE: The number of threads is not equal to the number of (logical) cpus 2: and the -pin option is set to auto: will not pin threads to cpus. 2: This can lead to significant performance degradation. 2: Consider using -pin on (and -pinoffset in case you run multiple jobs). 2: starting mdrun 'Water and methane' 2: 4 steps, 0.0 ps. 2: 2: 2: Dynamic load balancing report: 2: DLB was off during the run due to low measured imbalance. 2: Average load imbalance: 0.1%. 2: The balanceable part of the MD step is 10%, load imbalance is computed from this. 2: Part of the total run time spent waiting due to load imbalance: 0.0%. 2: 2: 2: NOTE: 49 % of the run time was spent communicating energies, 2: you might want to increase some nst* mdp options 2: 2: Core t (s) Wall t (s) (%) 2: Time: 0.261 0.065 398.5 2: (ns/day) (hour/ns) 2: Performance: 5.155 4.655 2: [ OK ] GmxApiTest.ApiRunnerStopSignalClient (851 ms) 2: [ RUN ] GmxApiTest.SystemConstruction 2: Setting the LD random seed to -1077952513 2: Setting the LD random seed to -295305313 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: Generating 1-4 interactions: fudge = 0.5 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: Generating 1-4 interactions: fudge = 0.5 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: [ OK ] GmxApiTest.SystemConstruction (664 ms) 2: [ RUN ] GmxApiTest.SaneVersionComparisons 2: [ OK ] GmxApiTest.SaneVersionComparisons (0 ms) 2: [ RUN ] GmxApiTest.VersionNamed0_1_Features 2: [ OK ] GmxApiTest.VersionNamed0_1_Features (0 ms) 2: [----------] 13 tests from GmxApiTest (4697 ms total) 2: 2: [----------] Global test environment tear-down 2: [==========] 13 tests from 1 test suite ran. (4771 ms total) 2: [ PASSED ] 13 tests. 2/94 Test #2: GmxapiMpiTests ............................... Passed 5.24 sec test 3 Start 3: GmxapiInternalInterfaceTests 3: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/workflow-details-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/GmxapiInternalInterfaceTests.xml" 3: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/workflow/tests 3: Test timeout computed to be: 600 3: [==========] Running 2 tests from 1 test suite. 3: [----------] Global test environment set-up. 3: [----------] 2 tests from GmxApiTest 3: [ RUN ] GmxApiTest.BuildApiWorkflowImpl 3: Generating 1-4 interactions: fudge = 0.5 3: 3: NOTE 1 [file spc_and_methane.top, line 33]: 3: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 3: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 3: the time step of 2.0e-03 ps. 3: Maybe you forgot to change the constraints mdp option. 3: 3: Number of degrees of freedom in T-Coupling group System is 18.00 3: 3: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]: 3: You are using a plain Coulomb cut-off, which might produce artifacts. 3: You might want to consider using PME electrostatics. 3: 3: 3: 3: There were 2 NOTEs 3: Setting the LD random seed to 1572494821 3: 3: Generated 331705 of the 331705 non-bonded parameter combinations 3: 3: Generated 331705 of the 331705 1-4 parameter combinations 3: 3: Excluding 2 bonded neighbours molecule type 'SOL' 3: 3: Excluding 3 bonded neighbours molecule type 'methane' 3: 3: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 3: 3: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 3: 3: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 3: 3: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 3: 3: Note that mdrun will redetermine rlist based on the actual pair-list setup 3: 3: This run will generate roughly 0 Mb of data 3: [ OK ] GmxApiTest.BuildApiWorkflowImpl (470 ms) 3: [ RUN ] GmxApiTest.CreateApiWorkflow 3: Generating 1-4 interactions: fudge = 0.5 3: 3: NOTE 1 [file spc_and_methane.top, line 33]: 3: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 3: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 3: the time step of 2.0e-03 ps. 3: Maybe you forgot to change the constraints mdp option. 3: 3: Number of degrees of freedom in T-Coupling group System is 18.00 3: 3: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]: 3: You are using a plain Coulomb cut-off, which might produce artifacts. 3: You might want to consider using PME electrostatics. 3: 3: 3: 3: There were 2 NOTEs 3: Setting the LD random seed to -67211521 3: 3: Generated 331705 of the 331705 non-bonded parameter combinations 3: 3: Generated 331705 of the 331705 1-4 parameter combinations 3: 3: Excluding 2 bonded neighbours molecule type 'SOL' 3: 3: Excluding 3 bonded neighbours molecule type 'methane' 3: 3: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 3: 3: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 3: 3: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 3: 3: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 3: 3: Note that mdrun will redetermine rlist based on the actual pair-list setup 3: 3: This run will generate roughly 0 Mb of data 3: [ OK ] GmxApiTest.CreateApiWorkflow (475 ms) 3: [----------] 2 tests from GmxApiTest (945 ms total) 3: 3: [----------] Global test environment tear-down 3: [==========] 2 tests from 1 test suite ran. (994 ms total) 3: [ PASSED ] 2 tests. 3/94 Test #3: GmxapiInternalInterfaceTests ................. Passed 1.35 sec test 4 Start 4: GmxapiInternalsMpiTests 4: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2025.0/build/mpi/bin/workflow-details-mpi-test" "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/GmxapiInternalsMpiTests.xml" 4: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/workflow/tests 4: Test timeout computed to be: 600 4: [==========] Running 2 tests from 1 test suite. 4: [----------] Global test environment set-up. 4: [----------] 2 tests from GmxApiTest 4: [ RUN ] GmxApiTest.BuildApiWorkflowImpl 4: Setting the LD random seed to -713318434 4: Setting the LD random seed to -102860451 4: 4: Generated 331705 of the 331705 non-bonded parameter combinations 4: Generating 1-4 interactions: fudge = 0.5 4: 4: Generated 331705 of the 331705 non-bonded parameter combinations 4: Generating 1-4 interactions: fudge = 0.5 4: 4: Generated 331705 of the 331705 1-4 parameter combinations 4: 4: Excluding 2 bonded neighbours molecule type 'SOL' 4: 4: Excluding 3 bonded neighbours molecule type 'methane' 4: 4: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 4: 4: Generated 331705 of the 331705 1-4 parameter combinations 4: 4: Excluding 2 bonded neighbours molecule type 'SOL' 4: 4: Excluding 3 bonded neighbours molecule type 'methane' 4: 4: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 4: 4: NOTE 1 [file spc_and_methane.top, line 33]: 4: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 4: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 4: the time step of 2.0e-03 ps. 4: Maybe you forgot to change the constraints mdp option. 4: 4: Number of degrees of freedom in T-Coupling group System is 18.00 4: 4: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 4: 4: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 4: 4: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 4: 4: Note that mdrun will redetermine rlist based on the actual pair-list setup 4: 4: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]: 4: You are using a plain Coulomb cut-off, which might produce artifacts. 4: You might want to consider using PME electrostatics. 4: 4: 4: 4: There were 2 NOTEs 4: 4: This run will generate roughly 0 Mb of data 4: 4: NOTE 1 [file spc_and_methane.top, line 33]: 4: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 4: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 4: the time step of 2.0e-03 ps. 4: Maybe you forgot to change the constraints mdp option. 4: 4: Number of degrees of freedom in T-Coupling group System is 18.00 4: 4: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 4: 4: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 4: 4: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 4: 4: Note that mdrun will redetermine rlist based on the actual pair-list setup 4: 4: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]: 4: You are using a plain Coulomb cut-off, which might produce artifacts. 4: You might want to consider using PME electrostatics. 4: 4: 4: 4: This run will generate roughly 0 Mb of data 4: 4: There were 2 NOTEs 4: [ OK ] GmxApiTest.BuildApiWorkflowImpl (741 ms) 4: [ RUN ] GmxApiTest.CreateApiWorkflow 4: Setting the LD random seed to 531619835 4: Setting the LD random seed to -270541193 4: 4: Generated 331705 of the 331705 non-bonded parameter combinations 4: Generating 1-4 interactions: fudge = 0.5 4: 4: Generated 331705 of the 331705 non-bonded parameter combinations 4: Generating 1-4 interactions: fudge = 0.5 4: 4: Generated 331705 of the 331705 1-4 parameter combinations 4: 4: Excluding 2 bonded neighbours molecule type 'SOL' 4: 4: Excluding 3 bonded neighbours molecule type 'methane' 4: 4: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 4: 4: NOTE 1 [file spc_and_methane.top, line 33]: 4: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 4: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 4: the time step of 2.0e-03 ps. 4: Maybe you forgot to change the constraints mdp option. 4: 4: Number of degrees of freedom in T-Coupling group System is 18.00 4: 4: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 4: 4: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 4: 4: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 4: 4: Note that mdrun will redetermine rlist based on the actual pair-list setup 4: 4: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]: 4: You are using a plain Coulomb cut-off, which might produce artifacts. 4: You might want to consider using PME electrostatics. 4: 4: 4: 4: There were 2 NOTEs 4: 4: This run will generate roughly 0 Mb of data 4: 4: Generated 331705 of the 331705 1-4 parameter combinations 4: 4: Excluding 2 bonded neighbours molecule type 'SOL' 4: 4: Excluding 3 bonded neighbours molecule type 'methane' 4: 4: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc_and_methane.gro' 4: 4: NOTE 1 [file spc_and_methane.top, line 33]: 4: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 4: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 4: the time step of 2.0e-03 ps. 4: Maybe you forgot to change the constraints mdp option. 4: 4: Number of degrees of freedom in T-Coupling group System is 18.00 4: 4: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 4: 4: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 4: 4: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 4: 4: Note that mdrun will redetermine rlist based on the actual pair-list setup 4: 4: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]: 4: You are using a plain Coulomb cut-off, which might produce artifacts. 4: You might want to consider using PME electrostatics. 4: 4: 4: 4: There were 2 NOTEs 4: 4: This run will generate roughly 0 Mb of data 4: [ OK ] GmxApiTest.CreateApiWorkflow (680 ms) 4: [----------] 2 tests from GmxApiTest (1423 ms total) 4: 4: [----------] Global test environment tear-down 4: [==========] 2 tests from 1 test suite ran. (1480 ms total) 4: [ PASSED ] 2 tests. 4/94 Test #4: GmxapiInternalsMpiTests ...................... Passed 2.12 sec test 5 Start 5: NbLibListedForcesTests 5: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/nblib-listed-forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/NbLibListedForcesTests.xml" 5: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/listed_forces/tests 5: Test timeout computed to be: 600 5: [==========] Running 44 tests from 22 test suites. 5: [----------] Global test environment set-up. 5: [----------] 8 tests from NBlibTest 5: [ RUN ] NBlibTest.BondTypesOperatorEqualWorks 5: [ OK ] NBlibTest.BondTypesOperatorEqualWorks (0 ms) 5: [ RUN ] NBlibTest.BondTypesLessThanWorks 5: [ OK ] NBlibTest.BondTypesLessThanWorks (0 ms) 5: [ RUN ] NBlibTest.CanSplitListedWork 5: [ OK ] NBlibTest.CanSplitListedWork (0 ms) 5: [ RUN ] NBlibTest.ListedForceBuffer 5: [ OK ] NBlibTest.ListedForceBuffer (0 ms) 5: [ RUN ] NBlibTest.ListedForceCalculatorCanConstruct 5: [ OK ] NBlibTest.ListedForceCalculatorCanConstruct (0 ms) 5: [ RUN ] NBlibTest.GmxToNblibConversionAllTypes 5: [ OK ] NBlibTest.GmxToNblibConversionAllTypes (0 ms) 5: [ RUN ] NBlibTest.EndToEndListedComparison 5: [ OK ] NBlibTest.EndToEndListedComparison (0 ms) 5: [ RUN ] NBlibTest.shiftForcesAreCorrect 5: [ OK ] NBlibTest.shiftForcesAreCorrect (24 ms) 5: [----------] 8 tests from NBlibTest (24 ms total) 5: 5: [----------] 1 test from Kernels 5: [ RUN ] Kernels.HarmonicScalarKernelCanCompute 5: [ OK ] Kernels.HarmonicScalarKernelCanCompute (0 ms) 5: [----------] 1 test from Kernels (0 ms total) 5: 5: [----------] 1 test from FourCenter 5: [ RUN ] FourCenter.ListedForcesProperDihedralTest 5: [ OK ] FourCenter.ListedForcesProperDihedralTest (0 ms) 5: [----------] 1 test from FourCenter (0 ms total) 5: 5: [----------] 7 tests from ThreeCenter 5: [ RUN ] ThreeCenter.ListedForcesG96AngleTest 5: [ OK ] ThreeCenter.ListedForcesG96AngleTest (0 ms) 5: [ RUN ] ThreeCenter.ListedForcesHarmonicAngleTest 5: [ OK ] ThreeCenter.ListedForcesHarmonicAngleTest (0 ms) 5: [ RUN ] ThreeCenter.ListedForcesLinearAngleTest 5: [ OK ] ThreeCenter.ListedForcesLinearAngleTest (0 ms) 5: [ RUN ] ThreeCenter.ListedForcesCrossBondBondTest 5: [ OK ] ThreeCenter.ListedForcesCrossBondBondTest (0 ms) 5: [ RUN ] ThreeCenter.ListedForcesCrossBondAngleTest 5: [ OK ] ThreeCenter.ListedForcesCrossBondAngleTest (0 ms) 5: [ RUN ] ThreeCenter.ListedForcesQuarticAngleTest 5: [ OK ] ThreeCenter.ListedForcesQuarticAngleTest (0 ms) 5: [ RUN ] ThreeCenter.ListedForcesRestrictedAngleTest 5: [ OK ] ThreeCenter.ListedForcesRestrictedAngleTest (0 ms) 5: [----------] 7 tests from ThreeCenter (0 ms total) 5: 5: [----------] 5 tests from TwoCenter 5: [ RUN ] TwoCenter.ListedForcesHarmonicBondTest 5: [ OK ] TwoCenter.ListedForcesHarmonicBondTest (0 ms) 5: [ RUN ] TwoCenter.ListedForcesG96BondTest 5: [ OK ] TwoCenter.ListedForcesG96BondTest (0 ms) 5: [ RUN ] TwoCenter.ListedForcesCubicBondTest 5: [ OK ] TwoCenter.ListedForcesCubicBondTest (0 ms) 5: [ RUN ] TwoCenter.ListedForcesMorseBondTest 5: [ OK ] TwoCenter.ListedForcesMorseBondTest (0 ms) 5: [ RUN ] TwoCenter.ListedForcesFeneBondTest 5: [ OK ] TwoCenter.ListedForcesFeneBondTest (0 ms) 5: [----------] 5 tests from TwoCenter (0 ms total) 5: 5: [----------] 5 tests from ListedExampleData 5: [ RUN ] ListedExampleData.ComputeHarmonicBondForces 5: [ OK ] ListedExampleData.ComputeHarmonicBondForces (0 ms) 5: [ RUN ] ListedExampleData.ComputeHarmonicBondEnergies 5: [ OK ] ListedExampleData.ComputeHarmonicBondEnergies (0 ms) 5: [ RUN ] ListedExampleData.ComputeHarmonicAngleForces 5: [ OK ] ListedExampleData.ComputeHarmonicAngleForces (0 ms) 5: [ RUN ] ListedExampleData.CanReduceForces 5: [ OK ] ListedExampleData.CanReduceForces (0 ms) 5: [ RUN ] ListedExampleData.CanReduceEnergies 5: [ OK ] ListedExampleData.CanReduceEnergies (0 ms) 5: [----------] 5 tests from ListedExampleData (0 ms total) 5: 5: [----------] 1 test from LinearChainDataFixture 5: [ RUN ] LinearChainDataFixture.Multithreading 5: [ OK ] LinearChainDataFixture.Multithreading (0 ms) 5: [----------] 1 test from LinearChainDataFixture (0 ms total) 5: 5: [----------] 2 tests from ListedShims 5: [ RUN ] ListedShims.ParameterConversion 5: [ OK ] ListedShims.ParameterConversion (0 ms) 5: [ RUN ] ListedShims.GmxToNblibConversion 5: [ OK ] ListedShims.GmxToNblibConversion (0 ms) 5: [----------] 2 tests from ListedShims (0 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/0, where TypeParam = nblib::TwoParameterInteraction 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/0.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/0.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/0 (0 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/1, where TypeParam = nblib::G96BondType 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/1.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/1.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/1 (0 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/2, where TypeParam = nblib::CubicBondType 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/2.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/2.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/2 (0 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/3, where TypeParam = nblib::MorseBondType 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/3.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/3.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/3 (0 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/4, where TypeParam = nblib::TwoParameterInteraction 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/4.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/4.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/4 (0 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/5, where TypeParam = nblib::AngleInteractionType 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/5.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/5.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/5 (0 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/6, where TypeParam = nblib::CosineParamAngle 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/6.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/6.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/6 (0 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/7, where TypeParam = nblib::CosineParamAngle 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/7.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/7.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/7 (0 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/8, where TypeParam = nblib::TwoParameterInteraction 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/8.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/8.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/8 (0 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/9, where TypeParam = nblib::QuarticAngle 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/9.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/9.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/9 (0 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/10, where TypeParam = nblib::CrossBondBond 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/10.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/10.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/10 (0 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/11, where TypeParam = nblib::CrossBondAngle 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/11.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/11.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/11 (0 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/12, where TypeParam = nblib::ProperDihedral 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/12.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/12.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/12 (0 ms total) 5: 5: [----------] 1 test from ListedTransformations 5: [ RUN ] ListedTransformations.SortInteractionIndices 5: [ OK ] ListedTransformations.SortInteractionIndices (0 ms) 5: [----------] 1 test from ListedTransformations (0 ms total) 5: 5: [----------] Global test environment tear-down 5: [==========] 44 tests from 22 test suites ran. (27 ms total) 5: [ PASSED ] 44 tests. 5/94 Test #5: NbLibListedForcesTests ....................... Passed 0.37 sec test 6 Start 6: NbLibSamplesTestArgon 6: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/argon-forces-integration 6: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/samples 6: Test timeout computed to be: 1500 6: initial forces on particle 0: x 0.000000 y 0.000000 z 0.000000 6: final forces on particle 0: x -0.412993 y -1.098256 z -0.113191 6: initial position of particle 0: x 0.794000 y 1.439000 z 0.610000 6: final position of particle 0: x 0.789162 y 1.271508 z 0.819867 6/94 Test #6: NbLibSamplesTestArgon ........................ Passed 0.30 sec test 7 Start 7: NbLibSamplesTestMethaneWater 7: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/methane-water-integration 7: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/samples 7: Test timeout computed to be: 1500 7: initial position of particle 0: x 0.005000 y 0.600000 z 0.244000 7: final position of particle 9: x 77.358398 y 5.324913 z -80.600098 7/94 Test #7: NbLibSamplesTestMethaneWater ................. Passed 0.27 sec test 8 Start 8: NbLibUtilTests 8: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/nblib-util-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/NbLibUtilTests.xml" 8: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/util/tests 8: Test timeout computed to be: 30 8: [==========] Running 16 tests from 2 test suites. 8: [----------] Global test environment set-up. 8: [----------] 6 tests from NBlibTest 8: [ RUN ] NBlibTest.isRealValued 8: [ OK ] NBlibTest.isRealValued (0 ms) 8: [ RUN ] NBlibTest.checkNumericValuesHasNan 8: [ OK ] NBlibTest.checkNumericValuesHasNan (0 ms) 8: [ RUN ] NBlibTest.checkNumericValuesHasInf 8: [ OK ] NBlibTest.checkNumericValuesHasInf (0 ms) 8: [ RUN ] NBlibTest.GeneratedVelocitiesAreCorrect 8: Velocities were taken from a Maxwell distribution at 300 K 8: [ OK ] NBlibTest.GeneratedVelocitiesAreCorrect (0 ms) 8: [ RUN ] NBlibTest.generateVelocitySize 8: Velocities were taken from a Maxwell distribution at 300 K 8: [ OK ] NBlibTest.generateVelocitySize (0 ms) 8: [ RUN ] NBlibTest.generateVelocityCheckNumbers 8: Velocities were taken from a Maxwell distribution at 300 K 8: [ OK ] NBlibTest.generateVelocityCheckNumbers (0 ms) 8: [----------] 6 tests from NBlibTest (0 ms total) 8: 8: [----------] 10 tests from NblibTraitsUtils 8: [ RUN ] NblibTraitsUtils.FuseTwo 8: [ OK ] NblibTraitsUtils.FuseTwo (0 ms) 8: [ RUN ] NblibTraitsUtils.Fuse 8: [ OK ] NblibTraitsUtils.Fuse (0 ms) 8: [ RUN ] NblibTraitsUtils.Repeat 8: [ OK ] NblibTraitsUtils.Repeat (0 ms) 8: [ RUN ] NblibTraitsUtils.FindIndexTuple1 8: [ OK ] NblibTraitsUtils.FindIndexTuple1 (0 ms) 8: [ RUN ] NblibTraitsUtils.FindIndexTuple2 8: [ OK ] NblibTraitsUtils.FindIndexTuple2 (0 ms) 8: [ RUN ] NblibTraitsUtils.FindIndexTypeList1 8: [ OK ] NblibTraitsUtils.FindIndexTypeList1 (0 ms) 8: [ RUN ] NblibTraitsUtils.FindIndexTypeList2 8: [ OK ] NblibTraitsUtils.FindIndexTypeList2 (0 ms) 8: [ RUN ] NblibTraitsUtils.Contains 8: [ OK ] NblibTraitsUtils.Contains (0 ms) 8: [ RUN ] NblibTraitsUtils.FindIndexTupleRepeated 8: [ OK ] NblibTraitsUtils.FindIndexTupleRepeated (0 ms) 8: [ RUN ] NblibTraitsUtils.FindIndexTypeListRepeated 8: [ OK ] NblibTraitsUtils.FindIndexTypeListRepeated (0 ms) 8: [----------] 10 tests from NblibTraitsUtils (0 ms total) 8: 8: [----------] Global test environment tear-down 8: [==========] 16 tests from 2 test suites ran. (0 ms total) 8: [ PASSED ] 16 tests. 8/94 Test #8: NbLibUtilTests ............................... Passed 0.34 sec test 9 Start 9: NbLibSetupTests 9: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/nblib-setup-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/NbLibSetupTests.xml" 9: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests 9: Test timeout computed to be: 600 9: [==========] Running 57 tests from 3 test suites. 9: [----------] Global test environment set-up. 9: [----------] 41 tests from NBlibTest 9: [ RUN ] NBlibTest.CubicBoxCannotHaveNaN 9: [ OK ] NBlibTest.CubicBoxCannotHaveNaN (0 ms) 9: [ RUN ] NBlibTest.CubicBoxCannotHaveInf 9: [ OK ] NBlibTest.CubicBoxCannotHaveInf (0 ms) 9: [ RUN ] NBlibTest.RectangularBoxCannotHaveNaN 9: [ OK ] NBlibTest.RectangularBoxCannotHaveNaN (0 ms) 9: [ RUN ] NBlibTest.RectangularBoxCannotHaveInf 9: [ OK ] NBlibTest.RectangularBoxCannotHaveInf (0 ms) 9: [ RUN ] NBlibTest.CubicBoxWorks 9: [ OK ] NBlibTest.CubicBoxWorks (0 ms) 9: [ RUN ] NBlibTest.BoxEqual 9: [ OK ] NBlibTest.BoxEqual (0 ms) 9: [ RUN ] NBlibTest.NonBondedForceParamsCorrect 9: [ OK ] NBlibTest.NonBondedForceParamsCorrect (0 ms) 9: [ RUN ] NBlibTest.CanMergeInteractions 9: [ OK ] NBlibTest.CanMergeInteractions (0 ms) 9: [ RUN ] NBlibTest.ParticleTypeNameCanBeConstructed 9: [ OK ] NBlibTest.ParticleTypeNameCanBeConstructed (0 ms) 9: [ RUN ] NBlibTest.ParticleTypeMassCanBeConstructed 9: [ OK ] NBlibTest.ParticleTypeMassCanBeConstructed (0 ms) 9: [ RUN ] NBlibTest.PbcHolderWorks 9: [ OK ] NBlibTest.PbcHolderWorks (0 ms) 9: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName 9: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName (0 ms) 9: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName 9: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName (0 ms) 9: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName 9: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName (0 ms) 9: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName 9: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName (0 ms) 9: [ RUN ] NBlibTest.CanGetNumParticlesInMolecule 9: [ OK ] NBlibTest.CanGetNumParticlesInMolecule (0 ms) 9: [ RUN ] NBlibTest.CanConstructExclusionListFromNames 9: [ OK ] NBlibTest.CanConstructExclusionListFromNames (0 ms) 9: [ RUN ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed 9: [ OK ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed (0 ms) 9: [ RUN ] NBlibTest.AtWorks 9: [ OK ] NBlibTest.AtWorks (0 ms) 9: [ RUN ] NBlibTest.AtThrows 9: [ OK ] NBlibTest.AtThrows (0 ms) 9: [ RUN ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass 9: [ OK ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass (0 ms) 9: [ RUN ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass 9: [ OK ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass (0 ms) 9: [ RUN ] NBlibTest.MoleculeNoThrowsSameParticleTypeName 9: [ OK ] NBlibTest.MoleculeNoThrowsSameParticleTypeName (0 ms) 9: [ RUN ] NBlibTest.CanAddInteractions 9: [ OK ] NBlibTest.CanAddInteractions (0 ms) 9: [ RUN ] NBlibTest.CanAddUreyBradley 9: [ OK ] NBlibTest.CanAddUreyBradley (0 ms) 9: [ RUN ] NBlibTest.TopologyHasNumParticles 9: [ OK ] NBlibTest.TopologyHasNumParticles (0 ms) 9: [ RUN ] NBlibTest.TopologyHasCharges 9: [ OK ] NBlibTest.TopologyHasCharges (0 ms) 9: [ RUN ] NBlibTest.TopologyHasMasses 9: [ OK ] NBlibTest.TopologyHasMasses (0 ms) 9: [ RUN ] NBlibTest.TopologyHasParticleTypes 9: [ OK ] NBlibTest.TopologyHasParticleTypes (0 ms) 9: [ RUN ] NBlibTest.TopologyHasParticleTypeIds 9: [ OK ] NBlibTest.TopologyHasParticleTypeIds (0 ms) 9: [ RUN ] NBlibTest.TopologyThrowsIdenticalParticleType 9: [ OK ] NBlibTest.TopologyThrowsIdenticalParticleType (0 ms) 9: [ RUN ] NBlibTest.TopologyHasExclusions 9: [ OK ] NBlibTest.TopologyHasExclusions (0 ms) 9: [ RUN ] NBlibTest.TopologyHasSequencing 9: [ OK ] NBlibTest.TopologyHasSequencing (0 ms) 9: [ RUN ] NBlibTest.TopologyCanAggregateBonds 9: [ OK ] NBlibTest.TopologyCanAggregateBonds (0 ms) 9: [ RUN ] NBlibTest.TopologyCanSequencePairIDs 9: [ OK ] NBlibTest.TopologyCanSequencePairIDs (0 ms) 9: [ RUN ] NBlibTest.TopologySequenceIdThrows 9: No particle O-Atom in residue SOL in molecule SOL found 9: [ OK ] NBlibTest.TopologySequenceIdThrows (0 ms) 9: [ RUN ] NBlibTest.TopologyCanEliminateDuplicateBonds 9: [ OK ] NBlibTest.TopologyCanEliminateDuplicateBonds (0 ms) 9: [ RUN ] NBlibTest.TopologyListedInteractions 9: [ OK ] NBlibTest.TopologyListedInteractions (0 ms) 9: [ RUN ] NBlibTest.TopologyListedInteractionsMultipleTypes 9: [ OK ] NBlibTest.TopologyListedInteractionsMultipleTypes (0 ms) 9: [ RUN ] NBlibTest.TopologyInvalidParticleInInteractionThrows 9: No particle Iron in residue SOL in molecule SOL found 9: [ OK ] NBlibTest.TopologyInvalidParticleInInteractionThrows (0 ms) 9: [ RUN ] NBlibTest.toGmxExclusionBlockWorks 9: [ OK ] NBlibTest.toGmxExclusionBlockWorks (0 ms) 9: [----------] 41 tests from NBlibTest (1 ms total) 9: 9: [----------] 15 tests from NbnxmSetupTest 9: [ RUN ] NbnxmSetupTest.findNumEnergyGroups 9: [ OK ] NbnxmSetupTest.findNumEnergyGroups (0 ms) 9: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnumAuto 9: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnumAuto (0 ms) 9: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnumNo 9: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnumNo (0 ms) 9: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnum2XM 9: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnum2XM (0 ms) 9: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnum4XM 9: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnum4XM (0 ms) 9: [ RUN ] NbnxmSetupTest.CheckKernelSetupThrowsAuto 9: [ OK ] NbnxmSetupTest.CheckKernelSetupThrowsAuto (0 ms) 9: [ RUN ] NbnxmSetupTest.CheckKernelSetupThrowsCount 9: [ OK ] NbnxmSetupTest.CheckKernelSetupThrowsCount (0 ms) 9: [ RUN ] NbnxmSetupTest.canCreateKernelSetupPlain 9: [ OK ] NbnxmSetupTest.canCreateKernelSetupPlain (0 ms) 9: [ RUN ] NbnxmSetupTest.canCreateParticleInfoAllVdv 9: [ OK ] NbnxmSetupTest.canCreateParticleInfoAllVdv (0 ms) 9: [ RUN ] NbnxmSetupTest.ewaldCoeffWorks 9: [ OK ] NbnxmSetupTest.ewaldCoeffWorks (0 ms) 9: [ RUN ] NbnxmSetupTest.updateForcerecWorks 9: [ OK ] NbnxmSetupTest.updateForcerecWorks (0 ms) 9: [ RUN ] NbnxmSetupTest.canCheckKernelSetup 9: [ OK ] NbnxmSetupTest.canCheckKernelSetup (0 ms) 9: [ RUN ] NbnxmSetupTest.cannotCreateKernelSetupCPU2XM 9: [ OK ] NbnxmSetupTest.cannotCreateKernelSetupCPU2XM (0 ms) 9: [ RUN ] NbnxmSetupTest.cannotCreateKernelSetupCPU4XM 9: [ OK ] NbnxmSetupTest.cannotCreateKernelSetupCPU4XM (0 ms) 9: [ RUN ] NbnxmSetupTest.CanCreateNbnxmCPU 9: [ OK ] NbnxmSetupTest.CanCreateNbnxmCPU (0 ms) 9: [----------] 15 tests from NbnxmSetupTest (0 ms total) 9: 9: [----------] 1 test from VirialsTest 9: [ RUN ] VirialsTest.computeVirialTensorWorks 9: [ OK ] VirialsTest.computeVirialTensorWorks (0 ms) 9: [----------] 1 test from VirialsTest (0 ms total) 9: 9: [----------] Global test environment tear-down 9: [==========] 57 tests from 3 test suites ran. (2 ms total) 9: [ PASSED ] 57 tests. 9/94 Test #9: NbLibSetupTests .............................. Passed 0.39 sec test 10 Start 10: NbLibTprTests 10: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/nblib-tpr-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/NbLibTprTests.xml" 10: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests 10: Test timeout computed to be: 30 10: [==========] Running 4 tests from 1 test suite. 10: [----------] Global test environment set-up. 10: [----------] 4 tests from TprReaderTest 10: [ RUN ] TprReaderTest.SimDBTprIsCreated 10: 10: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 10: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 10: that with the Verlet scheme, nstlist has no effect on the accuracy of 10: your simulation. 10: 10: 10: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 10: Setting nstcalcenergy (100) equal to nstenergy (4) 10: 10: Number of degrees of freedom in T-Coupling group System is 33.00 10: 10: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 10: NVE simulation: will use the initial temperature of 68.810 K for 10: determining the Verlet buffer size 10: 10: 10: There were 3 NOTEs 10: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 10: Generated 1 of the 1 non-bonded parameter combinations 10: 10: Excluding 1 bonded neighbours molecule type 'Argon' 10: 10: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 10: 10: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 10: 10: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 10: 10: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 10: 10: Note that mdrun will redetermine rlist based on the actual pair-list setup 10: 10: This run will generate roughly 0 Mb of data 10: [ OK ] TprReaderTest.SimDBTprIsCreated (31 ms) 10: [ RUN ] TprReaderTest.Spc2Reads 10: 10: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 10: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 10: that with the Verlet scheme, nstlist has no effect on the accuracy of 10: your simulation. 10: 10: 10: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 10: Setting nstcalcenergy (100) equal to nstenergy (4) 10: 10: Generating 1-4 interactions: fudge = 0.5 10: Number of degrees of freedom in T-Coupling group System is 9.00 10: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 10: 10: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 10: NVE simulation: will use the initial temperature of 2573.591 K for 10: determining the Verlet buffer size 10: 10: 10: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 10: You are using a plain Coulomb cut-off, which might produce artifacts. 10: You might want to consider using PME electrostatics. 10: 10: 10: 10: There were 4 NOTEs 10: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 10: Generated 3 of the 3 non-bonded parameter combinations 10: 10: Generated 3 of the 3 1-4 parameter combinations 10: 10: Excluding 2 bonded neighbours molecule type 'SOL' 10: 10: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 10: 10: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 10: 10: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 10: 10: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 10: 10: Note that mdrun will redetermine rlist based on the actual pair-list setup 10: 10: This run will generate roughly 0 Mb of data 10: [ OK ] TprReaderTest.Spc2Reads (15 ms) 10: [ RUN ] TprReaderTest.ArgonImportedDataIsCorrect 10: 10: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 10: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 10: that with the Verlet scheme, nstlist has no effect on the accuracy of 10: your simulation. 10: 10: 10: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 10: Setting nstcalcenergy (100) equal to nstenergy (4) 10: 10: Number of degrees of freedom in T-Coupling group System is 33.00 10: 10: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 10: NVE simulation: will use the initial temperature of 68.810 K for 10: determining the Verlet buffer size 10: 10: 10: There were 3 NOTEs 10: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 10: Generated 1 of the 1 non-bonded parameter combinations 10: 10: Excluding 1 bonded neighbours molecule type 'Argon' 10: 10: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 10: 10: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 10: 10: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 10: 10: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 10: 10: Note that mdrun will redetermine rlist based on the actual pair-list setup 10: 10: This run will generate roughly 0 Mb of data 10: [ OK ] TprReaderTest.ArgonImportedDataIsCorrect (114 ms) 10: [ RUN ] TprReaderTest.FCfromTprDataWorks 10: 10: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 10: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 10: that with the Verlet scheme, nstlist has no effect on the accuracy of 10: your simulation. 10: 10: 10: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 10: Setting nstcalcenergy (100) equal to nstenergy (4) 10: 10: Number of degrees of freedom in T-Coupling group System is 33.00 10: 10: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 10: NVE simulation: will use the initial temperature of 68.810 K for 10: determining the Verlet buffer size 10: 10: 10: There were 3 NOTEs 10: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 10: Generated 1 of the 1 non-bonded parameter combinations 10: 10: Excluding 1 bonded neighbours molecule type 'Argon' 10: 10: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 10: 10: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 10: 10: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 10: 10: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 10: 10: Note that mdrun will redetermine rlist based on the actual pair-list setup 10: 10: This run will generate roughly 0 Mb of data 10: [ OK ] TprReaderTest.FCfromTprDataWorks (40 ms) 10: [----------] 4 tests from TprReaderTest (203 ms total) 10: 10: [----------] Global test environment tear-down 10: [==========] 4 tests from 1 test suite ran. (262 ms total) 10: [ PASSED ] 4 tests. 10/94 Test #10: NbLibTprTests ................................ Passed 0.60 sec test 11 Start 11: NbLibIntegrationTests 11: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/nblib-integration-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/NbLibIntegrationTests.xml" 11: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests 11: Test timeout computed to be: 600 11: [==========] Running 20 tests from 1 test suite. 11: [----------] Global test environment set-up. 11: [----------] 20 tests from NBlibTest 11: [ RUN ] NBlibTest.GmxForceCalculatorCanCompute 11: [ OK ] NBlibTest.GmxForceCalculatorCanCompute (0 ms) 11: [ RUN ] NBlibTest.ArgonVirialsAreCorrect 11: [ OK ] NBlibTest.ArgonVirialsAreCorrect (0 ms) 11: [ RUN ] NBlibTest.ArgonEnergiesAreCorrect 11: [ OK ] NBlibTest.ArgonEnergiesAreCorrect (0 ms) 11: [ RUN ] NBlibTest.SpcMethanolEnergiesAreCorrect 11: [ OK ] NBlibTest.SpcMethanolEnergiesAreCorrect (0 ms) 11: [ RUN ] NBlibTest.SpcMethanolForcesAreCorrect 11: [ OK ] NBlibTest.SpcMethanolForcesAreCorrect (0 ms) 11: [ RUN ] NBlibTest.ExpectedNumberOfForces 11: [ OK ] NBlibTest.ExpectedNumberOfForces (0 ms) 11: [ RUN ] NBlibTest.CanIntegrateSystem 11: [ OK ] NBlibTest.CanIntegrateSystem (0 ms) 11: [ RUN ] NBlibTest.UpdateChangesForces 11: [ OK ] NBlibTest.UpdateChangesForces (0 ms) 11: [ RUN ] NBlibTest.ArgonOplsaForcesAreCorrect 11: [ OK ] NBlibTest.ArgonOplsaForcesAreCorrect (0 ms) 11: [ RUN ] NBlibTest.ArgonGromos43A1ForcesAreCorrect 11: [ OK ] NBlibTest.ArgonGromos43A1ForcesAreCorrect (0 ms) 11: [ RUN ] NBlibTest.CanConstructSimulationState 11: [ OK ] NBlibTest.CanConstructSimulationState (0 ms) 11: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateNAN 11: [ OK ] NBlibTest.SimulationStateThrowsCoordinateNAN (0 ms) 11: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateINF 11: [ OK ] NBlibTest.SimulationStateThrowsCoordinateINF (0 ms) 11: [ RUN ] NBlibTest.SimulationStateThrowsVelocityNAN 11: [ OK ] NBlibTest.SimulationStateThrowsVelocityNAN (0 ms) 11: [ RUN ] NBlibTest.SimulationStateThrowsVelocityINF 11: [ OK ] NBlibTest.SimulationStateThrowsVelocityINF (0 ms) 11: [ RUN ] NBlibTest.SimulationStateCanMove 11: [ OK ] NBlibTest.SimulationStateCanMove (0 ms) 11: [ RUN ] NBlibTest.SimulationStateCanAssign 11: [ OK ] NBlibTest.SimulationStateCanAssign (0 ms) 11: [ RUN ] NBlibTest.SimulationStateHasBox 11: [ OK ] NBlibTest.SimulationStateHasBox (0 ms) 11: [ RUN ] NBlibTest.SimulationStateHasCorrectCoordinates 11: [ OK ] NBlibTest.SimulationStateHasCorrectCoordinates (0 ms) 11: [ RUN ] NBlibTest.SimulationStateHasCorrectVelocities 11: [ OK ] NBlibTest.SimulationStateHasCorrectVelocities (0 ms) 11: [----------] 20 tests from NBlibTest (6 ms total) 11: 11: [----------] Global test environment tear-down 11: [==========] 20 tests from 1 test suite ran. (6 ms total) 11: [ PASSED ] 20 tests. 11/94 Test #11: NbLibIntegrationTests ........................ Passed 0.35 sec test 12 Start 12: NbLibIntegratorTests 12: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/nblib-integrator-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/NbLibIntegratorTests.xml" 12: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/tests 12: Test timeout computed to be: 600 12: [==========] Running 1 test from 1 test suite. 12: [----------] Global test environment set-up. 12: [----------] 1 test from NBlibTest 12: [ RUN ] NBlibTest.IntegratorWorks 12: [ OK ] NBlibTest.IntegratorWorks (0 ms) 12: [----------] 1 test from NBlibTest (0 ms total) 12: 12: [----------] Global test environment tear-down 12: [==========] 1 test from 1 test suite ran. (0 ms total) 12: [ PASSED ] 1 test. 12/94 Test #12: NbLibIntegratorTests ......................... Passed 0.36 sec test 13 Start 13: TestUtilsUnitTests 13: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/testutils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/TestUtilsUnitTests.xml" 13: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/testutils/tests 13: Test timeout computed to be: 30 13: [==========] Running 75 tests from 7 test suites. 13: [----------] Global test environment set-up. 13: [----------] 10 tests from InteractiveTestHelperTest 13: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession 13: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (0 ms) 13: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline 13: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (0 ms) 13: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput 13: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (0 ms) 13: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput 13: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (0 ms) 13: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput 13: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (0 ms) 13: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput 13: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (0 ms) 13: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput 13: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (0 ms) 13: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput 13: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (0 ms) 13: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput 13: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (0 ms) 13: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput 13: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (0 ms) 13: [----------] 10 tests from InteractiveTestHelperTest (2 ms total) 13: 13: [----------] 10 tests from NameOfTestFromTupleTest 13: [ RUN ] NameOfTestFromTupleTest.WorksWithEmptyTuple 13: [ OK ] NameOfTestFromTupleTest.WorksWithEmptyTuple (0 ms) 13: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFunction 13: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFunction (0 ms) 13: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFunctionOfEnumVariable 13: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFunctionOfEnumVariable (0 ms) 13: [ RUN ] NameOfTestFromTupleTest.RejectsNullptrFormatFunction 13: [ OK ] NameOfTestFromTupleTest.RejectsNullptrFormatFunction (0 ms) 13: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatLambda 13: [ OK ] NameOfTestFromTupleTest.WorksWithFormatLambda (0 ms) 13: [ RUN ] NameOfTestFromTupleTest.WorksWithUseStringFormat 13: [ OK ] NameOfTestFromTupleTest.WorksWithUseStringFormat (0 ms) 13: [ RUN ] NameOfTestFromTupleTest.WorksWithPrefixFormatter 13: [ OK ] NameOfTestFromTupleTest.WorksWithPrefixFormatter (0 ms) 13: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFunctor 13: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFunctor (0 ms) 13: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFromEnumerationArray 13: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFromEnumerationArray (0 ms) 13: [ RUN ] NameOfTestFromTupleTest.WorksWithMixtureOfFormatters 13: [ OK ] NameOfTestFromTupleTest.WorksWithMixtureOfFormatters (0 ms) 13: [----------] 10 tests from NameOfTestFromTupleTest (0 ms total) 13: 13: [----------] 3 tests from RefDataFilenameMakerTest 13: [ RUN ] RefDataFilenameMakerTest.WorksWithFormatFunction 13: [ OK ] RefDataFilenameMakerTest.WorksWithFormatFunction (0 ms) 13: [ RUN ] RefDataFilenameMakerTest.WorksWithMixtureOfFormatters 13: [ OK ] RefDataFilenameMakerTest.WorksWithMixtureOfFormatters (0 ms) 13: [ RUN ] RefDataFilenameMakerTest.WorksWithToEmpty 13: [ OK ] RefDataFilenameMakerTest.WorksWithToEmpty (0 ms) 13: [----------] 3 tests from RefDataFilenameMakerTest (0 ms total) 13: 13: [----------] 37 tests from ReferenceDataTest 13: [ RUN ] ReferenceDataTest.HandlesSimpleData 13: [ OK ] ReferenceDataTest.HandlesSimpleData (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesFloatingPointData 13: [ OK ] ReferenceDataTest.HandlesFloatingPointData (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesPresenceChecks 13: [ OK ] ReferenceDataTest.HandlesPresenceChecks (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesStringBlockData 13: [ OK ] ReferenceDataTest.HandlesStringBlockData (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesVectorData 13: [ OK ] ReferenceDataTest.HandlesVectorData (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesSequenceData 13: [ OK ] ReferenceDataTest.HandlesSequenceData (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData 13: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (0 ms) 13: [ RUN ] ReferenceDataTest.CheckSequenceArrayRef 13: [ OK ] ReferenceDataTest.CheckSequenceArrayRef (0 ms) 13: [ RUN ] ReferenceDataTest.CheckSequenceArrayRefHandlesIncorrectData 13: [ OK ] ReferenceDataTest.CheckSequenceArrayRefHandlesIncorrectData (0 ms) 13: [ RUN ] ReferenceDataTest.CheckSequenceArrayRefHandlesSequenceOfCustomData 13: [ OK ] ReferenceDataTest.CheckSequenceArrayRefHandlesSequenceOfCustomData (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesIncorrectData 13: [ OK ] ReferenceDataTest.HandlesIncorrectData (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType 13: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesMissingData 13: [ OK ] ReferenceDataTest.HandlesMissingData (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesUncheckedData 13: [ OK ] ReferenceDataTest.HandlesUncheckedData (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence 13: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound 13: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesAnys 13: [ OK ] ReferenceDataTest.HandlesAnys (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesKeyValueTree 13: [ OK ] ReferenceDataTest.HandlesKeyValueTree (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey 13: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey 13: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectValue 13: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectValue (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectType 13: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectType (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile 13: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings 13: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace 13: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesEmptyStrings 13: [ OK ] ReferenceDataTest.HandlesEmptyStrings (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock 13: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices 13: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData 13: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds 13: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds 13: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesReadingValues 13: [ OK ] ReferenceDataTest.HandlesReadingValues (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges 13: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (59 ms) 13: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges 13: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (14 ms) 13: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges 13: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (35 ms) 13: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges 13: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (80 ms) 13: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries 13: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (58 ms) 13: [----------] 37 tests from ReferenceDataTest (254 ms total) 13: 13: [----------] 7 tests from FloatingPointDifferenceTest 13: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues 13: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms) 13: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues 13: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms) 13: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign 13: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms) 13: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero 13: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms) 13: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences 13: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms) 13: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero 13: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms) 13: [ RUN ] FloatingPointDifferenceTest.HandlesNaN 13: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms) 13: [----------] 7 tests from FloatingPointDifferenceTest (0 ms total) 13: 13: [----------] 4 tests from FloatingPointToleranceTest 13: [ RUN ] FloatingPointToleranceTest.UlpTolerance 13: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms) 13: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint 13: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms) 13: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp 13: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms) 13: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance 13: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms) 13: [----------] 4 tests from FloatingPointToleranceTest (0 ms total) 13: 13: [----------] 4 tests from XvgTests 13: [ RUN ] XvgTests.CreateFile 13: [ OK ] XvgTests.CreateFile (0 ms) 13: [ RUN ] XvgTests.CheckMissing 13: [ OK ] XvgTests.CheckMissing (0 ms) 13: [ RUN ] XvgTests.CheckExtra 13: [ OK ] XvgTests.CheckExtra (0 ms) 13: [ RUN ] XvgTests.ReadIncorrect 13: [ OK ] XvgTests.ReadIncorrect (0 ms) 13: [----------] 4 tests from XvgTests (1 ms total) 13: 13: [----------] Global test environment tear-down 13: [==========] 75 tests from 7 test suites ran. (259 ms total) 13: [ PASSED ] 75 tests. 13/94 Test #13: TestUtilsUnitTests ........................... Passed 0.57 sec test 14 Start 14: TestUtilsMpiUnitTests 14: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2025.0/build/mpi/bin/testutils-mpi-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/TestUtilsMpiUnitTests.xml" 14: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/testutils/tests 14: Test timeout computed to be: 30 14: [==========] Running 1 test from 1 test suite. 14: [----------] Global test environment set-up. 14: [----------] 1 test from MpiSelfTest 14: [ RUN ] MpiSelfTest.Runs 14: [ OK ] MpiSelfTest.Runs (11 ms) 14: [----------] 1 test from MpiSelfTest (19 ms total) 14: 14: [----------] Global test environment tear-down 14: [==========] 1 test from 1 test suite ran. (19 ms total) 14: [ PASSED ] 1 test. 14/94 Test #14: TestUtilsMpiUnitTests ........................ Passed 0.81 sec test 15 Start 15: UtilityUnitTests 15: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/utility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/UtilityUnitTests.xml" 15: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests 15: Test timeout computed to be: 30 15: [==========] Running 420 tests from 65 test suites. 15: [----------] Global test environment set-up. 15: [----------] 6 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 15: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 15: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 15: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 15: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/0.Move 15: [ OK ] AllocatorTest/0.Move (0 ms) 15: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory 15: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms) 15: [ RUN ] AllocatorTest/0.Comparison 15: [ OK ] AllocatorTest/0.Comparison (0 ms) 15: [----------] 6 tests from AllocatorTest/0 (0 ms total) 15: 15: [----------] 6 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 15: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 15: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 15: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 15: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/1.Move 15: [ OK ] AllocatorTest/1.Move (0 ms) 15: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory 15: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms) 15: [ RUN ] AllocatorTest/1.Comparison 15: [ OK ] AllocatorTest/1.Comparison (0 ms) 15: [----------] 6 tests from AllocatorTest/1 (0 ms total) 15: 15: [----------] 6 tests from AllocatorTest/2, where TypeParam = gmx::Allocator 15: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 15: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 15: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 15: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/2.Move 15: [ OK ] AllocatorTest/2.Move (0 ms) 15: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory 15: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms) 15: [ RUN ] AllocatorTest/2.Comparison 15: [ OK ] AllocatorTest/2.Comparison (0 ms) 15: [----------] 6 tests from AllocatorTest/2 (0 ms total) 15: 15: [----------] 6 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 15: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 15: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 15: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 15: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/3.Move 15: [ OK ] AllocatorTest/3.Move (0 ms) 15: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory 15: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms) 15: [ RUN ] AllocatorTest/3.Comparison 15: [ OK ] AllocatorTest/3.Comparison (0 ms) 15: [----------] 6 tests from AllocatorTest/3 (0 ms total) 15: 15: [----------] 6 tests from AllocatorTest/4, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 15: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment 15: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment 15: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment 15: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/4.Move 15: [ OK ] AllocatorTest/4.Move (0 ms) 15: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory 15: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms) 15: [ RUN ] AllocatorTest/4.Comparison 15: [ OK ] AllocatorTest/4.Comparison (0 ms) 15: [----------] 6 tests from AllocatorTest/4 (0 ms total) 15: 15: [----------] 6 tests from AllocatorTest/5, where TypeParam = gmx::Allocator, gmx::PageAlignedAllocationPolicy> 15: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment 15: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment 15: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment 15: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/5.Move 15: [ OK ] AllocatorTest/5.Move (0 ms) 15: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory 15: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms) 15: [ RUN ] AllocatorTest/5.Comparison 15: [ OK ] AllocatorTest/5.Comparison (0 ms) 15: [----------] 6 tests from AllocatorTest/5 (0 ms total) 15: 15: [----------] 1 test from AllocatorUntypedTest 15: [ RUN ] AllocatorUntypedTest.Comparison 15: [ OK ] AllocatorUntypedTest.Comparison (0 ms) 15: [----------] 1 test from AllocatorUntypedTest (0 ms total) 15: 15: [----------] 4 tests from EmptyArrayRefTest 15: [ RUN ] EmptyArrayRefTest.IsEmpty 15: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 15: [ RUN ] EmptyArrayRefTest.ConstructFromNullptrIsEmpty 15: [ OK ] EmptyArrayRefTest.ConstructFromNullptrIsEmpty (0 ms) 15: [ RUN ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForNullptr 15: [ OK ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForNullptr (0 ms) 15: [ RUN ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForSizeNull 15: [ OK ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForSizeNull (0 ms) 15: [----------] 4 tests from EmptyArrayRefTest (0 ms total) 15: 15: [----------] 1 test from EmptyConstArrayRefTest 15: [ RUN ] EmptyConstArrayRefTest.IsEmpty 15: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms) 15: [----------] 1 test from EmptyConstArrayRefTest (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/0 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/1 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/2 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/3 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/4 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/5 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/6 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/7 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/8 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/9 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/10 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/11 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/12 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/13 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/14 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/15 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/16 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/17 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/18 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/19 (0 ms total) 15: 15: [----------] 8 tests from BoolType 15: [ RUN ] BoolType.ImplicitConversion 15: [ OK ] BoolType.ImplicitConversion (0 ms) 15: [ RUN ] BoolType.FalseByDefault 15: [ OK ] BoolType.FalseByDefault (0 ms) 15: [ RUN ] BoolType.Assignment 15: [ OK ] BoolType.Assignment (0 ms) 15: [ RUN ] BoolType.Copy 15: [ OK ] BoolType.Copy (0 ms) 15: [ RUN ] BoolType.ArrayRefCanBeCreated 15: [ OK ] BoolType.ArrayRefCanBeCreated (0 ms) 15: [ RUN ] BoolType.CanBeCastToBool 15: [ OK ] BoolType.CanBeCastToBool (0 ms) 15: [ RUN ] BoolType.HasSizeOfBool 15: [ OK ] BoolType.HasSizeOfBool (0 ms) 15: [ RUN ] BoolType.HasAlignmentOfBool 15: [ OK ] BoolType.HasAlignmentOfBool (0 ms) 15: [----------] 8 tests from BoolType (0 ms total) 15: 15: [----------] 4 tests from ArrayRefFromBoolTypeVector 15: [ RUN ] ArrayRefFromBoolTypeVector.CanConstructEmpty 15: [ OK ] ArrayRefFromBoolTypeVector.CanConstructEmpty (0 ms) 15: [ RUN ] ArrayRefFromBoolTypeVector.Works 15: [ OK ] ArrayRefFromBoolTypeVector.Works (0 ms) 15: [ RUN ] ArrayRefFromBoolTypeVector.CanConstructConstEmpty 15: [ OK ] ArrayRefFromBoolTypeVector.CanConstructConstEmpty (0 ms) 15: [ RUN ] ArrayRefFromBoolTypeVector.ConstWorks 15: [ OK ] ArrayRefFromBoolTypeVector.ConstWorks (0 ms) 15: [----------] 4 tests from ArrayRefFromBoolTypeVector (0 ms total) 15: 15: [----------] 7 tests from CStringUtilityTest 15: [ RUN ] CStringUtilityTest.CaseInsensitiveComparison 15: [ OK ] CStringUtilityTest.CaseInsensitiveComparison (0 ms) 15: [ RUN ] CStringUtilityTest.CaseInsensitiveComparisonInLength 15: [ OK ] CStringUtilityTest.CaseInsensitiveComparisonInLength (0 ms) 15: [ RUN ] CStringUtilityTest.strip_comment 15: [ OK ] CStringUtilityTest.strip_comment (0 ms) 15: [ RUN ] CStringUtilityTest.upstring 15: [ OK ] CStringUtilityTest.upstring (0 ms) 15: [ RUN ] CStringUtilityTest.ltrim 15: [ OK ] CStringUtilityTest.ltrim (0 ms) 15: [ RUN ] CStringUtilityTest.rtrim 15: [ OK ] CStringUtilityTest.rtrim (0 ms) 15: [ RUN ] CStringUtilityTest.trim 15: [ OK ] CStringUtilityTest.trim (0 ms) 15: [----------] 7 tests from CStringUtilityTest (0 ms total) 15: 15: [----------] 2 tests from DefaultInitializationAllocator 15: [ RUN ] DefaultInitializationAllocator.PerformsValueInitialization 15: [ OK ] DefaultInitializationAllocator.PerformsValueInitialization (0 ms) 15: [ RUN ] DefaultInitializationAllocator.PerformsNoInitialization 15: [ OK ] DefaultInitializationAllocator.PerformsNoInitialization (0 ms) 15: [----------] 2 tests from DefaultInitializationAllocator (0 ms total) 15: 15: [----------] 4 tests from EnumerationHelpersTest 15: [ RUN ] EnumerationHelpersTest.EnumerationWrapperWorks 15: [ OK ] EnumerationHelpersTest.EnumerationWrapperWorks (0 ms) 15: [ RUN ] EnumerationHelpersTest.EnumerationArrayWorks 15: [ OK ] EnumerationHelpersTest.EnumerationArrayWorks (0 ms) 15: [ RUN ] EnumerationHelpersTest.EnumerationArrayCountIsSafe 15: [ OK ] EnumerationHelpersTest.EnumerationArrayCountIsSafe (0 ms) 15: [ RUN ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks 15: [ OK ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks (0 ms) 15: [----------] 4 tests from EnumerationHelpersTest (0 ms total) 15: 15: [----------] 1 test from EnumClassSuitsEnumerationArray 15: [ RUN ] EnumClassSuitsEnumerationArray.Works 15: [ OK ] EnumClassSuitsEnumerationArray.Works (0 ms) 15: [----------] 1 test from EnumClassSuitsEnumerationArray (0 ms total) 15: 15: [----------] 18 tests from FixedCapacityVectorTest 15: [ RUN ] FixedCapacityVectorTest.IsEmpty 15: [ OK ] FixedCapacityVectorTest.IsEmpty (0 ms) 15: [ RUN ] FixedCapacityVectorTest.ConstructorWorks 15: [ OK ] FixedCapacityVectorTest.ConstructorWorks (0 ms) 15: [ RUN ] FixedCapacityVectorTest.PushWorks 15: [ OK ] FixedCapacityVectorTest.PushWorks (0 ms) 15: [ RUN ] FixedCapacityVectorTest.PopWorks 15: [ OK ] FixedCapacityVectorTest.PopWorks (0 ms) 15: [ RUN ] FixedCapacityVectorTest.ResizeWorks 15: [ OK ] FixedCapacityVectorTest.ResizeWorks (0 ms) 15: [ RUN ] FixedCapacityVectorTest.ClearWorks 15: [ OK ] FixedCapacityVectorTest.ClearWorks (0 ms) 15: [ RUN ] FixedCapacityVectorTest.EmplaceBackWorks 15: [ OK ] FixedCapacityVectorTest.EmplaceBackWorks (0 ms) 15: [ RUN ] FixedCapacityVectorTest.AtThrows 15: [ OK ] FixedCapacityVectorTest.AtThrows (0 ms) 15: [ RUN ] FixedCapacityVectorTest.IteratorWorks 15: [ OK ] FixedCapacityVectorTest.IteratorWorks (0 ms) 15: [ RUN ] FixedCapacityVectorTest.ReverseIteratorWorks 15: [ OK ] FixedCapacityVectorTest.ReverseIteratorWorks (0 ms) 15: [ RUN ] FixedCapacityVectorTest.ZeroCapacityWorks 15: [ OK ] FixedCapacityVectorTest.ZeroCapacityWorks (0 ms) 15: [ RUN ] FixedCapacityVectorTest.CopyConstructorWorks 15: [ OK ] FixedCapacityVectorTest.CopyConstructorWorks (0 ms) 15: [ RUN ] FixedCapacityVectorTest.CopyAssignmentWorks 15: [ OK ] FixedCapacityVectorTest.CopyAssignmentWorks (0 ms) 15: [ RUN ] FixedCapacityVectorTest.MoveConstructorWorks 15: [ OK ] FixedCapacityVectorTest.MoveConstructorWorks (0 ms) 15: [ RUN ] FixedCapacityVectorTest.MoveAssignmentWorks 15: [ OK ] FixedCapacityVectorTest.MoveAssignmentWorks (0 ms) 15: [ RUN ] FixedCapacityVectorTest.ElementAssignmentWorks 15: [ OK ] FixedCapacityVectorTest.ElementAssignmentWorks (0 ms) 15: [ RUN ] FixedCapacityVectorTest.DataWorks 15: [ OK ] FixedCapacityVectorTest.DataWorks (0 ms) 15: [ RUN ] FixedCapacityVectorTest.ConstMethodsWork 15: [ OK ] FixedCapacityVectorTest.ConstMethodsWork (0 ms) 15: [----------] 18 tests from FixedCapacityVectorTest (0 ms total) 15: 15: [----------] 5 tests from InMemorySerializerTest 15: [ RUN ] InMemorySerializerTest.Roundtrip 15: [ OK ] InMemorySerializerTest.Roundtrip (0 ms) 15: [ RUN ] InMemorySerializerTest.RoundtripWithEndianessSwap 15: [ OK ] InMemorySerializerTest.RoundtripWithEndianessSwap (0 ms) 15: [ RUN ] InMemorySerializerTest.SerializerExplicitEndianessSwap 15: [ OK ] InMemorySerializerTest.SerializerExplicitEndianessSwap (0 ms) 15: [ RUN ] InMemorySerializerTest.DeserializerExplicitEndianessSwap 15: [ OK ] InMemorySerializerTest.DeserializerExplicitEndianessSwap (0 ms) 15: [ RUN ] InMemorySerializerTest.SizeIsCorrect 15: [ OK ] InMemorySerializerTest.SizeIsCorrect (0 ms) 15: [----------] 5 tests from InMemorySerializerTest (0 ms total) 15: 15: [----------] 4 tests from KeyValueTreeSerializerTest 15: [ RUN ] KeyValueTreeSerializerTest.EmptyTree 15: [ OK ] KeyValueTreeSerializerTest.EmptyTree (0 ms) 15: [ RUN ] KeyValueTreeSerializerTest.SimpleObject 15: [ OK ] KeyValueTreeSerializerTest.SimpleObject (0 ms) 15: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays 15: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (0 ms) 15: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects 15: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (0 ms) 15: [----------] 4 tests from KeyValueTreeSerializerTest (0 ms total) 15: 15: [----------] 7 tests from TreeValueTransformTest 15: [ RUN ] TreeValueTransformTest.SimpleTransforms 15: [ OK ] TreeValueTransformTest.SimpleTransforms (1 ms) 15: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive 15: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (0 ms) 15: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject 15: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (0 ms) 15: [ RUN ] TreeValueTransformTest.ObjectFromString 15: [ OK ] TreeValueTransformTest.ObjectFromString (0 ms) 15: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings 15: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (0 ms) 15: [ RUN ] TreeValueTransformTest.ScopedTransformRules 15: [ OK ] TreeValueTransformTest.ScopedTransformRules (0 ms) 15: [ RUN ] TreeValueTransformTest.CanAssignUserMultiValue 15: [ OK ] TreeValueTransformTest.CanAssignUserMultiValue (0 ms) 15: [----------] 7 tests from TreeValueTransformTest (2 ms total) 15: 15: [----------] 1 test from TreeValueTransformErrorTest 15: [ RUN ] TreeValueTransformErrorTest.ConversionError 15: [ OK ] TreeValueTransformErrorTest.ConversionError (0 ms) 15: [----------] 1 test from TreeValueTransformErrorTest (0 ms total) 15: 15: [----------] 9 tests from ListOfLists 15: [ RUN ] ListOfLists.EmptyListOfListsWorks 15: [ OK ] ListOfLists.EmptyListOfListsWorks (0 ms) 15: [ RUN ] ListOfLists.AppendWorks 15: [ OK ] ListOfLists.AppendWorks (0 ms) 15: [ RUN ] ListOfLists.EmptyListWorks 15: [ OK ] ListOfLists.EmptyListWorks (0 ms) 15: [ RUN ] ListOfLists.AppendAccessWorks 15: [ OK ] ListOfLists.AppendAccessWorks (0 ms) 15: [ RUN ] ListOfLists.ClearWorks 15: [ OK ] ListOfLists.ClearWorks (0 ms) 15: [ RUN ] ListOfLists.OutOfRangeAccessThrows 15: [ OK ] ListOfLists.OutOfRangeAccessThrows (0 ms) 15: [ RUN ] ListOfLists.FrontAndBackWork 15: [ OK ] ListOfLists.FrontAndBackWork (0 ms) 15: [ RUN ] ListOfLists.ExtractsAndRestores 15: [ OK ] ListOfLists.ExtractsAndRestores (0 ms) 15: [ RUN ] ListOfLists.AppendsListOfListsWithOffset 15: [ OK ] ListOfLists.AppendsListOfListsWithOffset (0 ms) 15: [----------] 9 tests from ListOfLists (0 ms total) 15: 15: [----------] 7 tests from LoggerTest 15: [ RUN ] LoggerTest.EmptyLoggerWorks 15: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms) 15: [ RUN ] LoggerTest.LogsToStream 15: [ OK ] LoggerTest.LogsToStream (0 ms) 15: [ RUN ] LoggerTest.LogsToFile 15: [ OK ] LoggerTest.LogsToFile (1 ms) 15: [ RUN ] LoggerTest.LevelFilteringWorks 15: [ OK ] LoggerTest.LevelFilteringWorks (0 ms) 15: [ RUN ] LoggerTest.LogsToMultipleStreams 15: [ OK ] LoggerTest.LogsToMultipleStreams (0 ms) 15: [ RUN ] LoggerTest.LogsToMultipleFiles 15: [ OK ] LoggerTest.LogsToMultipleFiles (0 ms) 15: [ RUN ] LoggerTest.LogsToStreamAndFile 15: [ OK ] LoggerTest.LogsToStreamAndFile (0 ms) 15: [----------] 7 tests from LoggerTest (2 ms total) 15: 15: [----------] 7 tests from MessageStringCollectorTest 15: [ RUN ] MessageStringCollectorTest.CanAddAndClearMessagesNoContext 15: [ OK ] MessageStringCollectorTest.CanAddAndClearMessagesNoContext (0 ms) 15: [ RUN ] MessageStringCollectorTest.CanAddAndClearMessagesWithContext 15: [ OK ] MessageStringCollectorTest.CanAddAndClearMessagesWithContext (0 ms) 15: [ RUN ] MessageStringCollectorTest.CanAddStringMessages 15: [ OK ] MessageStringCollectorTest.CanAddStringMessages (0 ms) 15: [ RUN ] MessageStringCollectorTest.CanAddCharMessagesConditionally 15: [ OK ] MessageStringCollectorTest.CanAddCharMessagesConditionally (0 ms) 15: [ RUN ] MessageStringCollectorTest.CanAddStringMessagesConditionally 15: [ OK ] MessageStringCollectorTest.CanAddStringMessagesConditionally (0 ms) 15: [ RUN ] MessageStringCollectorTest.CanMoveConstruct 15: [ OK ] MessageStringCollectorTest.CanMoveConstruct (0 ms) 15: [ RUN ] MessageStringCollectorTest.CanMoveAssign 15: [ OK ] MessageStringCollectorTest.CanMoveAssign (0 ms) 15: [----------] 7 tests from MessageStringCollectorTest (0 ms total) 15: 15: [----------] 1 test from PathTest 15: [ RUN ] PathTest.StripSourcePrefixWorks 15: [ OK ] PathTest.StripSourcePrefixWorks (0 ms) 15: [----------] 1 test from PathTest (0 ms total) 15: 15: [----------] 2 tests from PhysicalNodeCommunicatorTest 15: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 15: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms) 15: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 15: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) 15: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total) 15: 15: [----------] 5 tests from Range 15: [ RUN ] Range.EmptyRangeWorks 15: [ OK ] Range.EmptyRangeWorks (0 ms) 15: [ RUN ] Range.NonEmptyRangeWorks 15: [ OK ] Range.NonEmptyRangeWorks (0 ms) 15: [ RUN ] Range.BeginEnd 15: [ OK ] Range.BeginEnd (0 ms) 15: [ RUN ] Range.IsInRangeWorks 15: [ OK ] Range.IsInRangeWorks (0 ms) 15: [ RUN ] Range.IteratorWorks 15: [ OK ] Range.IteratorWorks (0 ms) 15: [----------] 5 tests from Range (0 ms total) 15: 15: [----------] 3 tests from ScopeGuardTest 15: [ RUN ] ScopeGuardTest.ScopeGuardExecutesCallbackOnExit 15: [ OK ] ScopeGuardTest.ScopeGuardExecutesCallbackOnExit (0 ms) 15: [ RUN ] ScopeGuardTest.ScopeGuardCanFreePointers 15: [ OK ] ScopeGuardTest.ScopeGuardCanFreePointers (0 ms) 15: [ RUN ] ScopeGuardTest.ScopeGuardsCanBeCreatedByHelperFunctions 15: [ OK ] ScopeGuardTest.ScopeGuardsCanBeCreatedByHelperFunctions (0 ms) 15: [----------] 3 tests from ScopeGuardTest (0 ms total) 15: 15: [----------] 7 tests from StringConvert 15: [ RUN ] StringConvert.NoResultFromEptyString 15: [ OK ] StringConvert.NoResultFromEptyString (0 ms) 15: [ RUN ] StringConvert.ThreeFloatsSuccessfully 15: [ OK ] StringConvert.ThreeFloatsSuccessfully (0 ms) 15: [ RUN ] StringConvert.OneIntSucessfully 15: [ OK ] StringConvert.OneIntSucessfully (0 ms) 15: [ RUN ] StringConvert.FloatAsStringToIntArrayThrows 15: [ OK ] StringConvert.FloatAsStringToIntArrayThrows (0 ms) 15: [ RUN ] StringConvert.ThrowsWhenWrongSize 15: [ OK ] StringConvert.ThrowsWhenWrongSize (0 ms) 15: [ RUN ] StringConvert.StringIdentityTransformWithArrayThrows 15: [ OK ] StringConvert.StringIdentityTransformWithArrayThrows (0 ms) 15: [ RUN ] StringConvert.StringIdentityTransformWithArrayOkay 15: [ OK ] StringConvert.StringIdentityTransformWithArrayOkay (0 ms) 15: [----------] 7 tests from StringConvert (0 ms total) 15: 15: [----------] 7 tests from StringToEnumValueConverterTest 15: [ RUN ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithoutStripping 15: [ OK ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithoutStripping (0 ms) 15: [ RUN ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithoutStripping 15: [ OK ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithoutStripping (0 ms) 15: [ RUN ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithoutStripping 15: [ OK ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithoutStripping (0 ms) 15: [ RUN ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithStripping 15: [ OK ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithStripping (0 ms) 15: [ RUN ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithStripping 15: [ OK ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithStripping (0 ms) 15: [ RUN ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithStripping 15: [ OK ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithStripping (0 ms) 15: [ RUN ] StringToEnumValueConverterTest.CustomConverterWorks 15: [ OK ] StringToEnumValueConverterTest.CustomConverterWorks (0 ms) 15: [----------] 7 tests from StringToEnumValueConverterTest (3 ms total) 15: 15: [----------] 9 tests from StringUtilityTest 15: [ RUN ] StringUtilityTest.StartsWith 15: [ OK ] StringUtilityTest.StartsWith (0 ms) 15: [ RUN ] StringUtilityTest.EndsWith 15: [ OK ] StringUtilityTest.EndsWith (0 ms) 15: [ RUN ] StringUtilityTest.StripSuffixIfPresent 15: [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms) 15: [ RUN ] StringUtilityTest.StripString 15: [ OK ] StringUtilityTest.StripString (0 ms) 15: [ RUN ] StringUtilityTest.SplitString 15: [ OK ] StringUtilityTest.SplitString (0 ms) 15: [ RUN ] StringUtilityTest.SplitDelimitedString 15: [ OK ] StringUtilityTest.SplitDelimitedString (0 ms) 15: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString 15: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (0 ms) 15: [ RUN ] StringUtilityTest.CanCompareCaseInsensitive 15: [ OK ] StringUtilityTest.CanCompareCaseInsensitive (0 ms) 15: [ RUN ] StringUtilityTest.CanCompareCaseInsensitiveInLength 15: [ OK ] StringUtilityTest.CanCompareCaseInsensitiveInLength (0 ms) 15: [----------] 9 tests from StringUtilityTest (0 ms total) 15: 15: [----------] 2 tests from FormatStringTest 15: [ RUN ] FormatStringTest.HandlesBasicFormatting 15: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms) 15: [ RUN ] FormatStringTest.HandlesLongStrings 15: [ OK ] FormatStringTest.HandlesLongStrings (0 ms) 15: [----------] 2 tests from FormatStringTest (0 ms total) 15: 15: [----------] 1 test from StringFormatterTest 15: [ RUN ] StringFormatterTest.HandlesBasicFormatting 15: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms) 15: [----------] 1 test from StringFormatterTest (0 ms total) 15: 15: [----------] 1 test from formatAndJoinTest 15: [ RUN ] formatAndJoinTest.Works 15: [ OK ] formatAndJoinTest.Works (0 ms) 15: [----------] 1 test from formatAndJoinTest (0 ms total) 15: 15: [----------] 1 test from JoinStringsTest 15: [ RUN ] JoinStringsTest.Works 15: [ OK ] JoinStringsTest.Works (0 ms) 15: [----------] 1 test from JoinStringsTest (0 ms total) 15: 15: [----------] 6 tests from ReplaceAllTest 15: [ RUN ] ReplaceAllTest.HandlesEmptyStrings 15: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms) 15: [ RUN ] ReplaceAllTest.HandlesNoMatches 15: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms) 15: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds 15: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms) 15: [ RUN ] ReplaceAllTest.HandlesMultipleMatches 15: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms) 15: [ RUN ] ReplaceAllTest.HandlesWordBoundaries 15: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms) 15: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches 15: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms) 15: [----------] 6 tests from ReplaceAllTest (0 ms total) 15: 15: [----------] 10 tests from TextLineWrapperTest 15: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings 15: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms) 15: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace 15: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms) 15: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines 15: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms) 15: [ RUN ] TextLineWrapperTest.WrapsCorrectly 15: [ OK ] TextLineWrapperTest.WrapsCorrectly (0 ms) 15: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks 15: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (0 ms) 15: [ RUN ] TextLineWrapperTest.HandlesIndent 15: [ OK ] TextLineWrapperTest.HandlesIndent (0 ms) 15: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines 15: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (0 ms) 15: [ RUN ] TextLineWrapperTest.HandlesHangingIndent 15: [ OK ] TextLineWrapperTest.HandlesHangingIndent (0 ms) 15: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter 15: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (0 ms) 15: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace 15: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (0 ms) 15: [----------] 10 tests from TextLineWrapperTest (0 ms total) 15: 15: [----------] 1 test from CompileTimeStringJoin 15: [ RUN ] CompileTimeStringJoin.Works 15: [ OK ] CompileTimeStringJoin.Works (0 ms) 15: [----------] 1 test from CompileTimeStringJoin (0 ms total) 15: 15: [----------] 3 tests from TemplateMPTest 15: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionEnum 15: [ OK ] TemplateMPTest.DispatchTemplatedFunctionEnum (0 ms) 15: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionBool 15: [ OK ] TemplateMPTest.DispatchTemplatedFunctionBool (0 ms) 15: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionEnumBool 15: [ OK ] TemplateMPTest.DispatchTemplatedFunctionEnumBool (0 ms) 15: [----------] 3 tests from TemplateMPTest (0 ms total) 15: 15: [----------] 6 tests from TextWriterTest 15: [ RUN ] TextWriterTest.WritesLines 15: [ OK ] TextWriterTest.WritesLines (0 ms) 15: [ RUN ] TextWriterTest.WritesLinesInParts 15: [ OK ] TextWriterTest.WritesLinesInParts (0 ms) 15: [ RUN ] TextWriterTest.WritesWrappedLines 15: [ OK ] TextWriterTest.WritesWrappedLines (0 ms) 15: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper 15: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (0 ms) 15: [ RUN ] TextWriterTest.TracksNewlines 15: [ OK ] TextWriterTest.TracksNewlines (0 ms) 15: [ RUN ] TextWriterTest.PreservesTrailingWhitespace 15: [ OK ] TextWriterTest.PreservesTrailingWhitespace (0 ms) 15: [----------] 6 tests from TextWriterTest (0 ms total) 15: 15: [----------] 1 test from TypeTraitsTest 15: [ RUN ] TypeTraitsTest.IsIntegralConstant 15: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms) 15: [----------] 1 test from TypeTraitsTest (0 ms total) 15: 15: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 15: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 15: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms) 15: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0 15: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms) 15: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 15: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms) 15: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 15: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms) 15: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0 15: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms) 15: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0 15: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms) 15: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (0 ms total) 15: 15: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms) 15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms) 15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms) 15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms) 15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms) 15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms) 15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms) 15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms) 15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0 15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms) 15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1 15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms) 15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms) 15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms) 15: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (0 ms total) 15: 15: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms) 15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms) 15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms) 15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms) 15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms) 15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms) 15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms) 15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms) 15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0 15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms) 15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1 15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms) 15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms) 15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms) 15: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (0 ms total) 15: 15: [----------] 11 tests from WithInputPaths/PathSearchTest 15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/0 15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/0 (0 ms) 15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/1 15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/1 (0 ms) 15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/2 15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/2 (0 ms) 15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/3 15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/3 (0 ms) 15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/4 15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/4 (0 ms) 15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/5 15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/5 (0 ms) 15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/6 15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/6 (0 ms) 15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/7 15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/7 (0 ms) 15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/8 15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/8 (0 ms) 15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/9 15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/9 (0 ms) 15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/10 15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/10 (0 ms) 15: [----------] 11 tests from WithInputPaths/PathSearchTest (0 ms total) 15: 15: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest 15: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 15: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (0 ms) 15: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 15: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms) 15: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 15: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (0 ms) 15: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 15: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (0 ms) 15: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 15: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (0 ms) 15: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 15: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (0 ms) 15: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 15: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (0 ms) 15: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (0 ms total) 15: 15: [----------] Global test environment tear-down 15: [==========] 420 tests from 65 test suites ran. (14 ms total) 15: [ PASSED ] 420 tests. 15: 15: YOU HAVE 1 DISABLED TEST 15: 15/94 Test #15: UtilityUnitTests ............................. Passed 0.36 sec test 16 Start 16: UtilityMpiUnitTests 16: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2025.0/build/mpi/bin/utility-mpi-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/UtilityMpiUnitTests.xml" 16: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/utility/tests 16: Test timeout computed to be: 30 16: [==========] Running 2 tests from 1 test suite. 16: [----------] Global test environment set-up. 16: [----------] 2 tests from PhysicalNodeCommunicatorTest 16: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 16: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (1 ms) 16: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 16: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) 16: [----------] 2 tests from PhysicalNodeCommunicatorTest (1 ms total) 16: 16: [----------] Global test environment tear-down 16: [==========] 2 tests from 1 test suite ran. (1 ms total) 16: [ PASSED ] 2 tests. 16/94 Test #16: UtilityMpiUnitTests .......................... Passed 0.54 sec test 17 Start 17: GmxlibTests 17: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/nonbonded-fep-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/GmxlibTests.xml" 17: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxlib/nonbonded/tests 17: Test timeout computed to be: 30 17: [==========] Running 78 tests from 2 test suites. 17: [----------] Global test environment set-up. 17: [----------] 72 tests from NBInteraction/NonbondedFepTest 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/0 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/0 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/1 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/1 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/2 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/2 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/3 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/3 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/4 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/4 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/5 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/5 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/6 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/6 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/7 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/7 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/8 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/8 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/9 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/9 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/10 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/10 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/11 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/11 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/12 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/12 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/13 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/13 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/14 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/14 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/15 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/15 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/16 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/16 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/17 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/17 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/18 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/18 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/19 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/19 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/20 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/20 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/21 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/21 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/22 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/22 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/23 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/23 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/24 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/24 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/25 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/25 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/26 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/26 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/27 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/27 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/28 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/28 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/29 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/29 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/30 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/30 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/31 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/31 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/32 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/32 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/33 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/33 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/34 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/34 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/35 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/35 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/36 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/36 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/37 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/37 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/38 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/38 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/39 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/39 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/40 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/40 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/41 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/41 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/42 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/42 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/43 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/43 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/44 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/44 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/45 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/45 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/46 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/46 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/47 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/47 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/48 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/48 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/49 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/49 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/50 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/50 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/51 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/51 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/52 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/52 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/53 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/53 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/54 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/54 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/55 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/55 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/56 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/56 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/57 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/57 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/58 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/58 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/59 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/59 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/60 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/60 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/61 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/61 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/62 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/62 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/63 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/63 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/64 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/64 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/65 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/65 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/66 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/66 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/67 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/67 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/68 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/68 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/69 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/69 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/70 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/70 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/71 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/71 (0 ms) 17: [----------] 72 tests from NBInteraction/NonbondedFepTest (11 ms total) 17: 17: [----------] 6 tests from NBInteractionShortDistance/NonbondedFepTest 17: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/0 17: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/0 (0 ms) 17: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/1 17: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/1 (0 ms) 17: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/2 17: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/2 (0 ms) 17: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/3 17: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/3 (0 ms) 17: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/4 17: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/4 (0 ms) 17: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/5 17: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/5 (0 ms) 17: [----------] 6 tests from NBInteractionShortDistance/NonbondedFepTest (0 ms total) 17: 17: [----------] Global test environment tear-down 17: [==========] 78 tests from 2 test suites ran. (12 ms total) 17: [ PASSED ] 78 tests. 17/94 Test #17: GmxlibTests .................................. Passed 0.41 sec test 18 Start 18: MdlibUnitTest 18: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/mdlib-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/MdlibUnitTest.xml" 18: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests 18: Test timeout computed to be: 30 18: [==========] Running 1032 tests from 27 test suites. 18: [----------] Global test environment set-up. 18: [----------] 3 tests from EffectiveAtomDensity 18: [ RUN ] EffectiveAtomDensity.VolumeIndependence 18: [ OK ] EffectiveAtomDensity.VolumeIndependence (0 ms) 18: [ RUN ] EffectiveAtomDensity.WeightingWorks 18: [ OK ] EffectiveAtomDensity.WeightingWorks (0 ms) 18: [ RUN ] EffectiveAtomDensity.LargeValuesHandledWell 18: [ OK ] EffectiveAtomDensity.LargeValuesHandledWell (0 ms) 18: [----------] 3 tests from EffectiveAtomDensity (0 ms total) 18: 18: [----------] 2 tests from AtomNonbondedAndKineticProperties 18: [ RUN ] AtomNonbondedAndKineticProperties.IsAccurate 18: [ OK ] AtomNonbondedAndKineticProperties.IsAccurate (0 ms) 18: [ RUN ] AtomNonbondedAndKineticProperties.ConstraintsWork 18: [ OK ] AtomNonbondedAndKineticProperties.ConstraintsWork (0 ms) 18: [----------] 2 tests from AtomNonbondedAndKineticProperties (0 ms total) 18: 18: [----------] 1 test from VerletBufferConstraintTest 18: [ RUN ] VerletBufferConstraintTest.EqualMasses 18: [ OK ] VerletBufferConstraintTest.EqualMasses (0 ms) 18: [----------] 1 test from VerletBufferConstraintTest (0 ms total) 18: 18: [----------] 1 test from VerletBufferSize 18: [ RUN ] VerletBufferSize.SizeAboveFourIsEquivalent 18: [ OK ] VerletBufferSize.SizeAboveFourIsEquivalent (0 ms) 18: [----------] 1 test from VerletBufferSize (0 ms total) 18: 18: [----------] 6 tests from CalcvirTest 18: [ RUN ] CalcvirTest.CanCalculateVirialAllAtomsInBox 18: [ OK ] CalcvirTest.CanCalculateVirialAllAtomsInBox (0 ms) 18: [ RUN ] CalcvirTest.CanCalculateVirialAllAtomsInBoxScrew 18: [ OK ] CalcvirTest.CanCalculateVirialAllAtomsInBoxScrew (0 ms) 18: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewX 18: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewX (0 ms) 18: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewY 18: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewY (0 ms) 18: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewZ 18: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewZ (0 ms) 18: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewXYZ 18: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewXYZ (0 ms) 18: [----------] 6 tests from CalcvirTest (0 ms total) 18: 18: [----------] 2 tests from PrEbinTest 18: [ RUN ] PrEbinTest.HandlesAverages 18: [ OK ] PrEbinTest.HandlesAverages (1 ms) 18: [ RUN ] PrEbinTest.HandlesEmptyAverages 18: [ OK ] PrEbinTest.HandlesEmptyAverages (0 ms) 18: [----------] 2 tests from PrEbinTest (1 ms total) 18: 18: [----------] 3 tests from EnergyDriftTracker 18: [ RUN ] EnergyDriftTracker.emptyWorks 18: [ OK ] EnergyDriftTracker.emptyWorks (0 ms) 18: [ RUN ] EnergyDriftTracker.onePointWorks 18: [ OK ] EnergyDriftTracker.onePointWorks (0 ms) 18: [ RUN ] EnergyDriftTracker.manyPointsWorks 18: [ OK ] EnergyDriftTracker.manyPointsWorks (0 ms) 18: [----------] 3 tests from EnergyDriftTracker (0 ms total) 18: 18: [----------] 4 tests from ShakeTest 18: [ RUN ] ShakeTest.ConstrainsOneBond 18: [ OK ] ShakeTest.ConstrainsOneBond (0 ms) 18: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds 18: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms) 18: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom 18: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (0 ms) 18: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms 18: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms) 18: [----------] 4 tests from ShakeTest (0 ms total) 18: 18: [----------] 1 test from NullSignalTest 18: [ RUN ] NullSignalTest.NullSignallerWorks 18: [ OK ] NullSignalTest.NullSignallerWorks (0 ms) 18: [----------] 1 test from NullSignalTest (0 ms total) 18: 18: [----------] 7 tests from SignalTest 18: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace 18: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms) 18: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace 18: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms) 18: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace 18: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms) 18: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace 18: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms) 18: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace 18: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms) 18: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace 18: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms) 18: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace 18: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms) 18: [----------] 7 tests from SignalTest (0 ms total) 18: 18: [----------] 13 tests from UpdateGroupsTest 18: [ RUN ] UpdateGroupsTest.WithEthaneUA 18: [ OK ] UpdateGroupsTest.WithEthaneUA (0 ms) 18: [ RUN ] UpdateGroupsTest.WithMethane 18: [ OK ] UpdateGroupsTest.WithMethane (0 ms) 18: [ RUN ] UpdateGroupsTest.WithEthane 18: [ OK ] UpdateGroupsTest.WithEthane (0 ms) 18: [ RUN ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithEthane 18: [ OK ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithEthane (0 ms) 18: [ RUN ] UpdateGroupsTest.WithButaneUALogsThatUnsuitableForUpdateGroups 18: [ OK ] UpdateGroupsTest.WithButaneUALogsThatUnsuitableForUpdateGroups (0 ms) 18: [ RUN ] UpdateGroupsTest.WithWaterThreeSite 18: [ OK ] UpdateGroupsTest.WithWaterThreeSite (0 ms) 18: [ RUN ] UpdateGroupsTest.WithWaterFourSite 18: [ OK ] UpdateGroupsTest.WithWaterFourSite (0 ms) 18: [ RUN ] UpdateGroupsTest.WithFourAtomsWithSettle 18: [ OK ] UpdateGroupsTest.WithFourAtomsWithSettle (0 ms) 18: [ RUN ] UpdateGroupsTest.WithWaterFlexAngle 18: [ OK ] UpdateGroupsTest.WithWaterFlexAngle (0 ms) 18: [ RUN ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithWaterFlexAngle 18: [ OK ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithWaterFlexAngle (0 ms) 18: [ RUN ] UpdateGroupsTest.WithTwoMoltypes 18: [ OK ] UpdateGroupsTest.WithTwoMoltypes (0 ms) 18: [ RUN ] UpdateGroupsTest.LogsWhenSizesAreInvalid 18: [ OK ] UpdateGroupsTest.LogsWhenSizesAreInvalid (0 ms) 18: [ RUN ] UpdateGroupsTest.LogsWhenUpdateGroupsAreNotUseful 18: [ OK ] UpdateGroupsTest.LogsWhenUpdateGroupsAreNotUseful (0 ms) 18: [----------] 13 tests from UpdateGroupsTest (1 ms total) 18: 18: [----------] 1 test from UpdateGroupsCog 18: [ RUN ] UpdateGroupsCog.ComputesCogs 18: [ OK ] UpdateGroupsCog.ComputesCogs (0 ms) 18: [----------] 1 test from UpdateGroupsCog (1 ms total) 18: 18: [----------] 2 tests from WholeMoleculeTransform 18: [ RUN ] WholeMoleculeTransform.MakesMoleculesWhole 18: [ OK ] WholeMoleculeTransform.MakesMoleculesWhole (0 ms) 18: [ RUN ] WholeMoleculeTransform.HandlesReordering 18: [ OK ] WholeMoleculeTransform.HandlesReordering (0 ms) 18: [----------] 2 tests from WholeMoleculeTransform (0 ms total) 18: 18: [----------] 28 tests from WithParameters/ConstraintsTest 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/0 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/0 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/1 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/1 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/2 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/2 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/3 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/3 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/4 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/4 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/5 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/5 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/6 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/6 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/7 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/7 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/8 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/8 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/9 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/9 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/10 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/10 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/11 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/11 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/12 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/12 (10 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/13 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/13 (9 ms) 18: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/0 18: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/0 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/1 18: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/1 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/2 18: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/2 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/3 18: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/3 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/4 18: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/4 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/5 18: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/5 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/6 18: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/6 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/7 18: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/7 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/8 18: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/8 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/9 18: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/9 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/10 18: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/10 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/11 18: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/11 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/12 18: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/12 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.TriangleDetectionWorks/13 18: [ OK ] WithParameters/ConstraintsTest.TriangleDetectionWorks/13 (0 ms) 18: [----------] 28 tests from WithParameters/ConstraintsTest (26 ms total) 18: 18: [----------] 11 tests from WithParameters/EnergyOutputTest 18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/0 18: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_0.edr as single precision energy file 18: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/0 (3 ms) 18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/1 18: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_1.edr as single precision energy file 18: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/1 (1 ms) 18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/2 18: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_2.edr as single precision energy file 18: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/2 (1 ms) 18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/3 18: [ OK ] WithParameters/EnergyOutputTest.CheckOutput/3 (0 ms) 18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/4 18: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_4.edr as single precision energy file 18: Reading energy frame 0 time 10.100 Reading energy frame 1 time 27.500 Reading energy frame 2 time 44.900 Reading energy frame 3 time 62.300 Reading energy frame 4 time 79.700 Reading energy frame 5 time 97.100 Reading energy frame 6 time 114.500 Reading energy frame 7 time 131.900 Reading energy frame 8 time 149.300 Reading energy frame 9 time 166.700 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/4 (7 ms) 18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/5 18: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_5.edr as single precision energy file 18: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/5 (6 ms) 18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/6 18: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_6.edr as single precision energy file 18: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/6 (2 ms) 18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/7 18: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_7.edr as single precision energy file 18: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/7 (1 ms) 18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/8 18: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_8.edr as single precision energy file 18: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/8 (1 ms) 18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/9 18: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_9.edr as single precision energy file 18: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/9 (2 ms) 18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/10 18: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_10.edr as single precision energy file 18: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/10 (2 ms) 18: [----------] 11 tests from WithParameters/EnergyOutputTest (34 ms total) 18: 18: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 (0 ms) 18: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple (0 ms total) 18: 18: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 (0 ms) 18: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression (0 ms total) 18: 18: [----------] 23 tests from WithParameters/FreeEnergyParameterTest 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22 (0 ms) 18: [----------] 23 tests from WithParameters/FreeEnergyParameterTest (0 ms total) 18: 18: [----------] 17 tests from WithParameters/LangevinTest 18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/0 18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/0 (0 ms) 18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/1 18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/1 (0 ms) 18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/2 18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/2 (0 ms) 18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/3 18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/3 (0 ms) 18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/4 18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/4 (0 ms) 18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/5 18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/5 (0 ms) 18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/6 18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/6 (0 ms) 18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/7 18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/7 (0 ms) 18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/8 18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/8 (0 ms) 18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/9 18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/9 (0 ms) 18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/10 18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/10 (0 ms) 18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/11 18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/11 (0 ms) 18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/12 18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/12 (0 ms) 18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/13 18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/13 (0 ms) 18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/14 18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/14 (0 ms) 18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/15 18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/15 (0 ms) 18: [ RUN ] WithParameters/LangevinTest.SimpleIntegration/16 18: [ OK ] WithParameters/LangevinTest.SimpleIntegration/16 (0 ms) 18: [----------] 17 tests from WithParameters/LangevinTest (3 ms total) 18: 18: [----------] 16 tests from WithParameters/LeapFrogTest 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/0 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/0 (0 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/1 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/1 (0 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/2 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/2 (0 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/3 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/3 (0 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/4 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/4 (0 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/5 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/5 (2 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/6 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/6 (6 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/7 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/7 (0 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/8 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/8 (0 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/9 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/9 (0 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/10 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/10 (1 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/11 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/11 (1 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/12 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/12 (1 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/13 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/13 (1 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/14 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/14 (1 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/15 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/15 (1 ms) 18: [----------] 16 tests from WithParameters/LeapFrogTest (21 ms total) 18: 18: [----------] 140 tests from Cubic/ParrRahmTest 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 (0 ms) 18: [----------] 140 tests from Cubic/ParrRahmTest (10 ms total) 18: 18: [----------] 140 tests from Rectilinear/ParrRahmTest 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_100 (0 ms) 18: [----------] 140 tests from Rectilinear/ParrRahmTest (10 ms total) 18: 18: [----------] 140 tests from RhombDodecXYSquare/ParrRahmTest 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_100 (0 ms) 18: [----------] 140 tests from RhombDodecXYSquare/ParrRahmTest (8 ms total) 18: 18: [----------] 140 tests from RhombDodecXYHex/ParrRahmTest 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 (0 ms) 18: [----------] 140 tests from RhombDodecXYHex/ParrRahmTest (8 ms total) 18: 18: [----------] 140 tests from TruncOct/ParrRahmTest 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_100 (0 ms) 18: [----------] 140 tests from TruncOct/ParrRahmTest (8 ms total) 18: 18: [----------] 140 tests from Other/ParrRahmTest 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_100 (0 ms) 18: [----------] 140 tests from Other/ParrRahmTest (8 ms total) 18: 18: [----------] 13 tests from WithParameters/SettleTest 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (0 ms) 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (0 ms) 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (0 ms) 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (0 ms) 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (0 ms) 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (0 ms) 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (0 ms) 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (0 ms) 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (0 ms) 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (0 ms) 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (0 ms) 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (0 ms) 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (0 ms) 18: [----------] 13 tests from WithParameters/SettleTest (7 ms total) 18: 18: [----------] Global test environment tear-down 18: [==========] 1032 tests from 27 test suites ran. (153 ms total) 18: [ PASSED ] 1032 tests. 18/94 Test #18: MdlibUnitTest ................................ Passed 0.70 sec test 19 Start 19: AwhTest 19: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/awh-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/AwhTest.xml" 19: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/awh/tests 19: Test timeout computed to be: 30 19: [==========] Running 25 tests from 9 test suites. 19: [----------] Global test environment set-up. 19: [----------] 3 tests from SerializationTest 19: [ RUN ] SerializationTest.CanSerializeDimParams 19: [ OK ] SerializationTest.CanSerializeDimParams (0 ms) 19: [ RUN ] SerializationTest.CanSerializeBiasParams 19: [ OK ] SerializationTest.CanSerializeBiasParams (0 ms) 19: [ RUN ] SerializationTest.CanSerializeAwhParams 19: [ OK ] SerializationTest.CanSerializeAwhParams (0 ms) 19: [----------] 3 tests from SerializationTest (0 ms total) 19: 19: [----------] 1 test from BiasTest 19: [ RUN ] BiasTest.DetectsCovering 19: [ OK ] BiasTest.DetectsCovering (1 ms) 19: [----------] 1 test from BiasTest (1 ms total) 19: 19: [----------] 1 test from biasGridTest 19: [ RUN ] biasGridTest.neighborhood 19: [ OK ] biasGridTest.neighborhood (1 ms) 19: [----------] 1 test from biasGridTest (1 ms total) 19: 19: [----------] 2 tests from BiasFepLambdaStateTest 19: [ RUN ] BiasFepLambdaStateTest.DetectsCovering 19: [ OK ] BiasFepLambdaStateTest.DetectsCovering (3 ms) 19: [ RUN ] BiasFepLambdaStateTest.DetectsLargeNegativeForeignEnergy 19: [ OK ] BiasFepLambdaStateTest.DetectsLargeNegativeForeignEnergy (0 ms) 19: [----------] 2 tests from BiasFepLambdaStateTest (3 ms total) 19: 19: [----------] 8 tests from WithParameters/BiasTest 19: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/0 19: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/0 (0 ms) 19: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/1 19: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/1 (0 ms) 19: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/2 19: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/2 (0 ms) 19: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/3 19: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/3 (0 ms) 19: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/4 19: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/4 (0 ms) 19: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/5 19: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/5 (0 ms) 19: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/6 19: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/6 (0 ms) 19: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/7 19: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/7 (0 ms) 19: [----------] 8 tests from WithParameters/BiasTest (4 ms total) 19: 19: [----------] 2 tests from WithParameters/BiasStateTest 19: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0 19: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (0 ms) 19: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1 19: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (0 ms) 19: [----------] 2 tests from WithParameters/BiasStateTest (0 ms total) 19: 19: [----------] 1 test from WithParameters/UserInputTest 19: [ RUN ] WithParameters/UserInputTest.ParsesUser3DInput/0 19: [ OK ] WithParameters/UserInputTest.ParsesUser3DInput/0 (0 ms) 19: [----------] 1 test from WithParameters/UserInputTest (0 ms total) 19: 19: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest 19: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 19: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 (8 ms) 19: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 19: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 (7 ms) 19: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 19: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 (6 ms) 19: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 19: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 (7 ms) 19: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest (30 ms total) 19: 19: [----------] 3 tests from WithParameters/FrictionMetricTest 19: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/0 19: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/0 (0 ms) 19: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/1 19: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/1 (1 ms) 19: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/2 19: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/2 (28 ms) 19: [----------] 3 tests from WithParameters/FrictionMetricTest (32 ms total) 19: 19: [----------] Global test environment tear-down 19: [==========] 25 tests from 9 test suites ran. (75 ms total) 19: [ PASSED ] 25 tests. 19/94 Test #19: AwhTest ...................................... Passed 0.44 sec test 20 Start 20: DensityFittingAppliedForcesUnitTest 20: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/density_fitting_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/DensityFittingAppliedForcesUnitTest.xml" 20: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/densityfitting/tests 20: Test timeout computed to be: 30 20: [==========] Running 18 tests from 4 test suites. 20: [----------] Global test environment set-up. 20: [----------] 2 tests from DensityFittingTest 20: [ RUN ] DensityFittingTest.ForceProviderLackingInputThrows 20: [ OK ] DensityFittingTest.ForceProviderLackingInputThrows (0 ms) 20: [ RUN ] DensityFittingTest.SingleAtom 20: [ OK ] DensityFittingTest.SingleAtom (0 ms) 20: [----------] 2 tests from DensityFittingTest (0 ms total) 20: 20: [----------] 7 tests from DensityFittingAmplitudeLookupTest 20: [ RUN ] DensityFittingAmplitudeLookupTest.Unity 20: [ OK ] DensityFittingAmplitudeLookupTest.Unity (0 ms) 20: [ RUN ] DensityFittingAmplitudeLookupTest.Charge 20: [ OK ] DensityFittingAmplitudeLookupTest.Charge (0 ms) 20: [ RUN ] DensityFittingAmplitudeLookupTest.Masses 20: [ OK ] DensityFittingAmplitudeLookupTest.Masses (0 ms) 20: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyAssign 20: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyAssign (0 ms) 20: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyConstruct 20: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyConstruct (0 ms) 20: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveAssign 20: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveAssign (0 ms) 20: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveConstruct 20: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveConstruct (0 ms) 20: [----------] 7 tests from DensityFittingAmplitudeLookupTest (0 ms total) 20: 20: [----------] 1 test from DensityFittingForceProviderState 20: [ RUN ] DensityFittingForceProviderState.RoundTripSaving 20: [ OK ] DensityFittingForceProviderState.RoundTripSaving (0 ms) 20: [----------] 1 test from DensityFittingForceProviderState (0 ms total) 20: 20: [----------] 8 tests from DensityFittingOptionsTest 20: [ RUN ] DensityFittingOptionsTest.DefaultParameters 20: [ OK ] DensityFittingOptionsTest.DefaultParameters (0 ms) 20: [ RUN ] DensityFittingOptionsTest.OptionSetsActive 20: [ OK ] DensityFittingOptionsTest.OptionSetsActive (0 ms) 20: [ RUN ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive 20: [ OK ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 20: [ RUN ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive 20: [ OK ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive (0 ms) 20: [ RUN ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup 20: [ OK ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) 20: [ RUN ] DensityFittingOptionsTest.InternalsToKvt 20: [ OK ] DensityFittingOptionsTest.InternalsToKvt (0 ms) 20: [ RUN ] DensityFittingOptionsTest.KvtToInternal 20: [ OK ] DensityFittingOptionsTest.KvtToInternal (0 ms) 20: [ RUN ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent 20: [ OK ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent (0 ms) 20: [----------] 8 tests from DensityFittingOptionsTest (0 ms total) 20: 20: [----------] Global test environment tear-down 20: [==========] 18 tests from 4 test suites ran. (1 ms total) 20: [ PASSED ] 18 tests. 20/94 Test #20: DensityFittingAppliedForcesUnitTest .......... Passed 0.38 sec test 21 Start 21: QMMMAppliedForcesUnitTest 21: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/qmmm_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/QMMMAppliedForcesUnitTest.xml" 21: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests 21: Test timeout computed to be: 30 21: [==========] Running 21 tests from 5 test suites. 21: [----------] Global test environment set-up. 21: [----------] 3 tests from QMMMInputGeneratorTest 21: [ RUN ] QMMMInputGeneratorTest.CanConstruct 21: [ OK ] QMMMInputGeneratorTest.CanConstruct (0 ms) 21: [ RUN ] QMMMInputGeneratorTest.TwoWatersPBENoLink 21: [ OK ] QMMMInputGeneratorTest.TwoWatersPBENoLink (0 ms) 21: [ RUN ] QMMMInputGeneratorTest.TwoWatersPBEWithLink 21: [ OK ] QMMMInputGeneratorTest.TwoWatersPBEWithLink (0 ms) 21: [----------] 3 tests from QMMMInputGeneratorTest (0 ms total) 21: 21: [----------] 7 tests from QMMMTopologyPreprocessorTest 21: [ RUN ] QMMMTopologyPreprocessorTest.CanConstruct 21: [ OK ] QMMMTopologyPreprocessorTest.CanConstruct (0 ms) 21: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Generating 1-4 interactions: fudge = 0.5 21: Number of degrees of freedom in T-Coupling group rest is 21.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 21: NVE simulation with an initial temperature of zero: will use a Verlet 21: buffer of 10%. Check your energy drift! 21: 21: 21: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 21: You are using a plain Coulomb cut-off, which might produce artifacts. 21: You might want to consider using PME electrostatics. 21: 21: 21: 21: There were 3 NOTEs 21: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 21: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 21: Setting the LD random seed to -2577 21: 21: Generated 10 of the 10 non-bonded parameter combinations 21: 21: Generated 10 of the 10 1-4 parameter combinations 21: 21: Excluding 2 bonded neighbours molecule type 'SOL' 21: 21: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 21: Analysing residue names: 21: There are: 4 Water residues 21: 21: This run will generate roughly 0 Mb of data 21: [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink (10 ms) 21: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Generating 1-4 interactions: fudge = 0.5 21: Number of degrees of freedom in T-Coupling group rest is 21.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 21: NVE simulation with an initial temperature of zero: will use a Verlet 21: buffer of 10%. Check your energy drift! 21: 21: 21: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 21: You are using a plain Coulomb cut-off, which might produce artifacts. 21: You might want to consider using PME electrostatics. 21: 21: 21: 21: There were 3 NOTEs 21: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 21: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 21: Setting the LD random seed to -67191921 21: 21: Generated 10 of the 10 non-bonded parameter combinations 21: 21: Generated 10 of the 10 1-4 parameter combinations 21: 21: Excluding 2 bonded neighbours molecule type 'SOL' 21: 21: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 21: Analysing residue names: 21: There are: 4 Water residues 21: 21: This run will generate roughly 0 Mb of data 21: [ OK ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink (5 ms) 21: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Generating 1-4 interactions: fudge = 0.5 21: Number of degrees of freedom in T-Coupling group rest is 21.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 21: NVE simulation with an initial temperature of zero: will use a Verlet 21: buffer of 10%. Check your energy drift! 21: 21: 21: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 21: You are using a plain Coulomb cut-off, which might produce artifacts. 21: You might want to consider using PME electrostatics. 21: 21: 21: 21: There were 3 NOTEs 21: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 21: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 21: Setting the LD random seed to -1080181157 21: 21: Generated 10 of the 10 non-bonded parameter combinations 21: 21: Generated 10 of the 10 1-4 parameter combinations 21: 21: Excluding 2 bonded neighbours molecule type 'SOL' 21: 21: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 21: Analysing residue names: 21: There are: 4 Water residues 21: 21: This run will generate roughly 0 Mb of data 21: [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink (5 ms) 21: [ RUN ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksNoConstraints 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Generating 1-4 interactions: fudge = 0.5 21: Number of degrees of freedom in T-Coupling group rest is 63.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 21: NVE simulation: will use the initial temperature of 129.093 K for 21: determining the Verlet buffer size 21: 21: 21: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 21: You are using a plain Coulomb cut-off, which might produce artifacts. 21: You might want to consider using PME electrostatics. 21: 21: 21: 21: There were 3 NOTEs 21: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 21: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 21: Setting the LD random seed to 1073610742 21: 21: Generated 2145 of the 2145 non-bonded parameter combinations 21: 21: Generated 2145 of the 2145 1-4 parameter combinations 21: 21: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 21: 21: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 21: Analysing residue names: 21: There are: 3 Protein residues 21: Analysing Protein... 21: 21: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 129.093 K 21: 21: Calculated rlist for 1x1 atom pair-list as 1.021 nm, buffer size 0.021 nm 21: 21: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm 21: 21: Note that mdrun will redetermine rlist based on the actual pair-list setup 21: 21: This run will generate roughly 0 Mb of data 21: [ OK ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksNoConstraints (16 ms) 21: [ RUN ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksWithConstraints 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Generating 1-4 interactions: fudge = 0.5 21: 21: NOTE 2 [file unknown]: 21: You are using constraints on all bonds, whereas the forcefield has been 21: parametrized only with constraints involving hydrogen atoms. We suggest 21: using constraints = h-bonds instead, this will also improve performance. 21: 21: 21: NOTE 3 [file unknown]: 21: For energy conservation with LINCS, lincs_iter should be 2 or larger. 21: 21: 21: Number of degrees of freedom in T-Coupling group rest is 42.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 21: NVE simulation: will use the initial temperature of 193.640 K for 21: determining the Verlet buffer size 21: 21: 21: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 21: You are using a plain Coulomb cut-off, which might produce artifacts. 21: You might want to consider using PME electrostatics. 21: 21: 21: 21: There were 5 NOTEs 21: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 21: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 21: Setting the LD random seed to -4720036 21: 21: Generated 2145 of the 2145 non-bonded parameter combinations 21: 21: Generated 2145 of the 2145 1-4 parameter combinations 21: 21: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 21: 21: turning all bonds into constraints... 21: 21: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 21: Analysing residue names: 21: There are: 3 Protein residues 21: Analysing Protein... 21: 21: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 193.64 K 21: 21: Calculated rlist for 1x1 atom pair-list as 1.023 nm, buffer size 0.023 nm 21: 21: Set rlist, assuming 4x4 atom pair-list, to 1.015 nm, buffer size 0.015 nm 21: 21: Note that mdrun will redetermine rlist based on the actual pair-list setup 21: 21: This run will generate roughly 0 Mb of data 21: [ OK ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksWithConstraints (20 ms) 21: [ RUN ] QMMMTopologyPreprocessorTest.RemovingQMVsites 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Number of degrees of freedom in T-Coupling group rest is 45.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 21: NVE simulation with an initial temperature of zero: will use a Verlet 21: buffer of 10%. Check your energy drift! 21: 21: 21: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 21: You are using a plain Coulomb cut-off, which might produce artifacts. 21: You might want to consider using PME electrostatics. 21: 21: 21: 21: There were 3 NOTEs 21: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 21: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 21: Setting the LD random seed to -67109025 21: 21: Generated 3 of the 6 non-bonded parameter combinations 21: 21: Excluding 3 bonded neighbours molecule type 'VSTEST' 21: 21: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 21: 21: Cleaning up constraints and constant bonded interactions with virtual sites 21: Analysing residue names: 21: There are: 1 Other residues 21: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 21: 21: This run will generate roughly 0 Mb of data 21: [ OK ] QMMMTopologyPreprocessorTest.RemovingQMVsites (6 ms) 21: [----------] 7 tests from QMMMTopologyPreprocessorTest (66 ms total) 21: 21: [----------] 9 tests from QMMMOptionsTest 21: [ RUN ] QMMMOptionsTest.DefaultParameters 21: [ OK ] QMMMOptionsTest.DefaultParameters (0 ms) 21: [ RUN ] QMMMOptionsTest.OptionSetsActive 21: [ OK ] QMMMOptionsTest.OptionSetsActive (0 ms) 21: [ RUN ] QMMMOptionsTest.OutputNoDefaultValuesWhenInactive 21: [ OK ] QMMMOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 21: [ RUN ] QMMMOptionsTest.OutputDefaultValuesWhenActive 21: [ OK ] QMMMOptionsTest.OutputDefaultValuesWhenActive (0 ms) 21: [ RUN ] QMMMOptionsTest.CanConvertGroupStringToIndexGroup 21: [ OK ] QMMMOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) 21: [ RUN ] QMMMOptionsTest.NoQMGroupConvertGroupStringToIndexGroup 21: [ OK ] QMMMOptionsTest.NoQMGroupConvertGroupStringToIndexGroup (0 ms) 21: [ RUN ] QMMMOptionsTest.EmptyQMGroupConvertGroupStringToIndexGroup 21: [ OK ] QMMMOptionsTest.EmptyQMGroupConvertGroupStringToIndexGroup (0 ms) 21: [ RUN ] QMMMOptionsTest.InternalsToKvtAndBack 21: [ OK ] QMMMOptionsTest.InternalsToKvtAndBack (0 ms) 21: [ RUN ] QMMMOptionsTest.CP2KInputProcessing 21: [ OK ] QMMMOptionsTest.CP2KInputProcessing (0 ms) 21: [----------] 9 tests from QMMMOptionsTest (2 ms total) 21: 21: [----------] 1 test from QMMMForceProviderTest 21: [ RUN ] QMMMForceProviderTest.CanConstructOrNot 21: [ OK ] QMMMForceProviderTest.CanConstructOrNot (0 ms) 21: [----------] 1 test from QMMMForceProviderTest (0 ms total) 21: 21: [----------] 1 test from QMMMTest 21: [ RUN ] QMMMTest.ForceProviderLackingInputThrows 21: [ OK ] QMMMTest.ForceProviderLackingInputThrows (0 ms) 21: [----------] 1 test from QMMMTest (0 ms total) 21: 21: [----------] Global test environment tear-down 21: [==========] 21 tests from 5 test suites ran. (68 ms total) 21: [ PASSED ] 21 tests. 21/94 Test #21: QMMMAppliedForcesUnitTest .................... Passed 0.45 sec test 22 Start 22: ColvarsAppliedForcesUnitTest 22: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/colvars_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/ColvarsAppliedForcesUnitTest.xml" 22: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests 22: Test timeout computed to be: 30 22: [==========] Running 16 tests from 4 test suites. 22: [----------] Global test environment set-up. 22: [----------] 1 test from ColvarsTest 22: [ RUN ] ColvarsTest.ForceProviderLackingInputThrows 22: [ OK ] ColvarsTest.ForceProviderLackingInputThrows (0 ms) 22: [----------] 1 test from ColvarsTest (0 ms total) 22: 22: [----------] 6 tests from ColvarsOptionsTest 22: [ RUN ] ColvarsOptionsTest.OutputNoDefaultValuesWhenInactive 22: [ OK ] ColvarsOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 22: [ RUN ] ColvarsOptionsTest.OutputDefaultValuesWhenActive 22: [ OK ] ColvarsOptionsTest.OutputDefaultValuesWhenActive (0 ms) 22: [ RUN ] ColvarsOptionsTest.OutputValuesWhenActive 22: [ OK ] ColvarsOptionsTest.OutputValuesWhenActive (0 ms) 22: [ RUN ] ColvarsOptionsTest.OptionSetsActive 22: [ OK ] ColvarsOptionsTest.OptionSetsActive (0 ms) 22: [ RUN ] ColvarsOptionsTest.InternalsToKvtAndBack 22: 22: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 22: For a correct single-point energy evaluation with nsteps = 0, use 22: continuation = yes to avoid constraining the input coordinates. 22: 22: Generating 1-4 interactions: fudge = 0.5 22: Number of degrees of freedom in T-Coupling group rest is 21.00 22: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 22: 22: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 22: NVE simulation with an initial temperature of zero: will use a Verlet 22: buffer of 10%. Check your energy drift! 22: 22: 22: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 22: You are using a plain Coulomb cut-off, which might produce artifacts. 22: You might want to consider using PME electrostatics. 22: 22: 22: 22: There were 3 NOTEs 22: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 22: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 22: Setting the LD random seed to -287885578 22: 22: Generated 10 of the 10 non-bonded parameter combinations 22: 22: Generated 10 of the 10 1-4 parameter combinations 22: 22: Excluding 2 bonded neighbours molecule type 'SOL' 22: 22: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 22: Analysing residue names: 22: There are: 4 Water residues 22: 22: This run will generate roughly 0 Mb of data 22: [ OK ] ColvarsOptionsTest.InternalsToKvtAndBack (12 ms) 22: [ RUN ] ColvarsOptionsTest.RetrieveEdrFilename 22: [ OK ] ColvarsOptionsTest.RetrieveEdrFilename (0 ms) 22: [----------] 6 tests from ColvarsOptionsTest (13 ms total) 22: 22: [----------] 4 tests from ColvarsPreProcessorTest 22: [ RUN ] ColvarsPreProcessorTest.CanConstructColvarsPreProcess 22: 22: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 22: For a correct single-point energy evaluation with nsteps = 0, use 22: continuation = yes to avoid constraining the input coordinates. 22: 22: Generating 1-4 interactions: fudge = 0.5 22: Number of degrees of freedom in T-Coupling group rest is 21.00 22: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 22: 22: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 22: NVE simulation with an initial temperature of zero: will use a Verlet 22: buffer of 10%. Check your energy drift! 22: 22: 22: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 22: You are using a plain Coulomb cut-off, which might produce artifacts. 22: You might want to consider using PME electrostatics. 22: 22: 22: 22: There were 3 NOTEs 22: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 22: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 22: Setting the LD random seed to -356993162 22: 22: Generated 10 of the 10 non-bonded parameter combinations 22: 22: Generated 10 of the 10 1-4 parameter combinations 22: 22: Excluding 2 bonded neighbours molecule type 'SOL' 22: 22: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 22: Analysing residue names: 22: There are: 4 Water residues 22: 22: This run will generate roughly 0 Mb of data 22: [ OK ] ColvarsPreProcessorTest.CanConstructColvarsPreProcess (6 ms) 22: [ RUN ] ColvarsPreProcessorTest.CheckValuesFourWaters 22: 22: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 22: For a correct single-point energy evaluation with nsteps = 0, use 22: continuation = yes to avoid constraining the input coordinates. 22: 22: Generating 1-4 interactions: fudge = 0.5 22: Number of degrees of freedom in T-Coupling group rest is 21.00 22: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 22: 22: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 22: NVE simulation with an initial temperature of zero: will use a Verlet 22: buffer of 10%. Check your energy drift! 22: 22: 22: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 22: You are using a plain Coulomb cut-off, which might produce artifacts. 22: You might want to consider using PME electrostatics. 22: 22: 22: 22: There were 3 NOTEs 22: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 22: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 22: Setting the LD random seed to -625953 22: 22: Generated 10 of the 10 non-bonded parameter combinations 22: 22: Generated 10 of the 10 1-4 parameter combinations 22: 22: Excluding 2 bonded neighbours molecule type 'SOL' 22: 22: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 22: Analysing residue names: 22: There are: 4 Water residues 22: 22: This run will generate roughly 0 Mb of data 22: [ OK ] ColvarsPreProcessorTest.CheckValuesFourWaters (7 ms) 22: [ RUN ] ColvarsPreProcessorTest.CheckNestedInputFiles 22: 22: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 22: For a correct single-point energy evaluation with nsteps = 0, use 22: continuation = yes to avoid constraining the input coordinates. 22: 22: Generating 1-4 interactions: fudge = 0.5 22: Number of degrees of freedom in T-Coupling group rest is 21.00 22: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 22: 22: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 22: NVE simulation with an initial temperature of zero: will use a Verlet 22: buffer of 10%. Check your energy drift! 22: 22: 22: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 22: You are using a plain Coulomb cut-off, which might produce artifacts. 22: You might want to consider using PME electrostatics. 22: 22: 22: 22: There were 3 NOTEs 22: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 22: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 22: Setting the LD random seed to -2022703153 22: 22: Generated 10 of the 10 non-bonded parameter combinations 22: 22: Generated 10 of the 10 1-4 parameter combinations 22: 22: Excluding 2 bonded neighbours molecule type 'SOL' 22: 22: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 22: Analysing residue names: 22: There are: 4 Water residues 22: 22: This run will generate roughly 0 Mb of data 22: [ OK ] ColvarsPreProcessorTest.CheckNestedInputFiles (7 ms) 22: [ RUN ] ColvarsPreProcessorTest.WrongColvarsInput 22: 22: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 22: For a correct single-point energy evaluation with nsteps = 0, use 22: continuation = yes to avoid constraining the input coordinates. 22: 22: Generating 1-4 interactions: fudge = 0.5 22: Number of degrees of freedom in T-Coupling group rest is 21.00 22: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 22: 22: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 22: NVE simulation with an initial temperature of zero: will use a Verlet 22: buffer of 10%. Check your energy drift! 22: 22: 22: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 22: You are using a plain Coulomb cut-off, which might produce artifacts. 22: You might want to consider using PME electrostatics. 22: 22: 22: 22: There were 3 NOTEs 22: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 22: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 22: Setting the LD random seed to 1911685054 22: 22: Generated 10 of the 10 non-bonded parameter combinations 22: 22: Generated 10 of the 10 1-4 parameter combinations 22: 22: Excluding 2 bonded neighbours molecule type 'SOL' 22: 22: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 22: Analysing residue names: 22: There are: 4 Water residues 22: 22: This run will generate roughly 0 Mb of data 22: [ OK ] ColvarsPreProcessorTest.WrongColvarsInput (7 ms) 22: [----------] 4 tests from ColvarsPreProcessorTest (28 ms total) 22: 22: [----------] 5 tests from ColvarsForceProviderTest 22: [ RUN ] ColvarsForceProviderTest.CanConstructOrNot 22: [ OK ] ColvarsForceProviderTest.CanConstructOrNot (1 ms) 22: [ RUN ] ColvarsForceProviderTest.SimpleInputs 22: 22: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 22: For a correct single-point energy evaluation with nsteps = 0, use 22: continuation = yes to avoid constraining the input coordinates. 22: 22: Generating 1-4 interactions: fudge = 0.5 22: Number of degrees of freedom in T-Coupling group rest is 21.00 22: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 22: 22: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 22: NVE simulation with an initial temperature of zero: will use a Verlet 22: buffer of 10%. Check your energy drift! 22: 22: 22: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 22: You are using a plain Coulomb cut-off, which might produce artifacts. 22: You might want to consider using PME electrostatics. 22: 22: 22: 22: There were 3 NOTEs 22: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 22: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 22: Setting the LD random seed to -647565345 22: 22: Generated 10 of the 10 non-bonded parameter combinations 22: 22: Generated 10 of the 10 1-4 parameter combinations 22: 22: Excluding 2 bonded neighbours molecule type 'SOL' 22: 22: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 22: Analysing residue names: 22: There are: 4 Water residues 22: 22: This run will generate roughly 0 Mb of data 22: [ OK ] ColvarsForceProviderTest.SimpleInputs (9 ms) 22: [ RUN ] ColvarsForceProviderTest.WrongColvarsInput 22: 22: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 22: For a correct single-point energy evaluation with nsteps = 0, use 22: continuation = yes to avoid constraining the input coordinates. 22: 22: Generating 1-4 interactions: fudge = 0.5 22: Number of degrees of freedom in T-Coupling group rest is 21.00 22: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 22: 22: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 22: NVE simulation with an initial temperature of zero: will use a Verlet 22: buffer of 10%. Check your energy drift! 22: 22: 22: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 22: You are using a plain Coulomb cut-off, which might produce artifacts. 22: You might want to consider using PME electrostatics. 22: 22: 22: 22: There were 3 NOTEs 22: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 22: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 22: Setting the LD random seed to 938977257 22: 22: Generated 10 of the 10 non-bonded parameter combinations 22: 22: Generated 10 of the 10 1-4 parameter combinations 22: 22: Excluding 2 bonded neighbours molecule type 'SOL' 22: 22: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 22: Analysing residue names: 22: There are: 4 Water residues 22: 22: This run will generate roughly 0 Mb of data 22: [ OK ] ColvarsForceProviderTest.WrongColvarsInput (5 ms) 22: [ RUN ] ColvarsForceProviderTest.CalculateForces4water 22: 22: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 22: For a correct single-point energy evaluation with nsteps = 0, use 22: continuation = yes to avoid constraining the input coordinates. 22: 22: Generating 1-4 interactions: fudge = 0.5 22: Number of degrees of freedom in T-Coupling group rest is 21.00 22: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 22: 22: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 22: NVE simulation with an initial temperature of zero: will use a Verlet 22: buffer of 10%. Check your energy drift! 22: 22: 22: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 22: You are using a plain Coulomb cut-off, which might produce artifacts. 22: You might want to consider using PME electrostatics. 22: 22: 22: 22: There were 3 NOTEs 22: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 22: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 22: Setting the LD random seed to -323780757 22: 22: Generated 10 of the 10 non-bonded parameter combinations 22: 22: Generated 10 of the 10 1-4 parameter combinations 22: 22: Excluding 2 bonded neighbours molecule type 'SOL' 22: 22: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 22: Analysing residue names: 22: There are: 4 Water residues 22: 22: This run will generate roughly 0 Mb of data 22: [ OK ] ColvarsForceProviderTest.CalculateForces4water (48 ms) 22: [ RUN ] ColvarsForceProviderTest.CalculateForcesAlanine 22: 22: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 22: For a correct single-point energy evaluation with nsteps = 0, use 22: continuation = yes to avoid constraining the input coordinates. 22: 22: Generating 1-4 interactions: fudge = 0.5 22: Number of degrees of freedom in T-Coupling group rest is 66.00 22: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 22: 22: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 22: NVE simulation: will use the initial temperature of 300.368 K for 22: determining the Verlet buffer size 22: 22: 22: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 22: You are using a plain Coulomb cut-off, which might produce artifacts. 22: You might want to consider using PME electrostatics. 22: 22: 22: 22: There were 3 NOTEs 22: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 22: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 22: Setting the LD random seed to -1109918866 22: 22: Generated 2211 of the 2211 non-bonded parameter combinations 22: 22: Generated 2211 of the 2211 1-4 parameter combinations 22: 22: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 22: 22: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 22: Analysing residue names: 22: There are: 2 Protein residues 22: Analysing Protein... 22: 22: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 22: 22: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 22: 22: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 22: 22: Note that mdrun will redetermine rlist based on the actual pair-list setup 22: 22: This run will generate roughly 0 Mb of data 22: [ OK ] ColvarsForceProviderTest.CalculateForcesAlanine (79 ms) 22: [----------] 5 tests from ColvarsForceProviderTest (145 ms total) 22: 22: [----------] Global test environment tear-down 22: [==========] 16 tests from 4 test suites ran. (187 ms total) 22: [ PASSED ] 16 tests. 22/94 Test #22: ColvarsAppliedForcesUnitTest ................. Passed 0.55 sec test 23 Start 23: NNPotAppliedForcesUnitTest 23: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/nnpot_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/NNPotAppliedForcesUnitTest.xml" 23: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/nnpot/tests 23: Test timeout computed to be: 30 23: [==========] Running 12 tests from 4 test suites. 23: [----------] Global test environment set-up. 23: [----------] 1 test from NNPotTest 23: [ RUN ] NNPotTest.ForceProviderLackingInputThrows 23: [ OK ] NNPotTest.ForceProviderLackingInputThrows (0 ms) 23: [----------] 1 test from NNPotTest (0 ms total) 23: 23: [----------] 5 tests from NNPotOptionsTest 23: [ RUN ] NNPotOptionsTest.DefaultParameters 23: [ OK ] NNPotOptionsTest.DefaultParameters (0 ms) 23: [ RUN ] NNPotOptionsTest.OptionSetsActive 23: [ OK ] NNPotOptionsTest.OptionSetsActive (0 ms) 23: [ RUN ] NNPotOptionsTest.OutputNoDefaultValuesWhenInactive 23: [ OK ] NNPotOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 23: [ RUN ] NNPotOptionsTest.OutputDefaultValuesWhenActive 23: [ OK ] NNPotOptionsTest.OutputDefaultValuesWhenActive (0 ms) 23: [ RUN ] NNPotOptionsTest.InternalsToKvtAndBack 23: [ OK ] NNPotOptionsTest.InternalsToKvtAndBack (0 ms) 23: [----------] 5 tests from NNPotOptionsTest (0 ms total) 23: 23: [----------] 5 tests from NNPotTopologyPreprocessorTest 23: [ RUN ] NNPotTopologyPreprocessorTest.CanConstruct 23: [ OK ] NNPotTopologyPreprocessorTest.CanConstruct (0 ms) 23: [ RUN ] NNPotTopologyPreprocessorTest.FourWatersFirstInQMRegion 23: 23: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.mdp]: 23: For a correct single-point energy evaluation with nsteps = 0, use 23: continuation = yes to avoid constraining the input coordinates. 23: 23: Generating 1-4 interactions: fudge = 0.5 23: Number of degrees of freedom in T-Coupling group rest is 21.00 23: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 23: 23: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.mdp]: 23: NVE simulation with an initial temperature of zero: will use a Verlet 23: buffer of 10%. Check your energy drift! 23: 23: 23: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.mdp]: 23: You are using a plain Coulomb cut-off, which might produce artifacts. 23: You might want to consider using PME electrostatics. 23: 23: 23: 23: There were 3 NOTEs 23: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 23: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersFirstInQMRegion_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 23: Setting the LD random seed to -275547075 23: 23: Generated 10 of the 10 non-bonded parameter combinations 23: 23: Generated 10 of the 10 1-4 parameter combinations 23: 23: Excluding 2 bonded neighbours molecule type 'SOL' 23: 23: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 23: Analysing residue names: 23: There are: 4 Water residues 23: 23: This run will generate roughly 0 Mb of data 23: [ OK ] NNPotTopologyPreprocessorTest.FourWatersFirstInQMRegion (21 ms) 23: [ RUN ] NNPotTopologyPreprocessorTest.FourWatersSecondAndFourthInQMRegion 23: 23: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.mdp]: 23: For a correct single-point energy evaluation with nsteps = 0, use 23: continuation = yes to avoid constraining the input coordinates. 23: 23: Generating 1-4 interactions: fudge = 0.5 23: Number of degrees of freedom in T-Coupling group rest is 21.00 23: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 23: 23: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.mdp]: 23: NVE simulation with an initial temperature of zero: will use a Verlet 23: buffer of 10%. Check your energy drift! 23: 23: 23: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.mdp]: 23: You are using a plain Coulomb cut-off, which might produce artifacts. 23: You might want to consider using PME electrostatics. 23: 23: 23: 23: There were 3 NOTEs 23: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 23: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInQMRegion_4water.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 23: Setting the LD random seed to -277022723 23: 23: Generated 10 of the 10 non-bonded parameter combinations 23: 23: Generated 10 of the 10 1-4 parameter combinations 23: 23: Excluding 2 bonded neighbours molecule type 'SOL' 23: 23: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 23: Analysing residue names: 23: There are: 4 Water residues 23: 23: This run will generate roughly 0 Mb of data 23: [ OK ] NNPotTopologyPreprocessorTest.FourWatersSecondAndFourthInQMRegion (12 ms) 23: [ RUN ] NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsNoConstraints 23: 23: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.mdp]: 23: For a correct single-point energy evaluation with nsteps = 0, use 23: continuation = yes to avoid constraining the input coordinates. 23: 23: Generating 1-4 interactions: fudge = 0.5 23: Number of degrees of freedom in T-Coupling group rest is 63.00 23: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 23: 23: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.mdp]: 23: NVE simulation: will use the initial temperature of 129.093 K for 23: determining the Verlet buffer size 23: 23: 23: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.mdp]: 23: You are using a plain Coulomb cut-off, which might produce artifacts. 23: You might want to consider using PME electrostatics. 23: 23: 23: 23: There were 3 NOTEs 23: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 23: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_alanine_vacuo.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 23: Setting the LD random seed to -1485604993 23: 23: Generated 2145 of the 2145 non-bonded parameter combinations 23: 23: Generated 2145 of the 2145 1-4 parameter combinations 23: 23: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 23: 23: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 23: Analysing residue names: 23: There are: 3 Protein residues 23: Analysing Protein... 23: 23: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 129.093 K 23: 23: Calculated rlist for 1x1 atom pair-list as 1.021 nm, buffer size 0.021 nm 23: 23: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm 23: 23: Note that mdrun will redetermine rlist based on the actual pair-list setup 23: 23: This run will generate roughly 0 Mb of data 23: [ OK ] NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsNoConstraints (94 ms) 23: [ RUN ] NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsWithConstraints 23: 23: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.mdp]: 23: For a correct single-point energy evaluation with nsteps = 0, use 23: continuation = yes to avoid constraining the input coordinates. 23: 23: Generating 1-4 interactions: fudge = 0.5 23: 23: NOTE 2 [file unknown]: 23: You are using constraints on all bonds, whereas the forcefield has been 23: parametrized only with constraints involving hydrogen atoms. We suggest 23: using constraints = h-bonds instead, this will also improve performance. 23: 23: 23: NOTE 3 [file unknown]: 23: For energy conservation with LINCS, lincs_iter should be 2 or larger. 23: 23: 23: Number of degrees of freedom in T-Coupling group rest is 42.00 23: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 23: 23: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.mdp]: 23: NVE simulation: will use the initial temperature of 193.640 K for 23: determining the Verlet buffer size 23: 23: 23: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.mdp]: 23: You are using a plain Coulomb cut-off, which might produce artifacts. 23: You might want to consider using PME electrostatics. 23: 23: 23: 23: There were 5 NOTEs 23: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 23: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_alanine_vacuo.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 23: Setting the LD random seed to -438829377 23: 23: Generated 2145 of the 2145 non-bonded parameter combinations 23: 23: Generated 2145 of the 2145 1-4 parameter combinations 23: 23: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 23: 23: turning all bonds into constraints... 23: 23: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 23: Analysing residue names: 23: There are: 3 Protein residues 23: Analysing Protein... 23: 23: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 193.64 K 23: 23: Calculated rlist for 1x1 atom pair-list as 1.023 nm, buffer size 0.023 nm 23: 23: Set rlist, assuming 4x4 atom pair-list, to 1.015 nm, buffer size 0.015 nm 23: 23: Note that mdrun will redetermine rlist based on the actual pair-list setup 23: 23: This run will generate roughly 0 Mb of data 23: [ OK ] NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsWithConstraints (52 ms) 23: [----------] 5 tests from NNPotTopologyPreprocessorTest (181 ms total) 23: 23: [----------] 1 test from NNPotForceProviderTest 23: [ RUN ] NNPotForceProviderTest.CanConstruct 23: [ OK ] NNPotForceProviderTest.CanConstruct (0 ms) 23: [----------] 1 test from NNPotForceProviderTest (0 ms total) 23: 23: [----------] Global test environment tear-down 23: [==========] 12 tests from 4 test suites ran. (182 ms total) 23: [ PASSED ] 12 tests. 23/94 Test #23: NNPotAppliedForcesUnitTest ................... Passed 0.58 sec test 24 Start 24: AppliedForcesUnitTest 24: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/AppliedForcesUnitTest.xml" 24: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/applied_forces/tests 24: Test timeout computed to be: 30 24: [==========] Running 3 tests from 1 test suite. 24: [----------] Global test environment set-up. 24: [----------] 3 tests from ElectricFieldTest 24: [ RUN ] ElectricFieldTest.Static 24: [ OK ] ElectricFieldTest.Static (0 ms) 24: [ RUN ] ElectricFieldTest.Oscillating 24: [ OK ] ElectricFieldTest.Oscillating (0 ms) 24: [ RUN ] ElectricFieldTest.Pulsed 24: [ OK ] ElectricFieldTest.Pulsed (0 ms) 24: [----------] 3 tests from ElectricFieldTest (0 ms total) 24: 24: [----------] Global test environment tear-down 24: [==========] 3 tests from 1 test suite ran. (0 ms total) 24: [ PASSED ] 3 tests. 24/94 Test #24: AppliedForcesUnitTest ........................ Passed 0.35 sec test 25 Start 25: ListedForcesTest 25: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/listed_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/ListedForcesTest.xml" 25: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/listed_forces/tests 25: Test timeout computed to be: 30 25: [==========] Running 132 tests from 9 test suites. 25: [----------] Global test environment set-up. 25: [----------] 24 tests from Bond/ListedForcesTest 25: [ RUN ] Bond/ListedForcesTest.Ifunc/0 25: [ OK ] Bond/ListedForcesTest.Ifunc/0 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/1 25: [ OK ] Bond/ListedForcesTest.Ifunc/1 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/2 25: [ OK ] Bond/ListedForcesTest.Ifunc/2 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/3 25: [ OK ] Bond/ListedForcesTest.Ifunc/3 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/4 25: [ OK ] Bond/ListedForcesTest.Ifunc/4 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/5 25: [ OK ] Bond/ListedForcesTest.Ifunc/5 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/6 25: [ OK ] Bond/ListedForcesTest.Ifunc/6 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/7 25: [ OK ] Bond/ListedForcesTest.Ifunc/7 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/8 25: [ OK ] Bond/ListedForcesTest.Ifunc/8 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/9 25: [ OK ] Bond/ListedForcesTest.Ifunc/9 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/10 25: [ OK ] Bond/ListedForcesTest.Ifunc/10 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/11 25: [ OK ] Bond/ListedForcesTest.Ifunc/11 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/12 25: [ OK ] Bond/ListedForcesTest.Ifunc/12 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/13 25: [ OK ] Bond/ListedForcesTest.Ifunc/13 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/14 25: [ OK ] Bond/ListedForcesTest.Ifunc/14 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/15 25: [ OK ] Bond/ListedForcesTest.Ifunc/15 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/16 25: [ OK ] Bond/ListedForcesTest.Ifunc/16 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/17 25: [ OK ] Bond/ListedForcesTest.Ifunc/17 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/18 25: [ OK ] Bond/ListedForcesTest.Ifunc/18 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/19 25: [ OK ] Bond/ListedForcesTest.Ifunc/19 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/20 25: [ OK ] Bond/ListedForcesTest.Ifunc/20 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/21 25: [ OK ] Bond/ListedForcesTest.Ifunc/21 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/22 25: [ OK ] Bond/ListedForcesTest.Ifunc/22 (0 ms) 25: [ RUN ] Bond/ListedForcesTest.Ifunc/23 25: [ OK ] Bond/ListedForcesTest.Ifunc/23 (0 ms) 25: [----------] 24 tests from Bond/ListedForcesTest (8 ms total) 25: 25: [----------] 33 tests from Angle/ListedForcesTest 25: [ RUN ] Angle/ListedForcesTest.Ifunc/0 25: [ OK ] Angle/ListedForcesTest.Ifunc/0 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/1 25: [ OK ] Angle/ListedForcesTest.Ifunc/1 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/2 25: [ OK ] Angle/ListedForcesTest.Ifunc/2 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/3 25: [ OK ] Angle/ListedForcesTest.Ifunc/3 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/4 25: [ OK ] Angle/ListedForcesTest.Ifunc/4 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/5 25: [ OK ] Angle/ListedForcesTest.Ifunc/5 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/6 25: [ OK ] Angle/ListedForcesTest.Ifunc/6 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/7 25: [ OK ] Angle/ListedForcesTest.Ifunc/7 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/8 25: [ OK ] Angle/ListedForcesTest.Ifunc/8 (5 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/9 25: [ OK ] Angle/ListedForcesTest.Ifunc/9 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/10 25: [ OK ] Angle/ListedForcesTest.Ifunc/10 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/11 25: [ OK ] Angle/ListedForcesTest.Ifunc/11 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/12 25: [ OK ] Angle/ListedForcesTest.Ifunc/12 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/13 25: [ OK ] Angle/ListedForcesTest.Ifunc/13 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/14 25: [ OK ] Angle/ListedForcesTest.Ifunc/14 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/15 25: [ OK ] Angle/ListedForcesTest.Ifunc/15 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/16 25: [ OK ] Angle/ListedForcesTest.Ifunc/16 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/17 25: [ OK ] Angle/ListedForcesTest.Ifunc/17 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/18 25: [ OK ] Angle/ListedForcesTest.Ifunc/18 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/19 25: [ OK ] Angle/ListedForcesTest.Ifunc/19 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/20 25: [ OK ] Angle/ListedForcesTest.Ifunc/20 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/21 25: [ OK ] Angle/ListedForcesTest.Ifunc/21 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/22 25: [ OK ] Angle/ListedForcesTest.Ifunc/22 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/23 25: [ OK ] Angle/ListedForcesTest.Ifunc/23 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/24 25: [ OK ] Angle/ListedForcesTest.Ifunc/24 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/25 25: [ OK ] Angle/ListedForcesTest.Ifunc/25 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/26 25: [ OK ] Angle/ListedForcesTest.Ifunc/26 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/27 25: [ OK ] Angle/ListedForcesTest.Ifunc/27 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/28 25: [ OK ] Angle/ListedForcesTest.Ifunc/28 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/29 25: [ OK ] Angle/ListedForcesTest.Ifunc/29 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/30 25: [ OK ] Angle/ListedForcesTest.Ifunc/30 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/31 25: [ OK ] Angle/ListedForcesTest.Ifunc/31 (0 ms) 25: [ RUN ] Angle/ListedForcesTest.Ifunc/32 25: [ OK ] Angle/ListedForcesTest.Ifunc/32 (0 ms) 25: [----------] 33 tests from Angle/ListedForcesTest (11 ms total) 25: 25: [----------] 18 tests from Dihedral/ListedForcesTest 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/0 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/0 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/1 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/1 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/2 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/2 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/3 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/3 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/4 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/4 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/5 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/5 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/6 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/6 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/7 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/7 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/8 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/8 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/9 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/9 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/10 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/10 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/11 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/11 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/12 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/12 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/13 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/13 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/14 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/14 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/15 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/15 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/16 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/16 (0 ms) 25: [ RUN ] Dihedral/ListedForcesTest.Ifunc/17 25: [ OK ] Dihedral/ListedForcesTest.Ifunc/17 (0 ms) 25: [----------] 18 tests from Dihedral/ListedForcesTest (3 ms total) 25: 25: [----------] 12 tests from Polarize/ListedForcesTest 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/0 25: [ OK ] Polarize/ListedForcesTest.Ifunc/0 (0 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/1 25: [ OK ] Polarize/ListedForcesTest.Ifunc/1 (0 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/2 25: [ OK ] Polarize/ListedForcesTest.Ifunc/2 (0 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/3 25: [ OK ] Polarize/ListedForcesTest.Ifunc/3 (0 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/4 25: [ OK ] Polarize/ListedForcesTest.Ifunc/4 (0 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/5 25: [ OK ] Polarize/ListedForcesTest.Ifunc/5 (0 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/6 25: [ OK ] Polarize/ListedForcesTest.Ifunc/6 (0 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/7 25: [ OK ] Polarize/ListedForcesTest.Ifunc/7 (0 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/8 25: [ OK ] Polarize/ListedForcesTest.Ifunc/8 (0 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/9 25: [ OK ] Polarize/ListedForcesTest.Ifunc/9 (0 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/10 25: [ OK ] Polarize/ListedForcesTest.Ifunc/10 (0 ms) 25: [ RUN ] Polarize/ListedForcesTest.Ifunc/11 25: [ OK ] Polarize/ListedForcesTest.Ifunc/11 (0 ms) 25: [----------] 12 tests from Polarize/ListedForcesTest (1 ms total) 25: 25: [----------] 18 tests from Restraints/ListedForcesTest 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/0 25: [ OK ] Restraints/ListedForcesTest.Ifunc/0 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/1 25: [ OK ] Restraints/ListedForcesTest.Ifunc/1 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/2 25: [ OK ] Restraints/ListedForcesTest.Ifunc/2 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/3 25: [ OK ] Restraints/ListedForcesTest.Ifunc/3 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/4 25: [ OK ] Restraints/ListedForcesTest.Ifunc/4 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/5 25: [ OK ] Restraints/ListedForcesTest.Ifunc/5 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/6 25: [ OK ] Restraints/ListedForcesTest.Ifunc/6 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/7 25: [ OK ] Restraints/ListedForcesTest.Ifunc/7 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/8 25: [ OK ] Restraints/ListedForcesTest.Ifunc/8 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/9 25: [ OK ] Restraints/ListedForcesTest.Ifunc/9 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/10 25: [ OK ] Restraints/ListedForcesTest.Ifunc/10 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/11 25: [ OK ] Restraints/ListedForcesTest.Ifunc/11 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/12 25: [ OK ] Restraints/ListedForcesTest.Ifunc/12 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/13 25: [ OK ] Restraints/ListedForcesTest.Ifunc/13 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/14 25: [ OK ] Restraints/ListedForcesTest.Ifunc/14 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/15 25: [ OK ] Restraints/ListedForcesTest.Ifunc/15 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/16 25: [ OK ] Restraints/ListedForcesTest.Ifunc/16 (0 ms) 25: [ RUN ] Restraints/ListedForcesTest.Ifunc/17 25: [ OK ] Restraints/ListedForcesTest.Ifunc/17 (0 ms) 25: [----------] 18 tests from Restraints/ListedForcesTest (3 ms total) 25: 25: [----------] 3 tests from BondZeroLength/ListedForcesTest 25: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/0 25: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/0 (0 ms) 25: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/1 25: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/1 (0 ms) 25: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/2 25: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/2 (0 ms) 25: [----------] 3 tests from BondZeroLength/ListedForcesTest (0 ms total) 25: 25: [----------] 3 tests from AngleZero/ListedForcesTest 25: [ RUN ] AngleZero/ListedForcesTest.Ifunc/0 25: [ OK ] AngleZero/ListedForcesTest.Ifunc/0 (0 ms) 25: [ RUN ] AngleZero/ListedForcesTest.Ifunc/1 25: [ OK ] AngleZero/ListedForcesTest.Ifunc/1 (0 ms) 25: [ RUN ] AngleZero/ListedForcesTest.Ifunc/2 25: [ OK ] AngleZero/ListedForcesTest.Ifunc/2 (0 ms) 25: [----------] 3 tests from AngleZero/ListedForcesTest (0 ms total) 25: 25: [----------] 12 tests from 14Interaction/ListedForcesPairsTest 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/0 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/0 (0 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/1 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/1 (0 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/2 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/2 (0 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/3 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/3 (0 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/4 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/4 (0 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/5 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/5 (0 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/6 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/6 (0 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/7 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/7 (0 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/8 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/8 (0 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/9 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/9 (0 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/10 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/10 (0 ms) 25: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/11 25: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/11 (0 ms) 25: [----------] 12 tests from 14Interaction/ListedForcesPairsTest (2 ms total) 25: 25: [----------] 9 tests from PosResBasicTest/PositionRestraintsTest 25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/0 25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/0 (0 ms) 25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/1 25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/1 (0 ms) 25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/2 25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/2 (0 ms) 25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/3 25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/3 (0 ms) 25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/4 25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/4 (0 ms) 25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/5 25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/5 (0 ms) 25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/6 25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/6 (0 ms) 25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/7 25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/7 (0 ms) 25: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/8 25: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/8 (0 ms) 25: [----------] 9 tests from PosResBasicTest/PositionRestraintsTest (0 ms total) 25: 25: [----------] Global test environment tear-down 25: [==========] 132 tests from 9 test suites ran. (32 ms total) 25: [ PASSED ] 132 tests. 25/94 Test #25: ListedForcesTest ............................. Passed 0.37 sec test 26 Start 26: NbnxmTests 26: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/nbnxm-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/NbnxmTests.xml" 26: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/nbnxm/tests 26: Test timeout computed to be: 30 26: [==========] Running 383 tests from 4 test suites. 26: [----------] Global test environment set-up. 26: [----------] 18 tests from KernelSetupTest 26: [ RUN ] KernelSetupTest.getCoulombKernelTypeRF 26: [ OK ] KernelSetupTest.getCoulombKernelTypeRF (0 ms) 26: [ RUN ] KernelSetupTest.getCoulombKernelTypeCut 26: [ OK ] KernelSetupTest.getCoulombKernelTypeCut (0 ms) 26: [ RUN ] KernelSetupTest.getCoulombKernelTypeTable 26: [ OK ] KernelSetupTest.getCoulombKernelTypeTable (0 ms) 26: [ RUN ] KernelSetupTest.getCoulombKernelTypeTableTwin 26: [ OK ] KernelSetupTest.getCoulombKernelTypeTableTwin (0 ms) 26: [ RUN ] KernelSetupTest.getCoulombKernelTypeEwald 26: [ OK ] KernelSetupTest.getCoulombKernelTypeEwald (0 ms) 26: [ RUN ] KernelSetupTest.getCoulombKernelTypeEwaldTwin 26: [ OK ] KernelSetupTest.getCoulombKernelTypeEwaldTwin (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomNone 26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomNone (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomPotShift 26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomPotShift (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombLBNone 26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombLBNone (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombLBPotShift 26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombLBPotShift (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombNoneNone 26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombNoneNone (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombNonePotShift 26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombNonePotShift (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutThrows 26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutThrows (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutForceSwitch 26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutForceSwitch (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypePmeGeom 26: [ OK ] KernelSetupTest.getVdwKernelTypePmeGeom (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypePmeNone 26: [ OK ] KernelSetupTest.getVdwKernelTypePmeNone (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutPotSwitch 26: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutPotSwitch (0 ms) 26: [ RUN ] KernelSetupTest.getVdwKernelTypeAllCountThrows 26: [ OK ] KernelSetupTest.getVdwKernelTypeAllCountThrows (0 ms) 26: [----------] 18 tests from KernelSetupTest (0 ms total) 26: 26: [----------] 2 tests from SimdEnergyAccumulatorTest 26: [ RUN ] SimdEnergyAccumulatorTest.SingleEnergyGroupSimd4xM 26: [ OK ] SimdEnergyAccumulatorTest.SingleEnergyGroupSimd4xM (0 ms) 26: [ RUN ] SimdEnergyAccumulatorTest.EnergyGroupsSimd4xM 26: [ OK ] SimdEnergyAccumulatorTest.EnergyGroupsSimd4xM (0 ms) 26: [----------] 2 tests from SimdEnergyAccumulatorTest (0 ms total) 26: 26: [----------] 3 tests from WithParameters/CpuListDiagonalExclusionsTest 26: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/0 26: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/0 (0 ms) 26: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/1 26: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/1 (0 ms) 26: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/2 26: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/2 (0 ms) 26: [----------] 3 tests from WithParameters/CpuListDiagonalExclusionsTest (0 ms total) 26: 26: [----------] 360 tests from Combinations/NbnxmKernelTest 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (4 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombNone (4 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (4 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (4 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwForceSwitch (4 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (4 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (4 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwPotSwitch (4 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (4 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (4 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (4 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (4 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (4 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombNone (4 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (4 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (4 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwForceSwitch (4 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (4 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (4 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwPotSwitch (4 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (4 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (5 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (5 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (4 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (4 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (4 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (4 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (4 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (4 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (4 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (4 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (4 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (4 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (5 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (5 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (4 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (3 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombNone (3 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (3 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (3 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwForceSwitch (4 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (3 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (3 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwPotSwitch (4 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (3 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (4 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (4 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (4 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 26: Analytical Ewald is not implemented for the plain-C kernel, skip this test 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (4 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombNone (3 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (4 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (4 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwForceSwitch (4 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (4 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (4 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwPotSwitch (4 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (4 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (4 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (4 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (4 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:540: Skipped 26: There are no combination rule versions of the plain-C kernel 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (4 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (4 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (4 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (4 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (4 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (4 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (4 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (4 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (4 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (5 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (5 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (4 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombLB 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombLB (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombNone (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwForceSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwPotSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombLB 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombLB (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombNone (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwForceSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (3 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwPotSwitch (3 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (3 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (3 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (3 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (3 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (3 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (3 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (3 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (3 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (3 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (3 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombLB 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombLB (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombNone (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwForceSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwPotSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (3 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (3 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (3 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (3 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: ./src/gromacs/nbnxm/tests/kernel_test.cpp:520: Skipped 26: Cannot test or generate data for 2xNN kernels without suitable SIMD support 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 26: [----------] 360 tests from Combinations/NbnxmKernelTest (614 ms total) 26: 26: [----------] Global test environment tear-down 26: [==========] 383 tests from 4 test suites ran. (615 ms total) 26: [ PASSED ] 185 tests. 26: [ SKIPPED ] 198 tests, listed below: 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 26: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 26/94 Test #26: NbnxmTests ................................... Passed 0.99 sec test 27 Start 27: NbnxmGpuTests 27: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/nbnxm-gpu-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/NbnxmGpuTests.xml" 27: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/nbnxm/tests 27: Test timeout computed to be: 30 27: [==========] Running 0 tests from 0 test suites. 27: [==========] 0 tests from 0 test suites ran. (0 ms total) 27: [ PASSED ] 0 tests. 27/94 Test #27: NbnxmGpuTests ................................ Passed 0.44 sec test 28 Start 28: CommandLineUnitTests 28: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/commandline-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/CommandLineUnitTests.xml" 28: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/commandline/tests 28: Test timeout computed to be: 30 28: [==========] Running 60 tests from 7 test suites. 28: [----------] Global test environment set-up. 28: [----------] 3 tests from CommandLineHelpModuleTest 28: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp 28: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (1 ms) 28: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic 28: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (0 ms) 28: [ RUN ] CommandLineHelpModuleTest.ExportsHelp 28: [ OK ] CommandLineHelpModuleTest.ExportsHelp (27 ms) 28: [----------] 3 tests from CommandLineHelpModuleTest (28 ms total) 28: 28: [----------] 7 tests from CommandLineHelpWriterTest 28: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes 28: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (0 ms) 28: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables 28: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (0 ms) 28: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions 28: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (0 ms) 28: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions 28: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (0 ms) 28: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups 28: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (0 ms) 28: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText 28: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (0 ms) 28: [ RUN ] CommandLineHelpWriterTest.HandlesKnownIssues 28: [ OK ] CommandLineHelpWriterTest.HandlesKnownIssues (0 ms) 28: [----------] 7 tests from CommandLineHelpWriterTest (1 ms total) 28: 28: [----------] 6 tests from CommandLineModuleManagerTest 28: [ RUN ] CommandLineModuleManagerTest.RunsModule 28: [ OK ] CommandLineModuleManagerTest.RunsModule (0 ms) 28: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp 28: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (0 ms) 28: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet 28: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (0 ms) 28: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH 28: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (0 ms) 28: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule 28: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (0 ms) 28: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames 28: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (0 ms) 28: [----------] 6 tests from CommandLineModuleManagerTest (0 ms total) 28: 28: [----------] 13 tests from CommandLineParserTest 28: [ RUN ] CommandLineParserTest.HandlesSingleValues 28: [ OK ] CommandLineParserTest.HandlesSingleValues (0 ms) 28: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument 28: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms) 28: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument 28: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms) 28: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument 28: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (0 ms) 28: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers 28: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (0 ms) 28: [ RUN ] CommandLineParserTest.HandlesString 28: [ OK ] CommandLineParserTest.HandlesString (0 ms) 28: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues 28: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (0 ms) 28: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix 28: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms) 28: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers 28: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms) 28: [ RUN ] CommandLineParserTest.HandlesSkipUnknown 28: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms) 28: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault 28: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms) 28: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments 28: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms) 28: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions 28: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (0 ms) 28: [----------] 13 tests from CommandLineParserTest (0 ms total) 28: 28: [----------] 6 tests from CommandLineProgramContextTest 28: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath 28: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (0 ms) 28: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath 28: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms) 28: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath 28: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (0 ms) 28: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory 28: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms) 28: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink 28: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (0 ms) 28: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink 28: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (0 ms) 28: [----------] 6 tests from CommandLineProgramContextTest (0 ms total) 28: 28: [----------] 3 tests from OutputNamesTest 28: [ RUN ] OutputNamesTest.CanBeSuffixed 28: [ OK ] OutputNamesTest.CanBeSuffixed (0 ms) 28: [ RUN ] OutputNamesTest.HasSuffixFromNoAppend 28: [ OK ] OutputNamesTest.HasSuffixFromNoAppend (0 ms) 28: [ RUN ] OutputNamesTest.CanHavePartNumberAdded 28: [ OK ] OutputNamesTest.CanHavePartNumberAdded (0 ms) 28: [----------] 3 tests from OutputNamesTest (0 ms total) 28: 28: [----------] 22 tests from ParseCommonArgsTest 28: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs 28: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesInt64Args 28: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesRealArgs 28: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesStringArgs 28: [ OK ] ParseCommonArgsTest.ParsesStringArgs (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs 28: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgsToValuesOfSuitableEnum 28: [ OK ] ParseCommonArgsTest.ParsesBooleanArgsToValuesOfSuitableEnum (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs 28: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs 28: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit 28: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs 28: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesFileArgs 28: [ OK ] ParseCommonArgsTest.ParsesFileArgs (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults 28: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName 28: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (0 ms) 28: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension 28: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms) 28: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles 28: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (0 ms) 28: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles 28: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (0 ms) 28: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified 28: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (0 ms) 28: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles 28: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (0 ms) 28: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension 28: Value is /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/commandline/tests/Testing/Temporary/ParseCommonArgsTest_AcceptsUnknownTrajectoryExtension.foo 28: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (0 ms) 28: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile 28: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (0 ms) 28: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName 28: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (1 ms) 28: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs 28: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (0 ms) 28: [----------] 22 tests from ParseCommonArgsTest (4 ms total) 28: 28: [----------] Global test environment tear-down 28: [==========] 60 tests from 7 test suites ran. (37 ms total) 28: [ PASSED ] 60 tests. 28/94 Test #28: CommandLineUnitTests ......................... Passed 0.41 sec test 29 Start 29: DomDecTests 29: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/domdec-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/DomDecTests.xml" 29: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/domdec/tests 29: Test timeout computed to be: 30 29: [==========] Running 9 tests from 2 test suites. 29: [----------] Global test environment set-up. 29: [----------] 7 tests from HashedMap 29: [ RUN ] HashedMap.InsertsFinds 29: [ OK ] HashedMap.InsertsFinds (0 ms) 29: [ RUN ] HashedMap.NegativeKeysWork 29: [ OK ] HashedMap.NegativeKeysWork (0 ms) 29: [ RUN ] HashedMap.InsertsErases 29: [ OK ] HashedMap.InsertsErases (0 ms) 29: [ RUN ] HashedMap.InsertsOrAssigns 29: [ OK ] HashedMap.InsertsOrAssigns (0 ms) 29: [ RUN ] HashedMap.Clears 29: [ OK ] HashedMap.Clears (0 ms) 29: [ RUN ] HashedMap.LinkedEntries 29: [ OK ] HashedMap.LinkedEntries (0 ms) 29: [ RUN ] HashedMap.ResizesTable 29: [ OK ] HashedMap.ResizesTable (0 ms) 29: [----------] 7 tests from HashedMap (0 ms total) 29: 29: [----------] 2 tests from LocalAtomSetManager 29: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet 29: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms) 29: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices 29: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms) 29: [----------] 2 tests from LocalAtomSetManager (0 ms total) 29: 29: [----------] Global test environment tear-down 29: [==========] 9 tests from 2 test suites ran. (0 ms total) 29: [ PASSED ] 9 tests. 29/94 Test #29: DomDecTests .................................. Passed 0.35 sec test 30 Start 30: DomDecMpiTests 30: Test command: /usr/bin/mpiexec "-n" "4" "/build/reproducible-path/gromacs-2025.0/build/mpi/bin/domdec-mpi-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/DomDecMpiTests.xml" 30: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/domdec/tests 30: Test timeout computed to be: 30 30: [==========] Running 4 tests from 1 test suite. 30: [----------] Global test environment set-up. 30: [----------] 4 tests from HaloExchangeTest 30: [ RUN ] HaloExchangeTest.Coordinates1dHaloWith1Pulse 30: [ OK ] HaloExchangeTest.Coordinates1dHaloWith1Pulse (0 ms) 30: [ RUN ] HaloExchangeTest.Coordinates1dHaloWith2Pulses 30: [ OK ] HaloExchangeTest.Coordinates1dHaloWith2Pulses (0 ms) 30: [ RUN ] HaloExchangeTest.Coordinates2dHaloWith1PulseInEachDim 30: [ OK ] HaloExchangeTest.Coordinates2dHaloWith1PulseInEachDim (0 ms) 30: [ RUN ] HaloExchangeTest.Coordinates2dHaloWith2PulsesInDim1 30: [ OK ] HaloExchangeTest.Coordinates2dHaloWith2PulsesInDim1 (0 ms) 30: [----------] 4 tests from HaloExchangeTest (0 ms total) 30: 30: [----------] Global test environment tear-down 30: [==========] 4 tests from 1 test suite ran. (0 ms total) 30: [ PASSED ] 4 tests. 30/94 Test #30: DomDecMpiTests ............................... Passed 0.59 sec test 31 Start 31: EwaldUnitTests 31: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/ewald-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/EwaldUnitTests.xml" 31: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/ewald/tests 31: Test timeout computed to be: 30 31: [==========] Running 407 tests from 9 test suites. 31: [----------] Global test environment set-up. 31: [----------] 6 tests from SeparatePmeRanksPermittedTest 31: [ RUN ] SeparatePmeRanksPermittedTest.ZeroPmeDisableReasons 31: [ OK ] SeparatePmeRanksPermittedTest.ZeroPmeDisableReasons (0 ms) 31: [ RUN ] SeparatePmeRanksPermittedTest.CanBeDisabled 31: [ OK ] SeparatePmeRanksPermittedTest.CanBeDisabled (0 ms) 31: [ RUN ] SeparatePmeRanksPermittedTest.OneDisableReasonFlag 31: [ OK ] SeparatePmeRanksPermittedTest.OneDisableReasonFlag (0 ms) 31: [ RUN ] SeparatePmeRanksPermittedTest.OneDisableReasonText 31: [ OK ] SeparatePmeRanksPermittedTest.OneDisableReasonText (0 ms) 31: [ RUN ] SeparatePmeRanksPermittedTest.TwoDisableReasonText 31: [ OK ] SeparatePmeRanksPermittedTest.TwoDisableReasonText (0 ms) 31: [ RUN ] SeparatePmeRanksPermittedTest.EmptyDisableReasonText 31: [ OK ] SeparatePmeRanksPermittedTest.EmptyDisableReasonText (0 ms) 31: [----------] 6 tests from SeparatePmeRanksPermittedTest (0 ms total) 31: 31: [----------] 108 tests from Pme_SplineAndSpreadTest 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spline (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spline (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spread (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spline (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spline (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spread (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_fused spline and spread (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spline (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spread (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spline (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spread (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_fused spline and spread (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spline (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spread (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_fused spline and spread (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spline (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spread (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_fused spline and spread (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spread (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spline (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spread (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_fused spline and spread (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spline (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spread (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spline (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spread (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_fused spline and spread (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spline (1 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spread (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_fused spline and spread (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spline (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spline 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spline (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spread (2 ms) 31: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_fused spline and spread 31: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_fused spline and spread (2 ms) 31: [----------] 108 tests from Pme_SplineAndSpreadTest (116 ms total) 31: 31: [----------] 64 tests from Pme_SolveTest 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (1 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 31: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 31: [----------] 64 tests from Pme_SolveTest (14 ms total) 31: 31: [----------] 32 tests from PmeDiffEwaldQ_SolveTest 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [----------] 32 tests from PmeDiffEwaldQ_SolveTest (5 ms total) 31: 31: [----------] 32 tests from PmeDiffEwaldLJ_SolveTest 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 31: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 31: [----------] 32 tests from PmeDiffEwaldLJ_SolveTest (7 ms total) 31: 31: [----------] 64 tests from PmeDiffEps_SolveTest 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 31: Test is being skipped because: 31: CPU PME solve does not implement XYZ grid ordering 31: 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 31: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 31: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 31: [----------] 64 tests from PmeDiffEps_SolveTest (13 ms total) 31: 31: [----------] 72 tests from Pme_GatherTest 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_1_atom 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_2_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 31: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_13_atoms 31: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 31: [----------] 72 tests from Pme_GatherTest (16 ms total) 31: 31: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest 31: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 31: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (0 ms) 31: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 31: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms) 31: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 31: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (0 ms) 31: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 31: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (2 ms) 31: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 31: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (0 ms) 31: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (2 ms total) 31: 31: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (2 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (2 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (2 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (2 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (2 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (2 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (2 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (2 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (2 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (2 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (2 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (2 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (5 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (2 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (2 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (2 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (2 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (2 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (2 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (2 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (2 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (2 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (3 ms) 31: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 31: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (2 ms) 31: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (68 ms total) 31: 31: [----------] Global test environment tear-down 31: [==========] 407 tests from 9 test suites ran. (245 ms total) 31: [ PASSED ] 311 tests. 31: [ SKIPPED ] 96 tests, listed below: 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 31: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 31/94 Test #31: EwaldUnitTests ............................... Passed 0.71 sec test 32 Start 32: FFTUnitTests 32: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/fft-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/FFTUnitTests.xml" 32: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/fft/tests 32: Test timeout computed to be: 1920 32: [==========] Running 15 tests from 4 test suites. 32: [----------] Global test environment set-up. 32: [----------] 2 tests from ManyFFTTest 32: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test 32: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (6 ms) 32: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test 32: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (18 ms) 32: [----------] 2 tests from ManyFFTTest (25 ms total) 32: 32: [----------] 1 test from FFTTest 32: [ RUN ] FFTTest.Real2DLength18_15Test 32: [ OK ] FFTTest.Real2DLength18_15Test (5 ms) 32: [----------] 1 test from FFTTest (5 ms total) 32: 32: [----------] 10 tests from 7_8_25_36_60/FFTTest1D 32: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0 32: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (0 ms) 32: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1 32: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (0 ms) 32: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2 32: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (1 ms) 32: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3 32: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (3 ms) 32: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4 32: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (1 ms) 32: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0 32: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (0 ms) 32: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1 32: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (0 ms) 32: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2 32: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (0 ms) 32: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3 32: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (10 ms) 32: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4 32: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (14 ms) 32: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (34 ms total) 32: 32: [----------] 2 tests from Works/ParameterizedFFTTest3D 32: [ RUN ] Works/ParameterizedFFTTest3D.RunsOnHost/5_6_9 32: [ OK ] Works/ParameterizedFFTTest3D.RunsOnHost/5_6_9 (1 ms) 32: [ RUN ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 32: [ OK ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 (1 ms) 32: [----------] 2 tests from Works/ParameterizedFFTTest3D (2 ms total) 32: 32: [----------] Global test environment tear-down 32: [==========] 15 tests from 4 test suites ran. (68 ms total) 32: [ PASSED ] 15 tests. 32/94 Test #32: FFTUnitTests ................................. Passed 0.57 sec test 33 Start 33: GpuUtilsUnitTests 33: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/gpu_utils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/GpuUtilsUnitTests.xml" 33: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gpu_utils/tests 33: Test timeout computed to be: 30 33: [==========] Running 67 tests from 22 test suites. 33: [----------] Global test environment set-up. 33: [----------] 2 tests from ClfftInitializer 33: [ RUN ] ClfftInitializer.SingleInitializationWorks 33: [ OK ] ClfftInitializer.SingleInitializationWorks (0 ms) 33: [ RUN ] ClfftInitializer.TwoInitializationsWork 33: [ OK ] ClfftInitializer.TwoInitializationsWork (0 ms) 33: [----------] 2 tests from ClfftInitializer (0 ms total) 33: 33: [----------] 1 test from DevicesAvailable 33: [ RUN ] DevicesAvailable.ShouldBeAbleToRunOnDevice 33: [ OK ] DevicesAvailable.ShouldBeAbleToRunOnDevice (0 ms) 33: [----------] 1 test from DevicesAvailable (0 ms total) 33: 33: [----------] 1 test from DeviceStreamManagerTest 33: [ RUN ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice 33: [ OK ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice (0 ms) 33: [----------] 1 test from DeviceStreamManagerTest (0 ms total) 33: 33: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int 33: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks 33: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms) 33: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory 33: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms) 33: [----------] 2 tests from HostAllocatorTest/0 (0 ms total) 33: 33: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = float 33: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks 33: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms) 33: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory 33: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms) 33: [----------] 2 tests from HostAllocatorTest/1 (0 ms total) 33: 33: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector 33: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks 33: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms) 33: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory 33: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms) 33: [----------] 2 tests from HostAllocatorTest/2 (0 ms total) 33: 33: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly 33: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks 33: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms) 33: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory 33: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms) 33: [----------] 2 tests from HostAllocatorTest/3 (0 ms total) 33: 33: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int 33: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks 33: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 33: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork 33: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms) 33: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve 33: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms) 33: [----------] 3 tests from HostAllocatorTestCopyable/0 (0 ms total) 33: 33: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = float 33: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks 33: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 33: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork 33: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms) 33: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve 33: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms) 33: [----------] 3 tests from HostAllocatorTestCopyable/1 (0 ms total) 33: 33: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector 33: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks 33: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 33: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork 33: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms) 33: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve 33: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms) 33: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total) 33: 33: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int 33: [ RUN ] HostAllocatorTestNoMem/0.CreateVector 33: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment 33: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction 33: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/0.Swap 33: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/0.Comparison 33: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms) 33: [----------] 5 tests from HostAllocatorTestNoMem/0 (0 ms total) 33: 33: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = float 33: [ RUN ] HostAllocatorTestNoMem/1.CreateVector 33: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment 33: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction 33: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/1.Swap 33: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/1.Comparison 33: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms) 33: [----------] 5 tests from HostAllocatorTestNoMem/1 (0 ms total) 33: 33: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector 33: [ RUN ] HostAllocatorTestNoMem/2.CreateVector 33: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment 33: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction 33: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/2.Swap 33: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/2.Comparison 33: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms) 33: [----------] 5 tests from HostAllocatorTestNoMem/2 (0 ms total) 33: 33: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly 33: [ RUN ] HostAllocatorTestNoMem/3.CreateVector 33: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment 33: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction 33: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/3.Swap 33: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms) 33: [ RUN ] HostAllocatorTestNoMem/3.Comparison 33: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms) 33: [----------] 5 tests from HostAllocatorTestNoMem/3 (0 ms total) 33: 33: [----------] 3 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int 33: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment 33: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms) 33: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction 33: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms) 33: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator 33: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator (0 ms) 33: [----------] 3 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total) 33: 33: [----------] 3 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = float 33: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment 33: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms) 33: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction 33: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms) 33: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator 33: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator (0 ms) 33: [----------] 3 tests from HostAllocatorTestNoMemCopyable/1 (0 ms total) 33: 33: [----------] 3 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector 33: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment 33: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms) 33: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction 33: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms) 33: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator 33: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator (0 ms) 33: [----------] 3 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total) 33: 33: [----------] 1 test from HostAllocatorUntypedTest 33: [ RUN ] HostAllocatorUntypedTest.Comparison 33: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms) 33: [----------] 1 test from HostAllocatorUntypedTest (0 ms total) 33: 33: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 33: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 33: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 33: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 33: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/0.Move 33: [ OK ] AllocatorTest/0.Move (0 ms) 33: [----------] 4 tests from AllocatorTest/0 (0 ms total) 33: 33: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 33: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 33: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 33: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 33: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/1.Move 33: [ OK ] AllocatorTest/1.Move (0 ms) 33: [----------] 4 tests from AllocatorTest/1 (0 ms total) 33: 33: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator, gmx::HostAllocationPolicy> 33: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 33: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 33: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 33: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/2.Move 33: [ OK ] AllocatorTest/2.Move (0 ms) 33: [----------] 4 tests from AllocatorTest/2 (0 ms total) 33: 33: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 33: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 33: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 33: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 33: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 33: [ RUN ] AllocatorTest/3.Move 33: [ OK ] AllocatorTest/3.Move (0 ms) 33: [----------] 4 tests from AllocatorTest/3 (0 ms total) 33: 33: [----------] Global test environment tear-down 33: [==========] 67 tests from 22 test suites ran. (1 ms total) 33: [ PASSED ] 67 tests. 33/94 Test #33: GpuUtilsUnitTests ............................ Passed 0.45 sec test 34 Start 34: HardwareUnitTests 34: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/hardware-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/HardwareUnitTests.xml" 34: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/hardware/tests 34: Test timeout computed to be: 30 34: [==========] Running 22 tests from 10 test suites. 34: [----------] Global test environment set-up. 34: [----------] 1 test from CpuInfoTest 34: [ RUN ] CpuInfoTest.SupportLevel 34: [ OK ] CpuInfoTest.SupportLevel (43 ms) 34: [----------] 1 test from CpuInfoTest (44 ms total) 34: 34: [----------] 4 tests from HardwareTopologyTest 34: [ RUN ] HardwareTopologyTest.Execute 34: [ OK ] HardwareTopologyTest.Execute (59 ms) 34: [ RUN ] HardwareTopologyTest.HwlocExecute 34: [ OK ] HardwareTopologyTest.HwlocExecute (39 ms) 34: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency 34: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (47 ms) 34: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency 34: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (43 ms) 34: [----------] 4 tests from HardwareTopologyTest (190 ms total) 34: 34: [----------] 1 test from DevicesManagerTest 34: [ RUN ] DevicesManagerTest.Serialization 34: [ OK ] DevicesManagerTest.Serialization (0 ms) 34: [ DISABLED ] DevicesManagerTest.DISABLED_DetectsUuid 34: [----------] 1 test from DevicesManagerTest (0 ms total) 34: 34: [----------] 1 test from UuidStringTest 34: [ RUN ] UuidStringTest.Works 34: [ OK ] UuidStringTest.Works (0 ms) 34: [----------] 1 test from UuidStringTest (0 ms total) 34: 34: [----------] 5 tests from XeonE52620/MockHardwareTopologyTest 34: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/0 34: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/0 (1 ms) 34: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/1 34: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/1 (0 ms) 34: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/2 34: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/2 (0 ms) 34: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/3 34: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/3 (0 ms) 34: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/4 34: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/4 (0 ms) 34: [----------] 5 tests from XeonE52620/MockHardwareTopologyTest (3 ms total) 34: 34: [----------] 5 tests from Xeon4116/MockHardwareTopologyTest 34: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/0 34: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/0 (1 ms) 34: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/1 34: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/1 (0 ms) 34: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/2 34: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/2 (0 ms) 34: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/3 34: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/3 (0 ms) 34: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/4 34: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/4 (0 ms) 34: [----------] 5 tests from Xeon4116/MockHardwareTopologyTest (4 ms total) 34: 34: [----------] 2 tests from Core12900K/MockHardwareTopologyTest 34: [ RUN ] Core12900K/MockHardwareTopologyTest.DetectsHardware/0 34: [ OK ] Core12900K/MockHardwareTopologyTest.DetectsHardware/0 (0 ms) 34: [ RUN ] Core12900K/MockHardwareTopologyTest.DetectsHardware/1 34: [ OK ] Core12900K/MockHardwareTopologyTest.DetectsHardware/1 (0 ms) 34: [----------] 2 tests from Core12900K/MockHardwareTopologyTest (1 ms total) 34: 34: [----------] 1 test from Core12900K/MockHardwareTopologySpecialSystemTest 34: [ RUN ] Core12900K/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 34: [ OK ] Core12900K/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (1 ms) 34: [----------] 1 test from Core12900K/MockHardwareTopologySpecialSystemTest (1 ms total) 34: 34: [----------] 1 test from Power9/MockHardwareTopologySpecialSystemTest 34: [ RUN ] Power9/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 34: [ OK ] Power9/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (1 ms) 34: [----------] 1 test from Power9/MockHardwareTopologySpecialSystemTest (1 ms total) 34: 34: [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest 34: [ RUN ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 34: [ OK ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (2 ms) 34: [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest (2 ms total) 34: 34: [----------] Global test environment tear-down 34: [==========] 22 tests from 10 test suites ran. (250 ms total) 34: [ PASSED ] 22 tests. 34: 34: YOU HAVE 1 DISABLED TEST 34: 34/94 Test #34: HardwareUnitTests ............................ Passed 0.61 sec test 35 Start 35: MathUnitTests 35: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/math-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/MathUnitTests.xml" 35: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/math/tests 35: Test timeout computed to be: 30 35: [==========] Running 328 tests from 41 test suites. 35: [----------] Global test environment set-up. 35: [----------] 1 test from EmptyArrayRefWithPaddingTest 35: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty 35: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms) 35: [----------] 1 test from EmptyArrayRefWithPaddingTest (0 ms total) 35: 35: [----------] 1 test from EmptyConstArrayRefWithPaddingTest 35: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty 35: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms) 35: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total) 35: 35: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding 35: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks 35: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms) 35: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks 35: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms) 35: [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total) 35: 35: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding 35: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks 35: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms) 35: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks 35: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms) 35: [----------] 2 tests from ArrayRefWithPaddingTest/1 (0 ms total) 35: 35: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding 35: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks 35: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms) 35: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks 35: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms) 35: [----------] 2 tests from ArrayRefWithPaddingTest/2 (0 ms total) 35: 35: [----------] 2 tests from InvertBoxMatrixTest 35: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent 35: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms) 35: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace 35: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms) 35: [----------] 2 tests from InvertBoxMatrixTest (0 ms total) 35: 35: [----------] 8 tests from ComplexNumberTest 35: [ RUN ] ComplexNumberTest.RealComplexMultiply 35: [ OK ] ComplexNumberTest.RealComplexMultiply (0 ms) 35: [ RUN ] ComplexNumberTest.RealComplexExp 35: [ OK ] ComplexNumberTest.RealComplexExp (0 ms) 35: [ RUN ] ComplexNumberTest.ComplexAdd 35: [ OK ] ComplexNumberTest.ComplexAdd (0 ms) 35: [ RUN ] ComplexNumberTest.ComplexSubtract 35: [ OK ] ComplexNumberTest.ComplexSubtract (0 ms) 35: [ RUN ] ComplexNumberTest.ComplexMultiply 35: [ OK ] ComplexNumberTest.ComplexMultiply (0 ms) 35: [ RUN ] ComplexNumberTest.ComplexDivision 35: [ OK ] ComplexNumberTest.ComplexDivision (0 ms) 35: [ RUN ] ComplexNumberTest.ComplexConjugate 35: [ OK ] ComplexNumberTest.ComplexConjugate (0 ms) 35: [ RUN ] ComplexNumberTest.ComplexAbs2 35: [ OK ] ComplexNumberTest.ComplexAbs2 (0 ms) 35: [----------] 8 tests from ComplexNumberTest (0 ms total) 35: 35: [----------] 11 tests from TranslateAndScaleTest 35: [ RUN ] TranslateAndScaleTest.identityTransformation 35: [ OK ] TranslateAndScaleTest.identityTransformation (0 ms) 35: [ RUN ] TranslateAndScaleTest.translationWithIdentityScaling 35: [ OK ] TranslateAndScaleTest.translationWithIdentityScaling (0 ms) 35: [ RUN ] TranslateAndScaleTest.scalingWithZeroTranslation 35: [ OK ] TranslateAndScaleTest.scalingWithZeroTranslation (0 ms) 35: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivial 35: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivial (0 ms) 35: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector 35: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector (0 ms) 35: [ RUN ] TranslateAndScaleTest.scalingIdentity 35: [ OK ] TranslateAndScaleTest.scalingIdentity (0 ms) 35: [ RUN ] TranslateAndScaleTest.scalingNonTrivial 35: [ OK ] TranslateAndScaleTest.scalingNonTrivial (0 ms) 35: [ RUN ] TranslateAndScaleTest.scalingNonTrivialSingleVector 35: [ OK ] TranslateAndScaleTest.scalingNonTrivialSingleVector (0 ms) 35: [ RUN ] TranslateAndScaleTest.scalingInverseNoZero 35: [ OK ] TranslateAndScaleTest.scalingInverseNoZero (0 ms) 35: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero 35: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero (0 ms) 35: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector 35: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector (0 ms) 35: [----------] 11 tests from TranslateAndScaleTest (0 ms total) 35: 35: [----------] 3 tests from AffineTransformationTest 35: [ RUN ] AffineTransformationTest.identityTransformYieldsSameVectors 35: [ OK ] AffineTransformationTest.identityTransformYieldsSameVectors (0 ms) 35: [ RUN ] AffineTransformationTest.applyTransformationToVectors 35: [ OK ] AffineTransformationTest.applyTransformationToVectors (0 ms) 35: [ RUN ] AffineTransformationTest.retrieveGradient 35: [ OK ] AffineTransformationTest.retrieveGradient (0 ms) 35: [----------] 3 tests from AffineTransformationTest (0 ms total) 35: 35: [----------] 14 tests from DensitySimilarityTest 35: [ RUN ] DensitySimilarityTest.InnerProductIsCorrect 35: [ OK ] DensitySimilarityTest.InnerProductIsCorrect (0 ms) 35: [ RUN ] DensitySimilarityTest.InnerProductGradientIsCorrect 35: [ OK ] DensitySimilarityTest.InnerProductGradientIsCorrect (0 ms) 35: [ RUN ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch 35: [ OK ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch (0 ms) 35: [ RUN ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch 35: [ OK ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch (0 ms) 35: [ RUN ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect 35: [ OK ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect (0 ms) 35: [ RUN ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero 35: [ OK ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero (0 ms) 35: [ RUN ] DensitySimilarityTest.RelativeEntropyIsCorrect 35: [ OK ] DensitySimilarityTest.RelativeEntropyIsCorrect (0 ms) 35: [ RUN ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect 35: [ OK ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect (0 ms) 35: [ RUN ] DensitySimilarityTest.CrossCorrelationIsOne 35: [ OK ] DensitySimilarityTest.CrossCorrelationIsOne (39 ms) 35: [ RUN ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated 35: [ OK ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated (42 ms) 35: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated 35: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated (2 ms) 35: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect 35: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect (0 ms) 35: [ RUN ] DensitySimilarityTest.NormalizationCorrect 35: [ OK ] DensitySimilarityTest.NormalizationCorrect (0 ms) 35: [ RUN ] DensitySimilarityTest.NormalizationAllNonPositive 35: [ OK ] DensitySimilarityTest.NormalizationAllNonPositive (0 ms) 35: [----------] 14 tests from DensitySimilarityTest (85 ms total) 35: 35: [----------] 6 tests from StructureSimilarityTest 35: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD 35: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms) 35: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho 35: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms) 35: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD 35: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms) 35: [ RUN ] StructureSimilarityTest.YieldsCorrectRho 35: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms) 35: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex 35: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms) 35: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex 35: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms) 35: [----------] 6 tests from StructureSimilarityTest (0 ms total) 35: 35: [----------] 8 tests from ExponentialMovingAverage 35: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero 35: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero (0 ms) 35: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative 35: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative (0 ms) 35: [ RUN ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue 35: [ OK ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue (0 ms) 35: [ RUN ] ExponentialMovingAverage.YieldsCorrectValue 35: [ OK ] ExponentialMovingAverage.YieldsCorrectValue (0 ms) 35: [ RUN ] ExponentialMovingAverage.SetAverageCorrectly 35: [ OK ] ExponentialMovingAverage.SetAverageCorrectly (0 ms) 35: [ RUN ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing 35: [ OK ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing (0 ms) 35: [ RUN ] ExponentialMovingAverage.InverseLagTimeCorrect 35: [ OK ] ExponentialMovingAverage.InverseLagTimeCorrect (0 ms) 35: [ RUN ] ExponentialMovingAverage.RoundTripAsKeyValueTree 35: [ OK ] ExponentialMovingAverage.RoundTripAsKeyValueTree (0 ms) 35: [----------] 8 tests from ExponentialMovingAverage (0 ms total) 35: 35: [----------] 21 tests from FunctionTest 35: [ RUN ] FunctionTest.StaticLog2 35: [ OK ] FunctionTest.StaticLog2 (0 ms) 35: [ RUN ] FunctionTest.Log2I32Bit 35: [ OK ] FunctionTest.Log2I32Bit (0 ms) 35: [ RUN ] FunctionTest.Log2I64Bit 35: [ OK ] FunctionTest.Log2I64Bit (0 ms) 35: [ RUN ] FunctionTest.GreatestCommonDivisor 35: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms) 35: [ RUN ] FunctionTest.InvsqrtFloat 35: [ OK ] FunctionTest.InvsqrtFloat (0 ms) 35: [ RUN ] FunctionTest.InvsqrtDouble 35: [ OK ] FunctionTest.InvsqrtDouble (0 ms) 35: [ RUN ] FunctionTest.InvsqrtInteger 35: [ OK ] FunctionTest.InvsqrtInteger (0 ms) 35: [ RUN ] FunctionTest.InvcbrtFloat 35: [ OK ] FunctionTest.InvcbrtFloat (0 ms) 35: [ RUN ] FunctionTest.InvcbrtDouble 35: [ OK ] FunctionTest.InvcbrtDouble (0 ms) 35: [ RUN ] FunctionTest.InvcbrtInteger 35: [ OK ] FunctionTest.InvcbrtInteger (0 ms) 35: [ RUN ] FunctionTest.SixthrootFloat 35: [ OK ] FunctionTest.SixthrootFloat (0 ms) 35: [ RUN ] FunctionTest.SixthrootDouble 35: [ OK ] FunctionTest.SixthrootDouble (0 ms) 35: [ RUN ] FunctionTest.SixthrootInteger 35: [ OK ] FunctionTest.SixthrootInteger (0 ms) 35: [ RUN ] FunctionTest.InvsixthrootFloat 35: [ OK ] FunctionTest.InvsixthrootFloat (0 ms) 35: [ RUN ] FunctionTest.InvsixthrootDouble 35: [ OK ] FunctionTest.InvsixthrootDouble (0 ms) 35: [ RUN ] FunctionTest.InvsixthrootInteger 35: [ OK ] FunctionTest.InvsixthrootInteger (0 ms) 35: [ RUN ] FunctionTest.Powers 35: [ OK ] FunctionTest.Powers (0 ms) 35: [ RUN ] FunctionTest.ErfInvFloat 35: [ OK ] FunctionTest.ErfInvFloat (0 ms) 35: [ RUN ] FunctionTest.ErfInvDouble 35: [ OK ] FunctionTest.ErfInvDouble (0 ms) 35: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat 35: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (0 ms) 35: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble 35: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (0 ms) 35: [----------] 21 tests from FunctionTest (1 ms total) 35: 35: [----------] 2 tests from FunctionTestIntegerTypes/0, where TypeParam = signed char 35: [ RUN ] FunctionTestIntegerTypes/0.IsPowerOfTwo 35: [ OK ] FunctionTestIntegerTypes/0.IsPowerOfTwo (0 ms) 35: [ RUN ] FunctionTestIntegerTypes/0.DivideRoundUp 35: [ OK ] FunctionTestIntegerTypes/0.DivideRoundUp (0 ms) 35: [----------] 2 tests from FunctionTestIntegerTypes/0 (0 ms total) 35: 35: [----------] 2 tests from FunctionTestIntegerTypes/1, where TypeParam = unsigned char 35: [ RUN ] FunctionTestIntegerTypes/1.IsPowerOfTwo 35: [ OK ] FunctionTestIntegerTypes/1.IsPowerOfTwo (0 ms) 35: [ RUN ] FunctionTestIntegerTypes/1.DivideRoundUp 35: [ OK ] FunctionTestIntegerTypes/1.DivideRoundUp (0 ms) 35: [----------] 2 tests from FunctionTestIntegerTypes/1 (0 ms total) 35: 35: [----------] 2 tests from FunctionTestIntegerTypes/2, where TypeParam = short 35: [ RUN ] FunctionTestIntegerTypes/2.IsPowerOfTwo 35: [ OK ] FunctionTestIntegerTypes/2.IsPowerOfTwo (0 ms) 35: [ RUN ] FunctionTestIntegerTypes/2.DivideRoundUp 35: [ OK ] FunctionTestIntegerTypes/2.DivideRoundUp (0 ms) 35: [----------] 2 tests from FunctionTestIntegerTypes/2 (0 ms total) 35: 35: [----------] 2 tests from FunctionTestIntegerTypes/3, where TypeParam = unsigned short 35: [ RUN ] FunctionTestIntegerTypes/3.IsPowerOfTwo 35: [ OK ] FunctionTestIntegerTypes/3.IsPowerOfTwo (0 ms) 35: [ RUN ] FunctionTestIntegerTypes/3.DivideRoundUp 35: [ OK ] FunctionTestIntegerTypes/3.DivideRoundUp (0 ms) 35: [----------] 2 tests from FunctionTestIntegerTypes/3 (0 ms total) 35: 35: [----------] 2 tests from FunctionTestIntegerTypes/4, where TypeParam = int 35: [ RUN ] FunctionTestIntegerTypes/4.IsPowerOfTwo 35: [ OK ] FunctionTestIntegerTypes/4.IsPowerOfTwo (0 ms) 35: [ RUN ] FunctionTestIntegerTypes/4.DivideRoundUp 35: [ OK ] FunctionTestIntegerTypes/4.DivideRoundUp (0 ms) 35: [----------] 2 tests from FunctionTestIntegerTypes/4 (0 ms total) 35: 35: [----------] 2 tests from FunctionTestIntegerTypes/5, where TypeParam = unsigned int 35: [ RUN ] FunctionTestIntegerTypes/5.IsPowerOfTwo 35: [ OK ] FunctionTestIntegerTypes/5.IsPowerOfTwo (0 ms) 35: [ RUN ] FunctionTestIntegerTypes/5.DivideRoundUp 35: [ OK ] FunctionTestIntegerTypes/5.DivideRoundUp (0 ms) 35: [----------] 2 tests from FunctionTestIntegerTypes/5 (0 ms total) 35: 35: [----------] 2 tests from FunctionTestIntegerTypes/6, where TypeParam = long 35: [ RUN ] FunctionTestIntegerTypes/6.IsPowerOfTwo 35: [ OK ] FunctionTestIntegerTypes/6.IsPowerOfTwo (0 ms) 35: [ RUN ] FunctionTestIntegerTypes/6.DivideRoundUp 35: [ OK ] FunctionTestIntegerTypes/6.DivideRoundUp (0 ms) 35: [----------] 2 tests from FunctionTestIntegerTypes/6 (0 ms total) 35: 35: [----------] 2 tests from FunctionTestIntegerTypes/7, where TypeParam = unsigned long 35: [ RUN ] FunctionTestIntegerTypes/7.IsPowerOfTwo 35: [ OK ] FunctionTestIntegerTypes/7.IsPowerOfTwo (0 ms) 35: [ RUN ] FunctionTestIntegerTypes/7.DivideRoundUp 35: [ OK ] FunctionTestIntegerTypes/7.DivideRoundUp (0 ms) 35: [----------] 2 tests from FunctionTestIntegerTypes/7 (0 ms total) 35: 35: [----------] 4 tests from GaussianOn1DLattice 35: [ RUN ] GaussianOn1DLattice.sumsCloseToOne 35: [ OK ] GaussianOn1DLattice.sumsCloseToOne (0 ms) 35: [ RUN ] GaussianOn1DLattice.isCorrect 35: [ OK ] GaussianOn1DLattice.isCorrect (0 ms) 35: [ RUN ] GaussianOn1DLattice.complementaryAmplitudesSumToZero 35: [ OK ] GaussianOn1DLattice.complementaryAmplitudesSumToZero (0 ms) 35: [ RUN ] GaussianOn1DLattice.doesNotOverflowForLargeRange 35: [ OK ] GaussianOn1DLattice.doesNotOverflowForLargeRange (0 ms) 35: [----------] 4 tests from GaussianOn1DLattice (0 ms total) 35: 35: [----------] 9 tests from GaussTransformTest 35: [ RUN ] GaussTransformTest.isZeroUponConstruction 35: [ OK ] GaussTransformTest.isZeroUponConstruction (0 ms) 35: [ RUN ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss 35: [ OK ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss (0 ms) 35: [ RUN ] GaussTransformTest.isZeroAfterSettingZero 35: [ OK ] GaussTransformTest.isZeroAfterSettingZero (0 ms) 35: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinX 35: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinX (0 ms) 35: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinY 35: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinY (0 ms) 35: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinZ 35: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinZ (0 ms) 35: [ RUN ] GaussTransformTest.complementaryGaussAddToZero 35: [ OK ] GaussTransformTest.complementaryGaussAddToZero (0 ms) 35: [ RUN ] GaussTransformTest.centerGaussianInCubeHasExpectedValues 35: [ OK ] GaussTransformTest.centerGaussianInCubeHasExpectedValues (0 ms) 35: [ RUN ] GaussTransformTest.view 35: [ OK ] GaussTransformTest.view (0 ms) 35: [----------] 9 tests from GaussTransformTest (0 ms total) 35: 35: [----------] 3 tests from DensityFittingForce 35: [ RUN ] DensityFittingForce.isZeroWhenMatchingDensity 35: [ OK ] DensityFittingForce.isZeroWhenMatchingDensity (0 ms) 35: [ RUN ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections 35: [ OK ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections (0 ms) 35: [ RUN ] DensityFittingForce.pullsTowardsDerivative 35: [ OK ] DensityFittingForce.pullsTowardsDerivative (0 ms) 35: [----------] 3 tests from DensityFittingForce (0 ms total) 35: 35: [----------] 2 tests from InvertMatrixTest 35: [ RUN ] InvertMatrixTest.IdentityIsImpotent 35: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms) 35: [ RUN ] InvertMatrixTest.ComputesInverse 35: [ OK ] InvertMatrixTest.ComputesInverse (0 ms) 35: [----------] 2 tests from InvertMatrixTest (0 ms total) 35: 35: [----------] 22 tests from MatrixTest 35: [ RUN ] MatrixTest.canSetFromArray 35: [ OK ] MatrixTest.canSetFromArray (0 ms) 35: [ RUN ] MatrixTest.canSetStaticallyFromList 35: [ OK ] MatrixTest.canSetStaticallyFromList (0 ms) 35: [ RUN ] MatrixTest.canConstructAndFill 35: [ OK ] MatrixTest.canConstructAndFill (0 ms) 35: [ RUN ] MatrixTest.canSetValues 35: [ OK ] MatrixTest.canSetValues (0 ms) 35: [ RUN ] MatrixTest.canCopyAssign 35: [ OK ] MatrixTest.canCopyAssign (0 ms) 35: [ RUN ] MatrixTest.canSwap 35: [ OK ] MatrixTest.canSwap (0 ms) 35: [ RUN ] MatrixTest.staticMultiDimArrayExtent 35: [ OK ] MatrixTest.staticMultiDimArrayExtent (0 ms) 35: [ RUN ] MatrixTest.canAddMatrix 35: [ OK ] MatrixTest.canAddMatrix (0 ms) 35: [ RUN ] MatrixTest.canSubstractMatrix 35: [ OK ] MatrixTest.canSubstractMatrix (0 ms) 35: [ RUN ] MatrixTest.canNegateMatrix 35: [ OK ] MatrixTest.canNegateMatrix (0 ms) 35: [ RUN ] MatrixTest.determinantWorks 35: [ OK ] MatrixTest.determinantWorks (0 ms) 35: [ RUN ] MatrixTest.noninvertableDeterminantIsZero 35: [ OK ] MatrixTest.noninvertableDeterminantIsZero (0 ms) 35: [ RUN ] MatrixTest.determinantOfDiagonalMatrix 35: [ OK ] MatrixTest.determinantOfDiagonalMatrix (0 ms) 35: [ RUN ] MatrixTest.traceWorks 35: [ OK ] MatrixTest.traceWorks (0 ms) 35: [ RUN ] MatrixTest.transposeWorks 35: [ OK ] MatrixTest.transposeWorks (0 ms) 35: [ RUN ] MatrixTest.transposeOfSymmetricMatrix 35: [ OK ] MatrixTest.transposeOfSymmetricMatrix (0 ms) 35: [ RUN ] MatrixTest.canCreateFromLegacyMatrix 35: [ OK ] MatrixTest.canCreateFromLegacyMatrix (0 ms) 35: [ RUN ] MatrixTest.canFillLegacyMatrix 35: [ OK ] MatrixTest.canFillLegacyMatrix (0 ms) 35: [ RUN ] MatrixTest.IdentityMatrix 35: [ OK ] MatrixTest.IdentityMatrix (0 ms) 35: [ RUN ] MatrixTest.MatrixMatrixInnerProduct 35: [ OK ] MatrixTest.MatrixMatrixInnerProduct (0 ms) 35: [ RUN ] MatrixTest.MatrixMatrixMultiplication 35: [ OK ] MatrixTest.MatrixMatrixMultiplication (0 ms) 35: [ RUN ] MatrixTest.MatrixVectorMultiplication 35: [ OK ] MatrixTest.MatrixVectorMultiplication (0 ms) 35: [----------] 22 tests from MatrixTest (0 ms total) 35: 35: [----------] 25 tests from MultiDimArrayTest 35: [ RUN ] MultiDimArrayTest.canConstructAndFillStatic 35: [ OK ] MultiDimArrayTest.canConstructAndFillStatic (0 ms) 35: [ RUN ] MultiDimArrayTest.canConstructAndFillDynamic 35: [ OK ] MultiDimArrayTest.canConstructAndFillDynamic (0 ms) 35: [ RUN ] MultiDimArrayTest.canSetValuesInStatic 35: [ OK ] MultiDimArrayTest.canSetValuesInStatic (0 ms) 35: [ RUN ] MultiDimArrayTest.canSetValuesInDynamic 35: [ OK ] MultiDimArrayTest.canSetValuesInDynamic (0 ms) 35: [ RUN ] MultiDimArrayTest.canMoveConstructStatic 35: [ OK ] MultiDimArrayTest.canMoveConstructStatic (0 ms) 35: [ RUN ] MultiDimArrayTest.canMoveConstructDynamic 35: [ OK ] MultiDimArrayTest.canMoveConstructDynamic (0 ms) 35: [ RUN ] MultiDimArrayTest.canMoveAssignStatic 35: [ OK ] MultiDimArrayTest.canMoveAssignStatic (0 ms) 35: [ RUN ] MultiDimArrayTest.canMoveAssignDynamic 35: [ OK ] MultiDimArrayTest.canMoveAssignDynamic (0 ms) 35: [ RUN ] MultiDimArrayTest.canCopyConstructStatic 35: [ OK ] MultiDimArrayTest.canCopyConstructStatic (0 ms) 35: [ RUN ] MultiDimArrayTest.canCopyConstructDynamic 35: [ OK ] MultiDimArrayTest.canCopyConstructDynamic (0 ms) 35: [ RUN ] MultiDimArrayTest.canCopyAssignStatic 35: [ OK ] MultiDimArrayTest.canCopyAssignStatic (0 ms) 35: [ RUN ] MultiDimArrayTest.canCopyAssignDynamic 35: [ OK ] MultiDimArrayTest.canCopyAssignDynamic (0 ms) 35: [ RUN ] MultiDimArrayTest.canSwapStatic 35: [ OK ] MultiDimArrayTest.canSwapStatic (0 ms) 35: [ RUN ] MultiDimArrayTest.canSwapDynamic 35: [ OK ] MultiDimArrayTest.canSwapDynamic (0 ms) 35: [ RUN ] MultiDimArrayTest.staticMultiDimArrayExtent 35: [ OK ] MultiDimArrayTest.staticMultiDimArrayExtent (0 ms) 35: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayExtent 35: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayExtent (0 ms) 35: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent 35: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent (0 ms) 35: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue 35: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue (0 ms) 35: [ RUN ] MultiDimArrayTest.staticMultiDimArrayFromArray 35: [ OK ] MultiDimArrayTest.staticMultiDimArrayFromArray (0 ms) 35: [ RUN ] MultiDimArrayTest.conversionToView 35: [ OK ] MultiDimArrayTest.conversionToView (0 ms) 35: [ RUN ] MultiDimArrayTest.conversionToConstView 35: [ OK ] MultiDimArrayTest.conversionToConstView (0 ms) 35: [ RUN ] MultiDimArrayTest.viewBegin 35: [ OK ] MultiDimArrayTest.viewBegin (0 ms) 35: [ RUN ] MultiDimArrayTest.viewEnd 35: [ OK ] MultiDimArrayTest.viewEnd (0 ms) 35: [ RUN ] MultiDimArrayTest.constViewConstBegin 35: [ OK ] MultiDimArrayTest.constViewConstBegin (0 ms) 35: [ RUN ] MultiDimArrayTest.constViewConstEnd 35: [ OK ] MultiDimArrayTest.constViewConstEnd (0 ms) 35: [----------] 25 tests from MultiDimArrayTest (0 ms total) 35: 35: [----------] 4 tests from MultiDimArrayToMdSpanTest 35: [ RUN ] MultiDimArrayToMdSpanTest.convertsToMdSpan 35: [ OK ] MultiDimArrayToMdSpanTest.convertsToMdSpan (0 ms) 35: [ RUN ] MultiDimArrayToMdSpanTest.constArrayToMdSpan 35: [ OK ] MultiDimArrayToMdSpanTest.constArrayToMdSpan (0 ms) 35: [ RUN ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan 35: [ OK ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan (0 ms) 35: [ RUN ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan 35: [ OK ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan (0 ms) 35: [----------] 4 tests from MultiDimArrayToMdSpanTest (0 ms total) 35: 35: [----------] 9 tests from NelderMeadSimplexTest 35: [ RUN ] NelderMeadSimplexTest.BestVertex 35: [ OK ] NelderMeadSimplexTest.BestVertex (0 ms) 35: [ RUN ] NelderMeadSimplexTest.WorstVertex 35: [ OK ] NelderMeadSimplexTest.WorstVertex (0 ms) 35: [ RUN ] NelderMeadSimplexTest.SecondWorstValue 35: [ OK ] NelderMeadSimplexTest.SecondWorstValue (0 ms) 35: [ RUN ] NelderMeadSimplexTest.ReflectionPoint 35: [ OK ] NelderMeadSimplexTest.ReflectionPoint (0 ms) 35: [ RUN ] NelderMeadSimplexTest.EvaluateExpansionPoint 35: [ OK ] NelderMeadSimplexTest.EvaluateExpansionPoint (0 ms) 35: [ RUN ] NelderMeadSimplexTest.EvaluateContractionPoint 35: [ OK ] NelderMeadSimplexTest.EvaluateContractionPoint (0 ms) 35: [ RUN ] NelderMeadSimplexTest.SwapOutWorst 35: [ OK ] NelderMeadSimplexTest.SwapOutWorst (0 ms) 35: [ RUN ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest 35: [ OK ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest (0 ms) 35: [ RUN ] NelderMeadSimplexTest.OrientedLength 35: [ OK ] NelderMeadSimplexTest.OrientedLength (0 ms) 35: [----------] 9 tests from NelderMeadSimplexTest (0 ms total) 35: 35: [----------] 2 tests from NelderMead 35: [ RUN ] NelderMead.Optimizes2DFunctionCorrectly 35: [ OK ] NelderMead.Optimizes2DFunctionCorrectly (0 ms) 35: [ RUN ] NelderMead.Optimizes3DFunctorCorrectly 35: [ OK ] NelderMead.Optimizes3DFunctorCorrectly (0 ms) 35: [----------] 2 tests from NelderMead (0 ms total) 35: 35: [----------] 11 tests from PaddedVectorTest/0, where TypeParam = std::allocator 35: [ RUN ] PaddedVectorTest/0.DefaultConstructorWorks 35: [ OK ] PaddedVectorTest/0.DefaultConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/0.ResizeWorks 35: [ OK ] PaddedVectorTest/0.ResizeWorks (0 ms) 35: [ RUN ] PaddedVectorTest/0.ReserveWorks 35: [ OK ] PaddedVectorTest/0.ReserveWorks (0 ms) 35: [ RUN ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve 35: [ OK ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve (0 ms) 35: [ RUN ] PaddedVectorTest/0.MoveConstructorWorks 35: [ OK ] PaddedVectorTest/0.MoveConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks 35: [ OK ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/0.MoveAssignmentWorks 35: [ OK ] PaddedVectorTest/0.MoveAssignmentWorks (0 ms) 35: [ RUN ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical 35: [ OK ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical (0 ms) 35: [ RUN ] PaddedVectorTest/0.CanCopyAssign 35: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms) 35: [ RUN ] PaddedVectorTest/0.CanMoveAssign 35: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms) 35: [ RUN ] PaddedVectorTest/0.CanSwap 35: [ OK ] PaddedVectorTest/0.CanSwap (0 ms) 35: [----------] 11 tests from PaddedVectorTest/0 (0 ms total) 35: 35: [----------] 11 tests from PaddedVectorTest/1, where TypeParam = std::allocator 35: [ RUN ] PaddedVectorTest/1.DefaultConstructorWorks 35: [ OK ] PaddedVectorTest/1.DefaultConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/1.ResizeWorks 35: [ OK ] PaddedVectorTest/1.ResizeWorks (0 ms) 35: [ RUN ] PaddedVectorTest/1.ReserveWorks 35: [ OK ] PaddedVectorTest/1.ReserveWorks (0 ms) 35: [ RUN ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve 35: [ OK ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve (0 ms) 35: [ RUN ] PaddedVectorTest/1.MoveConstructorWorks 35: [ OK ] PaddedVectorTest/1.MoveConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks 35: [ OK ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/1.MoveAssignmentWorks 35: [ OK ] PaddedVectorTest/1.MoveAssignmentWorks (0 ms) 35: [ RUN ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical 35: [ OK ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical (0 ms) 35: [ RUN ] PaddedVectorTest/1.CanCopyAssign 35: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms) 35: [ RUN ] PaddedVectorTest/1.CanMoveAssign 35: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms) 35: [ RUN ] PaddedVectorTest/1.CanSwap 35: [ OK ] PaddedVectorTest/1.CanSwap (0 ms) 35: [----------] 11 tests from PaddedVectorTest/1 (0 ms total) 35: 35: [----------] 11 tests from PaddedVectorTest/2, where TypeParam = std::allocator 35: [ RUN ] PaddedVectorTest/2.DefaultConstructorWorks 35: [ OK ] PaddedVectorTest/2.DefaultConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/2.ResizeWorks 35: [ OK ] PaddedVectorTest/2.ResizeWorks (0 ms) 35: [ RUN ] PaddedVectorTest/2.ReserveWorks 35: [ OK ] PaddedVectorTest/2.ReserveWorks (0 ms) 35: [ RUN ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve 35: [ OK ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve (0 ms) 35: [ RUN ] PaddedVectorTest/2.MoveConstructorWorks 35: [ OK ] PaddedVectorTest/2.MoveConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks 35: [ OK ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/2.MoveAssignmentWorks 35: [ OK ] PaddedVectorTest/2.MoveAssignmentWorks (0 ms) 35: [ RUN ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical 35: [ OK ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical (0 ms) 35: [ RUN ] PaddedVectorTest/2.CanCopyAssign 35: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms) 35: [ RUN ] PaddedVectorTest/2.CanMoveAssign 35: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms) 35: [ RUN ] PaddedVectorTest/2.CanSwap 35: [ OK ] PaddedVectorTest/2.CanSwap (0 ms) 35: [----------] 11 tests from PaddedVectorTest/2 (0 ms total) 35: 35: [----------] 11 tests from PaddedVectorTest/3, where TypeParam = std::allocator > 35: [ RUN ] PaddedVectorTest/3.DefaultConstructorWorks 35: [ OK ] PaddedVectorTest/3.DefaultConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/3.ResizeWorks 35: [ OK ] PaddedVectorTest/3.ResizeWorks (0 ms) 35: [ RUN ] PaddedVectorTest/3.ReserveWorks 35: [ OK ] PaddedVectorTest/3.ReserveWorks (0 ms) 35: [ RUN ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve 35: [ OK ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve (0 ms) 35: [ RUN ] PaddedVectorTest/3.MoveConstructorWorks 35: [ OK ] PaddedVectorTest/3.MoveConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks 35: [ OK ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/3.MoveAssignmentWorks 35: [ OK ] PaddedVectorTest/3.MoveAssignmentWorks (0 ms) 35: [ RUN ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical 35: [ OK ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical (0 ms) 35: [ RUN ] PaddedVectorTest/3.CanCopyAssign 35: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms) 35: [ RUN ] PaddedVectorTest/3.CanMoveAssign 35: [ OK ] PaddedVectorTest/3.CanMoveAssign (0 ms) 35: [ RUN ] PaddedVectorTest/3.CanSwap 35: [ OK ] PaddedVectorTest/3.CanSwap (0 ms) 35: [----------] 11 tests from PaddedVectorTest/3 (0 ms total) 35: 35: [----------] 11 tests from PaddedVectorTest/4, where TypeParam = std::allocator > 35: [ RUN ] PaddedVectorTest/4.DefaultConstructorWorks 35: [ OK ] PaddedVectorTest/4.DefaultConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/4.ResizeWorks 35: [ OK ] PaddedVectorTest/4.ResizeWorks (0 ms) 35: [ RUN ] PaddedVectorTest/4.ReserveWorks 35: [ OK ] PaddedVectorTest/4.ReserveWorks (0 ms) 35: [ RUN ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve 35: [ OK ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve (0 ms) 35: [ RUN ] PaddedVectorTest/4.MoveConstructorWorks 35: [ OK ] PaddedVectorTest/4.MoveConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks 35: [ OK ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/4.MoveAssignmentWorks 35: [ OK ] PaddedVectorTest/4.MoveAssignmentWorks (0 ms) 35: [ RUN ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical 35: [ OK ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical (0 ms) 35: [ RUN ] PaddedVectorTest/4.CanCopyAssign 35: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms) 35: [ RUN ] PaddedVectorTest/4.CanMoveAssign 35: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms) 35: [ RUN ] PaddedVectorTest/4.CanSwap 35: [ OK ] PaddedVectorTest/4.CanSwap (0 ms) 35: [----------] 11 tests from PaddedVectorTest/4 (0 ms total) 35: 35: [----------] 11 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator 35: [ RUN ] PaddedVectorTest/5.DefaultConstructorWorks 35: [ OK ] PaddedVectorTest/5.DefaultConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/5.ResizeWorks 35: [ OK ] PaddedVectorTest/5.ResizeWorks (0 ms) 35: [ RUN ] PaddedVectorTest/5.ReserveWorks 35: [ OK ] PaddedVectorTest/5.ReserveWorks (0 ms) 35: [ RUN ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve 35: [ OK ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve (0 ms) 35: [ RUN ] PaddedVectorTest/5.MoveConstructorWorks 35: [ OK ] PaddedVectorTest/5.MoveConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks 35: [ OK ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/5.MoveAssignmentWorks 35: [ OK ] PaddedVectorTest/5.MoveAssignmentWorks (0 ms) 35: [ RUN ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical 35: [ OK ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical (0 ms) 35: [ RUN ] PaddedVectorTest/5.CanCopyAssign 35: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms) 35: [ RUN ] PaddedVectorTest/5.CanMoveAssign 35: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms) 35: [ RUN ] PaddedVectorTest/5.CanSwap 35: [ OK ] PaddedVectorTest/5.CanSwap (0 ms) 35: [----------] 11 tests from PaddedVectorTest/5 (0 ms total) 35: 35: [----------] 11 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator 35: [ RUN ] PaddedVectorTest/6.DefaultConstructorWorks 35: [ OK ] PaddedVectorTest/6.DefaultConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/6.ResizeWorks 35: [ OK ] PaddedVectorTest/6.ResizeWorks (0 ms) 35: [ RUN ] PaddedVectorTest/6.ReserveWorks 35: [ OK ] PaddedVectorTest/6.ReserveWorks (0 ms) 35: [ RUN ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve 35: [ OK ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve (0 ms) 35: [ RUN ] PaddedVectorTest/6.MoveConstructorWorks 35: [ OK ] PaddedVectorTest/6.MoveConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks 35: [ OK ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/6.MoveAssignmentWorks 35: [ OK ] PaddedVectorTest/6.MoveAssignmentWorks (0 ms) 35: [ RUN ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical 35: [ OK ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical (0 ms) 35: [ RUN ] PaddedVectorTest/6.CanCopyAssign 35: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms) 35: [ RUN ] PaddedVectorTest/6.CanMoveAssign 35: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms) 35: [ RUN ] PaddedVectorTest/6.CanSwap 35: [ OK ] PaddedVectorTest/6.CanSwap (0 ms) 35: [----------] 11 tests from PaddedVectorTest/6 (0 ms total) 35: 35: [----------] 11 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator 35: [ RUN ] PaddedVectorTest/7.DefaultConstructorWorks 35: [ OK ] PaddedVectorTest/7.DefaultConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/7.ResizeWorks 35: [ OK ] PaddedVectorTest/7.ResizeWorks (0 ms) 35: [ RUN ] PaddedVectorTest/7.ReserveWorks 35: [ OK ] PaddedVectorTest/7.ReserveWorks (0 ms) 35: [ RUN ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve 35: [ OK ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve (0 ms) 35: [ RUN ] PaddedVectorTest/7.MoveConstructorWorks 35: [ OK ] PaddedVectorTest/7.MoveConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks 35: [ OK ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/7.MoveAssignmentWorks 35: [ OK ] PaddedVectorTest/7.MoveAssignmentWorks (0 ms) 35: [ RUN ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical 35: [ OK ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical (0 ms) 35: [ RUN ] PaddedVectorTest/7.CanCopyAssign 35: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms) 35: [ RUN ] PaddedVectorTest/7.CanMoveAssign 35: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms) 35: [ RUN ] PaddedVectorTest/7.CanSwap 35: [ OK ] PaddedVectorTest/7.CanSwap (0 ms) 35: [----------] 11 tests from PaddedVectorTest/7 (0 ms total) 35: 35: [----------] 11 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 35: [ RUN ] PaddedVectorTest/8.DefaultConstructorWorks 35: [ OK ] PaddedVectorTest/8.DefaultConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/8.ResizeWorks 35: [ OK ] PaddedVectorTest/8.ResizeWorks (0 ms) 35: [ RUN ] PaddedVectorTest/8.ReserveWorks 35: [ OK ] PaddedVectorTest/8.ReserveWorks (0 ms) 35: [ RUN ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve 35: [ OK ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve (0 ms) 35: [ RUN ] PaddedVectorTest/8.MoveConstructorWorks 35: [ OK ] PaddedVectorTest/8.MoveConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks 35: [ OK ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/8.MoveAssignmentWorks 35: [ OK ] PaddedVectorTest/8.MoveAssignmentWorks (0 ms) 35: [ RUN ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical 35: [ OK ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical (0 ms) 35: [ RUN ] PaddedVectorTest/8.CanCopyAssign 35: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms) 35: [ RUN ] PaddedVectorTest/8.CanMoveAssign 35: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms) 35: [ RUN ] PaddedVectorTest/8.CanSwap 35: [ OK ] PaddedVectorTest/8.CanSwap (0 ms) 35: [----------] 11 tests from PaddedVectorTest/8 (0 ms total) 35: 35: [----------] 11 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 35: [ RUN ] PaddedVectorTest/9.DefaultConstructorWorks 35: [ OK ] PaddedVectorTest/9.DefaultConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/9.ResizeWorks 35: [ OK ] PaddedVectorTest/9.ResizeWorks (0 ms) 35: [ RUN ] PaddedVectorTest/9.ReserveWorks 35: [ OK ] PaddedVectorTest/9.ReserveWorks (0 ms) 35: [ RUN ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve 35: [ OK ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve (0 ms) 35: [ RUN ] PaddedVectorTest/9.MoveConstructorWorks 35: [ OK ] PaddedVectorTest/9.MoveConstructorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks 35: [ OK ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks (0 ms) 35: [ RUN ] PaddedVectorTest/9.MoveAssignmentWorks 35: [ OK ] PaddedVectorTest/9.MoveAssignmentWorks (0 ms) 35: [ RUN ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical 35: [ OK ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical (0 ms) 35: [ RUN ] PaddedVectorTest/9.CanCopyAssign 35: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms) 35: [ RUN ] PaddedVectorTest/9.CanMoveAssign 35: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms) 35: [ RUN ] PaddedVectorTest/9.CanSwap 35: [ OK ] PaddedVectorTest/9.CanSwap (0 ms) 35: [----------] 11 tests from PaddedVectorTest/9 (0 ms total) 35: 35: [----------] 41 tests from RVecTest 35: [ RUN ] RVecTest.CanBeStoredInVector 35: [ OK ] RVecTest.CanBeStoredInVector (0 ms) 35: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec 35: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms) 35: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec 35: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms) 35: [ RUN ] RVecTest.WorksAsMutable_rvec 35: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms) 35: [ RUN ] RVecTest.WorksAs_rvec_Array 35: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms) 35: [ RUN ] RVecTest.ComparesEqual 35: [ OK ] RVecTest.ComparesEqual (0 ms) 35: [ RUN ] RVecTest.ComparesUnequal 35: [ OK ] RVecTest.ComparesUnequal (0 ms) 35: [ RUN ] RVecTest.CanAddRVecToRvec 35: [ OK ] RVecTest.CanAddRVecToRvec (0 ms) 35: [ RUN ] RVecTest.CanAddAssignRVecToRvec 35: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms) 35: [ RUN ] RVecTest.CanSubtractRVecFromRvec 35: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms) 35: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec 35: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms) 35: [ RUN ] RVecTest.CanDotProductRVecByRvec 35: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms) 35: [ RUN ] RVecTest.CanCrossProductRVecByRvec 35: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms) 35: [ RUN ] RVecTest.CanDivideRVecInplace 35: [ OK ] RVecTest.CanDivideRVecInplace (0 ms) 35: [ RUN ] RVecTest.CanScaleRVec 35: [ OK ] RVecTest.CanScaleRVec (0 ms) 35: [ RUN ] RVecTest.CanDivideRVec 35: [ OK ] RVecTest.CanDivideRVec (0 ms) 35: [ RUN ] RVecTest.CanDoUnitvFromRVec 35: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms) 35: [ RUN ] RVecTest.CanSqLengthOfRVec 35: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms) 35: [ RUN ] RVecTest.CanLengthOfRVec 35: [ OK ] RVecTest.CanLengthOfRVec (0 ms) 35: [ RUN ] RVecTest.CanCastToRVec 35: [ OK ] RVecTest.CanCastToRVec (0 ms) 35: [ RUN ] RVecTest.CanCastToDVec 35: [ OK ] RVecTest.CanCastToDVec (0 ms) 35: [ RUN ] RVecTest.CanLeftScalarMultiply 35: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms) 35: [ RUN ] RVecTest.CanRightScalarMultiply 35: [ OK ] RVecTest.CanRightScalarMultiply (0 ms) 35: [ RUN ] RVecTest.CanGetUnitvFromRVec 35: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms) 35: [ RUN ] RVecTest.CanGetSqLengthOfRVec 35: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms) 35: [ RUN ] RVecTest.CanGetLengthOfRVec 35: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms) 35: [ RUN ] RVecTest.CanDoCrossProductOfRVec 35: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms) 35: [ RUN ] RVecTest.CanDoDotProductOfRVec 35: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms) 35: [ RUN ] RVecTest.CanScaleByVector 35: [ OK ] RVecTest.CanScaleByVector (0 ms) 35: [ RUN ] RVecTest.CanNegate 35: [ OK ] RVecTest.CanNegate (0 ms) 35: [ RUN ] RVecTest.asIVec 35: [ OK ] RVecTest.asIVec (0 ms) 35: [ RUN ] RVecTest.elementWiseMin 35: [ OK ] RVecTest.elementWiseMin (0 ms) 35: [ RUN ] RVecTest.elementWiseMax 35: [ OK ] RVecTest.elementWiseMax (0 ms) 35: [ RUN ] RVecTest.WorksAs_dvec_Reference 35: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms) 35: [ RUN ] RVecTest.WorksAs_ivec_Reference 35: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms) 35: [ RUN ] RVecTest.WorksAs_rvec_Reference 35: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms) 35: [ RUN ] RVecTest.CopyConstructorWorks 35: [ OK ] RVecTest.CopyConstructorWorks (0 ms) 35: [ RUN ] RVecTest.CopyAssignmentWorks 35: [ OK ] RVecTest.CopyAssignmentWorks (0 ms) 35: [ RUN ] RVecTest.MoveConstructorWorks 35: [ OK ] RVecTest.MoveConstructorWorks (0 ms) 35: [ RUN ] RVecTest.MoveAssignmentWorks 35: [ OK ] RVecTest.MoveAssignmentWorks (0 ms) 35: [ RUN ] RVecTest.UsableInConstexpr 35: [ OK ] RVecTest.UsableInConstexpr (0 ms) 35: [----------] 41 tests from RVecTest (0 ms total) 35: 35: [----------] Global test environment tear-down 35: [==========] 328 tests from 41 test suites ran. (91 ms total) 35: [ PASSED ] 328 tests. 35/94 Test #35: MathUnitTests ................................ Passed 0.47 sec test 36 Start 36: MdrunUtilityUnitTests 36: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/mdrunutility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/MdrunUtilityUnitTests.xml" 36: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdrunutility/tests 36: Test timeout computed to be: 30 36: [==========] Running 21 tests from 2 test suites. 36: [----------] Global test environment set-up. 36: [----------] 4 tests from MDModulesNotifierTest 36: [ RUN ] MDModulesNotifierTest.AddConsumer 36: [ OK ] MDModulesNotifierTest.AddConsumer (0 ms) 36: [ RUN ] MDModulesNotifierTest.AddConsumerWithPointerParameter 36: [ OK ] MDModulesNotifierTest.AddConsumerWithPointerParameter (0 ms) 36: [ RUN ] MDModulesNotifierTest.AddTwoDifferentConsumers 36: [ OK ] MDModulesNotifierTest.AddTwoDifferentConsumers (0 ms) 36: [ RUN ] MDModulesNotifierTest.AddConsumerOfTwoResources 36: [ OK ] MDModulesNotifierTest.AddConsumerOfTwoResources (0 ms) 36: [----------] 4 tests from MDModulesNotifierTest (0 ms total) 36: 36: [----------] 17 tests from ThreadAffinityTest 36: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled 36: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (0 ms) 36: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported 36: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms) 36: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads 36: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (0 ms) 36: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads 36: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (0 ms) 36: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads 36: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (0 ms) 36: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware 36: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (0 ms) 36: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads 36: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (0 ms) 36: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset 36: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (0 ms) 36: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride 36: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (0 ms) 36: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto 36: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (0 ms) 36: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced 36: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (0 ms) 36: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced 36: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (0 ms) 36: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread 36: NOTE: Affinity setting failed. 36: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (0 ms) 36: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto 36: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (0 ms) 36: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced 36: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (0 ms) 36: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads 36: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (0 ms) 36: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing 36: NOTE: Affinity setting for 1/2 threads failed. 36: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (0 ms) 36: [----------] 17 tests from ThreadAffinityTest (4 ms total) 36: 36: [----------] Global test environment tear-down 36: [==========] 21 tests from 2 test suites ran. (4 ms total) 36: [ PASSED ] 21 tests. 36/94 Test #36: MdrunUtilityUnitTests ........................ Passed 0.52 sec test 37 Start 37: MdrunUtilityMpiUnitTests 37: Test command: /usr/bin/mpiexec "-n" "4" "/build/reproducible-path/gromacs-2025.0/build/mpi/bin/mdrunutility-mpi-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/MdrunUtilityMpiUnitTests.xml" 37: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdrunutility/tests 37: Test timeout computed to be: 30 37: [==========] Running 13 tests from 2 test suites. 37: [----------] Global test environment set-up. 37: [----------] 6 tests from ThreadAffinityMultiRankTest 37: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode 37: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (35 ms) 37: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride 37: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (0 ms) 37: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes 37: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (0 ms) 37: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled 37: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (0 ms) 37: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto 37: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (0 ms) 37: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce 37: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (0 ms) 37: [----------] 6 tests from ThreadAffinityMultiRankTest (37 ms total) 37: 37: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest 37: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMainOnly 37: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMainOnly (0 ms) 37: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMainOnly 37: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMainOnly (0 ms) 37: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMain 37: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMain (0 ms) 37: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMainOnly 37: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMainOnly (0 ms) 37: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMainOnly 37: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMainOnly (0 ms) 37: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMainOnly 37: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMainOnly (0 ms) 37: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMainOnly 37: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMainOnly (0 ms) 37: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (2 ms total) 37: 37: [----------] Global test environment tear-down 37: [==========] 13 tests from 2 test suites ran. (40 ms total) 37: [ PASSED ] 13 tests. 37/94 Test #37: MdrunUtilityMpiUnitTests ..................... Passed 0.73 sec test 38 Start 38: MDSpanTests 38: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/mdspan-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/MDSpanTests.xml" 38: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdspan/tests 38: Test timeout computed to be: 30 38: [==========] Running 32 tests from 7 test suites. 38: [----------] Global test environment set-up. 38: [----------] 4 tests from BasicAccessorPolicy 38: [ RUN ] BasicAccessorPolicy.Decay 38: [ OK ] BasicAccessorPolicy.Decay (0 ms) 38: [ RUN ] BasicAccessorPolicy.Access 38: [ OK ] BasicAccessorPolicy.Access (0 ms) 38: [ RUN ] BasicAccessorPolicy.Offset 38: [ OK ] BasicAccessorPolicy.Offset (0 ms) 38: [ RUN ] BasicAccessorPolicy.CopyAccessor 38: [ OK ] BasicAccessorPolicy.CopyAccessor (0 ms) 38: [----------] 4 tests from BasicAccessorPolicy (0 ms total) 38: 38: [----------] 4 tests from ExtentsTest 38: [ RUN ] ExtentsTest.Construction 38: [ OK ] ExtentsTest.Construction (0 ms) 38: [ RUN ] ExtentsTest.PurelyStatic 38: [ OK ] ExtentsTest.PurelyStatic (0 ms) 38: [ RUN ] ExtentsTest.RankNought 38: [ OK ] ExtentsTest.RankNought (0 ms) 38: [ RUN ] ExtentsTest.Assignment 38: [ OK ] ExtentsTest.Assignment (0 ms) 38: [----------] 4 tests from ExtentsTest (0 ms total) 38: 38: [----------] 8 tests from MdSpanExtension 38: [ RUN ] MdSpanExtension.SlicingAllStatic 38: [ OK ] MdSpanExtension.SlicingAllStatic (0 ms) 38: [ RUN ] MdSpanExtension.SlicingDynamic 38: [ OK ] MdSpanExtension.SlicingDynamic (0 ms) 38: [ RUN ] MdSpanExtension.SlicingAllStatic3D 38: [ OK ] MdSpanExtension.SlicingAllStatic3D (0 ms) 38: [ RUN ] MdSpanExtension.SlicingEqualsView3D 38: [ OK ] MdSpanExtension.SlicingEqualsView3D (0 ms) 38: [ RUN ] MdSpanExtension.additionWorks 38: [ OK ] MdSpanExtension.additionWorks (0 ms) 38: [ RUN ] MdSpanExtension.subtractionWorks 38: [ OK ] MdSpanExtension.subtractionWorks (0 ms) 38: [ RUN ] MdSpanExtension.multiplicationWorks 38: [ OK ] MdSpanExtension.multiplicationWorks (0 ms) 38: [ RUN ] MdSpanExtension.divisionWorks 38: [ OK ] MdSpanExtension.divisionWorks (0 ms) 38: [----------] 8 tests from MdSpanExtension (0 ms total) 38: 38: [----------] 3 tests from LayoutTests 38: [ RUN ] LayoutTests.LayoutRightConstruction 38: [ OK ] LayoutTests.LayoutRightConstruction (0 ms) 38: [ RUN ] LayoutTests.LayoutRightProperties 38: [ OK ] LayoutTests.LayoutRightProperties (0 ms) 38: [ RUN ] LayoutTests.LayoutRightOperator 38: [ OK ] LayoutTests.LayoutRightOperator (0 ms) 38: [----------] 3 tests from LayoutTests (0 ms total) 38: 38: [----------] 1 test from MdSpanTest 38: [ RUN ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly 38: [ OK ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly (0 ms) 38: [----------] 1 test from MdSpanTest (0 ms total) 38: 38: [----------] 6 tests from MdSpanTest/0, where TypeParam = gmx::basic_mdspan, gmx::layout_right, gmx::accessor_basic > 38: [ RUN ] MdSpanTest/0.Rank 38: [ OK ] MdSpanTest/0.Rank (0 ms) 38: [ RUN ] MdSpanTest/0.DynamicRank 38: [ OK ] MdSpanTest/0.DynamicRank (0 ms) 38: [ RUN ] MdSpanTest/0.Extents 38: [ OK ] MdSpanTest/0.Extents (0 ms) 38: [ RUN ] MdSpanTest/0.Strides 38: [ OK ] MdSpanTest/0.Strides (0 ms) 38: [ RUN ] MdSpanTest/0.Properties 38: [ OK ] MdSpanTest/0.Properties (0 ms) 38: [ RUN ] MdSpanTest/0.Operator 38: [ OK ] MdSpanTest/0.Operator (0 ms) 38: [----------] 6 tests from MdSpanTest/0 (0 ms total) 38: 38: [----------] 6 tests from MdSpanTest/1, where TypeParam = gmx::basic_mdspan, gmx::layout_right, gmx::accessor_basic > 38: [ RUN ] MdSpanTest/1.Rank 38: [ OK ] MdSpanTest/1.Rank (0 ms) 38: [ RUN ] MdSpanTest/1.DynamicRank 38: [ OK ] MdSpanTest/1.DynamicRank (0 ms) 38: [ RUN ] MdSpanTest/1.Extents 38: [ OK ] MdSpanTest/1.Extents (0 ms) 38: [ RUN ] MdSpanTest/1.Strides 38: [ OK ] MdSpanTest/1.Strides (0 ms) 38: [ RUN ] MdSpanTest/1.Properties 38: [ OK ] MdSpanTest/1.Properties (0 ms) 38: [ RUN ] MdSpanTest/1.Operator 38: [ OK ] MdSpanTest/1.Operator (0 ms) 38: [----------] 6 tests from MdSpanTest/1 (0 ms total) 38: 38: [----------] Global test environment tear-down 38: [==========] 32 tests from 7 test suites ran. (0 ms total) 38: [ PASSED ] 32 tests. 38/94 Test #38: MDSpanTests .................................. Passed 0.34 sec test 39 Start 39: MdtypesUnitTest 39: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/mdtypes-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/MdtypesUnitTest.xml" 39: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/mdtypes/tests 39: Test timeout computed to be: 30 39: [==========] Running 97 tests from 7 test suites. 39: [----------] Global test environment set-up. 39: [----------] 4 tests from ForeingLambdaTermsDhdl 39: [ RUN ] ForeingLambdaTermsDhdl.RateCheckWorks 39: [ OK ] ForeingLambdaTermsDhdl.RateCheckWorks (0 ms) 39: [ RUN ] ForeingLambdaTermsDhdl.AllLinear 39: [ OK ] ForeingLambdaTermsDhdl.AllLinear (0 ms) 39: [ RUN ] ForeingLambdaTermsDhdl.AllLinearNegative 39: [ OK ] ForeingLambdaTermsDhdl.AllLinearNegative (0 ms) 39: [ RUN ] ForeingLambdaTermsDhdl.SeparateVdwCoul 39: [ OK ] ForeingLambdaTermsDhdl.SeparateVdwCoul (0 ms) 39: [----------] 4 tests from ForeingLambdaTermsDhdl (0 ms total) 39: 39: [----------] 4 tests from ObservablesReducerTest 39: [ RUN ] ObservablesReducerTest.CanMoveAssign 39: [ OK ] ObservablesReducerTest.CanMoveAssign (0 ms) 39: [ RUN ] ObservablesReducerTest.CanMoveConstruct 39: [ OK ] ObservablesReducerTest.CanMoveConstruct (0 ms) 39: [ RUN ] ObservablesReducerTest.CanBuildAndUseWithNoSubscribers 39: [ OK ] ObservablesReducerTest.CanBuildAndUseWithNoSubscribers (0 ms) 39: [ RUN ] ObservablesReducerTest.CanBuildAndUseWithOneSubscriber 39: [ OK ] ObservablesReducerTest.CanBuildAndUseWithOneSubscriber (0 ms) 39: [----------] 4 tests from ObservablesReducerTest (0 ms total) 39: 39: [----------] 2 tests from CheckpointDataTest 39: [ RUN ] CheckpointDataTest.SingleDataTest 39: [ OK ] CheckpointDataTest.SingleDataTest (1329 ms) 39: [ RUN ] CheckpointDataTest.MultiDataTest 39: [ OK ] CheckpointDataTest.MultiDataTest (2298 ms) 39: [----------] 2 tests from CheckpointDataTest (3627 ms total) 39: 39: [----------] 7 tests from ForceBuffers 39: [ RUN ] ForceBuffers.ConstructsUnpinned 39: [ OK ] ForceBuffers.ConstructsUnpinned (0 ms) 39: [ RUN ] ForceBuffers.ConstructsPinned 39: [ OK ] ForceBuffers.ConstructsPinned (0 ms) 39: [ RUN ] ForceBuffers.ConstructsEmpty 39: [ OK ] ForceBuffers.ConstructsEmpty (0 ms) 39: [ RUN ] ForceBuffers.ResizeWorks 39: [ OK ] ForceBuffers.ResizeWorks (0 ms) 39: [ RUN ] ForceBuffers.PaddingWorks 39: [ OK ] ForceBuffers.PaddingWorks (0 ms) 39: [ RUN ] ForceBuffers.CopyWorks 39: [ OK ] ForceBuffers.CopyWorks (0 ms) 39: [ RUN ] ForceBuffers.CopyDoesNotPin 39: [ OK ] ForceBuffers.CopyDoesNotPin (0 ms) 39: [----------] 7 tests from ForceBuffers (0 ms total) 39: 39: [----------] 5 tests from MultipleTimeStepping 39: [ RUN ] MultipleTimeStepping.ChecksNumLevels 39: [ OK ] MultipleTimeStepping.ChecksNumLevels (0 ms) 39: [ RUN ] MultipleTimeStepping.SelectsForceGroups 39: [ OK ] MultipleTimeStepping.SelectsForceGroups (0 ms) 39: [ RUN ] MultipleTimeStepping.ChecksStepFactor 39: [ OK ] MultipleTimeStepping.ChecksStepFactor (0 ms) 39: [ RUN ] MultipleTimeStepping.ChecksPmeIsAtLastLevel 39: [ OK ] MultipleTimeStepping.ChecksPmeIsAtLastLevel (0 ms) 39: [ RUN ] MultipleTimeStepping.ChecksIntegrator 39: [ OK ] MultipleTimeStepping.ChecksIntegrator (0 ms) 39: [----------] 5 tests from MultipleTimeStepping (0 ms total) 39: 39: [----------] 60 tests from WithVariousSubscriberCounts/ObservablesReducerIntegrationTest 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks2 (1 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks3 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks1 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks1 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks2 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks2 (0 ms) 39: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks3 39: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks3 (0 ms) 39: [----------] 60 tests from WithVariousSubscriberCounts/ObservablesReducerIntegrationTest (9 ms total) 39: 39: [----------] 15 tests from ChecksStepInterval/MtsIntervalTest 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/0 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/0 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/1 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/1 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/2 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/2 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/3 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/3 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/4 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/4 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/5 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/5 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/6 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/6 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/7 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/7 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/8 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/8 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/9 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/9 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/10 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/10 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/11 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/11 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/12 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/12 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/13 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/13 (0 ms) 39: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/14 39: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/14 (0 ms) 39: [----------] 15 tests from ChecksStepInterval/MtsIntervalTest (1 ms total) 39: 39: [----------] Global test environment tear-down 39: [==========] 97 tests from 7 test suites ran. (3640 ms total) 39: [ PASSED ] 97 tests. 39/94 Test #39: MdtypesUnitTest .............................. Passed 3.98 sec test 40 Start 40: OnlineHelpUnitTests 40: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/onlinehelp-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/OnlineHelpUnitTests.xml" 40: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/onlinehelp/tests 40: Test timeout computed to be: 30 40: [==========] Running 22 tests from 4 test suites. 40: [----------] Global test environment set-up. 40: [----------] 6 tests from TextTableFormatterTest 40: [ RUN ] TextTableFormatterTest.HandlesBasicCase 40: [ OK ] TextTableFormatterTest.HandlesBasicCase (0 ms) 40: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles 40: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (0 ms) 40: [ RUN ] TextTableFormatterTest.HandlesIndentation 40: [ OK ] TextTableFormatterTest.HandlesIndentation (0 ms) 40: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines 40: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (0 ms) 40: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding 40: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (0 ms) 40: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns 40: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (0 ms) 40: [----------] 6 tests from TextTableFormatterTest (0 ms total) 40: 40: [----------] 3 tests from HelpManagerTest 40: [ RUN ] HelpManagerTest.HandlesRootTopic 40: [ OK ] HelpManagerTest.HandlesRootTopic (0 ms) 40: [ RUN ] HelpManagerTest.HandlesSubTopics 40: [ OK ] HelpManagerTest.HandlesSubTopics (0 ms) 40: [ RUN ] HelpManagerTest.HandlesInvalidTopics 40: [ OK ] HelpManagerTest.HandlesInvalidTopics (0 ms) 40: [----------] 3 tests from HelpManagerTest (0 ms total) 40: 40: [----------] 2 tests from HelpTopicFormattingTest 40: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic 40: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (1 ms) 40: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics 40: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (0 ms) 40: [----------] 2 tests from HelpTopicFormattingTest (1 ms total) 40: 40: [----------] 11 tests from HelpWriterContextTest 40: [ RUN ] HelpWriterContextTest.FormatsParagraphs 40: [ OK ] HelpWriterContextTest.FormatsParagraphs (0 ms) 40: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs 40: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (0 ms) 40: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace 40: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (0 ms) 40: [ RUN ] HelpWriterContextTest.FormatsLiteralText 40: [ OK ] HelpWriterContextTest.FormatsLiteralText (0 ms) 40: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning 40: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (0 ms) 40: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation 40: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (0 ms) 40: [ RUN ] HelpWriterContextTest.FormatsBulletList 40: [ OK ] HelpWriterContextTest.FormatsBulletList (0 ms) 40: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList 40: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (0 ms) 40: [ RUN ] HelpWriterContextTest.FormatsSimpleTable 40: [ OK ] HelpWriterContextTest.FormatsSimpleTable (0 ms) 40: [ RUN ] HelpWriterContextTest.FormatsGridTable 40: [ OK ] HelpWriterContextTest.FormatsGridTable (0 ms) 40: [ RUN ] HelpWriterContextTest.FormatsTitles 40: [ OK ] HelpWriterContextTest.FormatsTitles (0 ms) 40: [----------] 11 tests from HelpWriterContextTest (0 ms total) 40: 40: [----------] Global test environment tear-down 40: [==========] 22 tests from 4 test suites ran. (3 ms total) 40: [ PASSED ] 22 tests. 40/94 Test #40: OnlineHelpUnitTests .......................... Passed 0.39 sec test 41 Start 41: OptionsUnitTests 41: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/options-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/OptionsUnitTests.xml" 41: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/options/tests 41: Test timeout computed to be: 30 41: [==========] Running 112 tests from 18 test suites. 41: [----------] Global test environment set-up. 41: [----------] 5 tests from AbstractOptionStorageTest 41: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish 41: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (0 ms) 41: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval 41: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (0 ms) 41: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition 41: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (0 ms) 41: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition 41: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (0 ms) 41: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues 41: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (0 ms) 41: [----------] 5 tests from AbstractOptionStorageTest (0 ms total) 41: 41: [----------] 10 tests from FileNameOptionTest 41: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension 41: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (0 ms) 41: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue 41: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms) 41: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption 41: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms) 41: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension 41: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms) 41: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension 41: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms) 41: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension 41: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms) 41: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix 41: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (0 ms) 41: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix 41: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms) 41: [ RUN ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension 41: [ OK ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension (0 ms) 41: [ RUN ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue 41: [ OK ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue (0 ms) 41: [----------] 10 tests from FileNameOptionTest (0 ms total) 41: 41: [----------] 16 tests from FileNameOptionManagerTest 41: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension 41: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms) 41: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension 41: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms) 41: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile 41: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (0 ms) 41: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile 41: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (0 ms) 41: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile 41: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (0 ms) 41: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile 41: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms) 41: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified 41: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms) 41: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified 41: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms) 41: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified 41: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms) 41: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile 41: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms) 41: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile 41: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms) 41: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile 41: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms) 41: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile 41: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms) 41: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile 41: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms) 41: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking 41: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms) 41: [ RUN ] FileNameOptionManagerTest.AcceptsCompressedInputFile 41: [ OK ] FileNameOptionManagerTest.AcceptsCompressedInputFile (0 ms) 41: [----------] 16 tests from FileNameOptionManagerTest (0 ms total) 41: 41: [----------] 1 test from OptionsTest 41: [ RUN ] OptionsTest.FailsOnNonsafeStorage 41: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms) 41: [----------] 1 test from OptionsTest (0 ms total) 41: 41: [----------] 9 tests from OptionsAssignerTest 41: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter 41: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms) 41: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue 41: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms) 41: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter 41: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (0 ms) 41: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter 41: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms) 41: [ RUN ] OptionsAssignerTest.HandlesMissingValue 41: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms) 41: [ RUN ] OptionsAssignerTest.HandlesExtraValue 41: [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms) 41: [ RUN ] OptionsAssignerTest.HandlesGroups 41: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms) 41: [ RUN ] OptionsAssignerTest.HandlesSections 41: [ OK ] OptionsAssignerTest.HandlesSections (0 ms) 41: [ RUN ] OptionsAssignerTest.HandlesMultipleSources 41: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms) 41: [----------] 9 tests from OptionsAssignerTest (0 ms total) 41: 41: [----------] 4 tests from OptionsAssignerBooleanTest 41: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue 41: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms) 41: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue 41: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms) 41: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo 41: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms) 41: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue 41: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms) 41: [----------] 4 tests from OptionsAssignerBooleanTest (0 ms total) 41: 41: [----------] 13 tests from OptionsAssignerIntegerTest 41: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue 41: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue 41: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue 41: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow 41: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue 41: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet 41: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet 41: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues 41: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.StoresToVector 41: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors 41: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue 41: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue 41: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms) 41: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment 41: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms) 41: [----------] 13 tests from OptionsAssignerIntegerTest (0 ms total) 41: 41: [----------] 5 tests from OptionsAssignerDoubleTest 41: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue 41: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms) 41: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat 41: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms) 41: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue 41: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (0 ms) 41: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue 41: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms) 41: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue 41: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms) 41: [----------] 5 tests from OptionsAssignerDoubleTest (0 ms total) 41: 41: [----------] 9 tests from OptionsAssignerStringTest 41: [ RUN ] OptionsAssignerStringTest.StoresSingleValue 41: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms) 41: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue 41: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms) 41: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray 41: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms) 41: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue 41: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms) 41: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue 41: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms) 41: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue 41: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms) 41: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue 41: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms) 41: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable 41: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms) 41: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector 41: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms) 41: [----------] 9 tests from OptionsAssignerStringTest (0 ms total) 41: 41: [----------] 6 tests from OptionsAssignerEnumTest 41: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue 41: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms) 41: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues 41: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms) 41: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange 41: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms) 41: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue 41: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms) 41: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable 41: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms) 41: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector 41: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms) 41: [----------] 6 tests from OptionsAssignerEnumTest (0 ms total) 41: 41: [----------] 8 tests from RepeatingOptionSectionTest 41: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance 41: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms) 41: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption 41: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms) 41: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance 41: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms) 41: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue 41: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms) 41: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances 41: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms) 41: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault 41: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms) 41: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault 41: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms) 41: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections 41: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms) 41: [----------] 8 tests from RepeatingOptionSectionTest (0 ms total) 41: 41: [----------] 1 test from TimeUnitManagerTest 41: [ RUN ] TimeUnitManagerTest.BasicOperations 41: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms) 41: [----------] 1 test from TimeUnitManagerTest (0 ms total) 41: 41: [----------] 4 tests from TimeUnitBehaviorTest 41: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue 41: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms) 41: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues 41: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms) 41: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources 41: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms) 41: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks 41: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms) 41: [----------] 4 tests from TimeUnitBehaviorTest (0 ms total) 41: 41: [----------] 2 tests from TreeValueSupportAssignTest 41: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree 41: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (0 ms) 41: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays 41: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms) 41: [----------] 2 tests from TreeValueSupportAssignTest (0 ms total) 41: 41: [----------] 1 test from TreeValueSupportAssignErrorTest 41: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue 41: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (0 ms) 41: [----------] 1 test from TreeValueSupportAssignErrorTest (0 ms total) 41: 41: [----------] 5 tests from TreeValueSupportCheckTest 41: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty 41: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms) 41: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree 41: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms) 41: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1 41: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms) 41: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2 41: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms) 41: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue 41: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms) 41: [----------] 5 tests from TreeValueSupportCheckTest (0 ms total) 41: 41: [----------] 6 tests from TreeValueSupportAdjustTest 41: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues 41: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (0 ms) 41: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues 41: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (0 ms) 41: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues 41: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (0 ms) 41: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues 41: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (0 ms) 41: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues 41: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (0 ms) 41: [ RUN ] TreeValueSupportAdjustTest.OrdersValues 41: [ OK ] TreeValueSupportAdjustTest.OrdersValues (0 ms) 41: [----------] 6 tests from TreeValueSupportAdjustTest (0 ms total) 41: 41: [----------] 7 tests from TreeValueSupportTest 41: [ RUN ] TreeValueSupportTest.SupportsBooleanOption 41: [ OK ] TreeValueSupportTest.SupportsBooleanOption (0 ms) 41: [ RUN ] TreeValueSupportTest.SupportsIntegerOption 41: [ OK ] TreeValueSupportTest.SupportsIntegerOption (0 ms) 41: [ RUN ] TreeValueSupportTest.SupportsInt64Option 41: [ OK ] TreeValueSupportTest.SupportsInt64Option (0 ms) 41: [ RUN ] TreeValueSupportTest.SupportsStringOption 41: [ OK ] TreeValueSupportTest.SupportsStringOption (0 ms) 41: [ RUN ] TreeValueSupportTest.SupportsFloatOption 41: [ OK ] TreeValueSupportTest.SupportsFloatOption (0 ms) 41: [ RUN ] TreeValueSupportTest.SupportsDoubleOption 41: [ OK ] TreeValueSupportTest.SupportsDoubleOption (0 ms) 41: [ RUN ] TreeValueSupportTest.SupportsEnumOption 41: [ OK ] TreeValueSupportTest.SupportsEnumOption (0 ms) 41: [----------] 7 tests from TreeValueSupportTest (1 ms total) 41: 41: [----------] Global test environment tear-down 41: [==========] 112 tests from 18 test suites ran. (5 ms total) 41: [ PASSED ] 112 tests. 41/94 Test #41: OptionsUnitTests ............................. Passed 0.38 sec test 42 Start 42: PbcutilUnitTest 42: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/pbcutil-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/PbcutilUnitTest.xml" 42: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/pbcutil/tests 42: Test timeout computed to be: 30 42: [==========] Running 37 tests from 5 test suites. 42: [----------] Global test environment set-up. 42: [----------] 1 test from ShiftTest 42: [ RUN ] ShiftTest.CoordinateShiftWorks 42: [ OK ] ShiftTest.CoordinateShiftWorks (0 ms) 42: [----------] 1 test from ShiftTest (0 ms total) 42: 42: [----------] 2 tests from MShift 42: [ RUN ] MShift.shiftsAndUnshifts 42: [ OK ] MShift.shiftsAndUnshifts (0 ms) 42: [ RUN ] MShift.shiftsAndUnshiftsSelf 42: [ OK ] MShift.shiftsAndUnshiftsSelf (0 ms) 42: [----------] 2 tests from MShift (0 ms total) 42: 42: [----------] 5 tests from PbcTest 42: [ RUN ] PbcTest.CalcShiftsWorks 42: [ OK ] PbcTest.CalcShiftsWorks (0 ms) 42: [ RUN ] PbcTest.PutAtomsInCubicBoxAlreadyInBox 42: [ OK ] PbcTest.PutAtomsInCubicBoxAlreadyInBox (0 ms) 42: [ RUN ] PbcTest.PutAtomsInCubicBoxFromOutsideBox 42: [ OK ] PbcTest.PutAtomsInCubicBoxFromOutsideBox (0 ms) 42: [ RUN ] PbcTest.PutAtomsInTriclinicBoxFromOutsideBox 42: [ OK ] PbcTest.PutAtomsInTriclinicBoxFromOutsideBox (0 ms) 42: [ RUN ] PbcTest.PutAtomsInBoxHandlesInf 42: [ OK ] PbcTest.PutAtomsInBoxHandlesInf (0 ms) 42: [----------] 5 tests from PbcTest (0 ms total) 42: 42: [----------] 2 tests from PbcEnumsTest 42: [ RUN ] PbcEnumsTest.CenteringTypeNamesAreCorrect 42: [ OK ] PbcEnumsTest.CenteringTypeNamesAreCorrect (0 ms) 42: [ RUN ] PbcEnumsTest.UnitCellTypeNamesAreCorrect 42: [ OK ] PbcEnumsTest.UnitCellTypeNamesAreCorrect (0 ms) 42: [----------] 2 tests from PbcEnumsTest (0 ms total) 42: 42: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 (0 ms) 42: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 42: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 (0 ms) 42: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest (4 ms total) 42: 42: [----------] Global test environment tear-down 42: [==========] 37 tests from 5 test suites ran. (5 ms total) 42: [ PASSED ] 37 tests. 42/94 Test #42: PbcutilUnitTest .............................. Passed 0.34 sec test 43 Start 43: RandomUnitTests 43: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/random-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/RandomUnitTests.xml" 43: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/random/tests 43: Test timeout computed to be: 30 43: [==========] Running 44 tests from 10 test suites. 43: [----------] Global test environment set-up. 43: [----------] 4 tests from ExponentialDistributionTest 43: [ RUN ] ExponentialDistributionTest.Output 43: [ OK ] ExponentialDistributionTest.Output (0 ms) 43: [ RUN ] ExponentialDistributionTest.Logical 43: [ OK ] ExponentialDistributionTest.Logical (0 ms) 43: [ RUN ] ExponentialDistributionTest.Reset 43: [ OK ] ExponentialDistributionTest.Reset (0 ms) 43: [ RUN ] ExponentialDistributionTest.AltParam 43: [ OK ] ExponentialDistributionTest.AltParam (0 ms) 43: [----------] 4 tests from ExponentialDistributionTest (0 ms total) 43: 43: [----------] 4 tests from GammaDistributionTest 43: [ RUN ] GammaDistributionTest.Output 43: [ OK ] GammaDistributionTest.Output (0 ms) 43: [ RUN ] GammaDistributionTest.Logical 43: [ OK ] GammaDistributionTest.Logical (0 ms) 43: [ RUN ] GammaDistributionTest.Reset 43: [ OK ] GammaDistributionTest.Reset (0 ms) 43: [ RUN ] GammaDistributionTest.AltParam 43: [ OK ] GammaDistributionTest.AltParam (0 ms) 43: [----------] 4 tests from GammaDistributionTest (0 ms total) 43: 43: [----------] 4 tests from NormalDistributionTest 43: [ RUN ] NormalDistributionTest.Output 43: [ OK ] NormalDistributionTest.Output (0 ms) 43: [ RUN ] NormalDistributionTest.Logical 43: [ OK ] NormalDistributionTest.Logical (0 ms) 43: [ RUN ] NormalDistributionTest.Reset 43: [ OK ] NormalDistributionTest.Reset (0 ms) 43: [ RUN ] NormalDistributionTest.AltParam 43: [ OK ] NormalDistributionTest.AltParam (0 ms) 43: [----------] 4 tests from NormalDistributionTest (0 ms total) 43: 43: [----------] 1 test from SeedTest 43: [ RUN ] SeedTest.makeRandomSeed 43: [ OK ] SeedTest.makeRandomSeed (0 ms) 43: [----------] 1 test from SeedTest (0 ms total) 43: 43: [----------] 6 tests from TabulatedNormalDistributionTest 43: [ RUN ] TabulatedNormalDistributionTest.Output14 43: [ OK ] TabulatedNormalDistributionTest.Output14 (0 ms) 43: [ RUN ] TabulatedNormalDistributionTest.Output16 43: [ OK ] TabulatedNormalDistributionTest.Output16 (0 ms) 43: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14 43: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (0 ms) 43: [ RUN ] TabulatedNormalDistributionTest.Logical 43: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms) 43: [ RUN ] TabulatedNormalDistributionTest.Reset 43: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms) 43: [ RUN ] TabulatedNormalDistributionTest.AltParam 43: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms) 43: [----------] 6 tests from TabulatedNormalDistributionTest (0 ms total) 43: 43: [----------] 1 test from TabulatedNormalDistributionTableTest 43: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties 43: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (0 ms) 43: [----------] 1 test from TabulatedNormalDistributionTableTest (0 ms total) 43: 43: [----------] 6 tests from ThreeFry2x64Test 43: [ RUN ] ThreeFry2x64Test.Logical 43: [ OK ] ThreeFry2x64Test.Logical (0 ms) 43: [ RUN ] ThreeFry2x64Test.InternalCounterSequence 43: [ OK ] ThreeFry2x64Test.InternalCounterSequence (0 ms) 43: [ RUN ] ThreeFry2x64Test.Reseed 43: [ OK ] ThreeFry2x64Test.Reseed (0 ms) 43: [ RUN ] ThreeFry2x64Test.Discard 43: [ OK ] ThreeFry2x64Test.Discard (0 ms) 43: [ RUN ] ThreeFry2x64Test.InvalidCounter 43: [ OK ] ThreeFry2x64Test.InvalidCounter (0 ms) 43: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter 43: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms) 43: [----------] 6 tests from ThreeFry2x64Test (0 ms total) 43: 43: [----------] 4 tests from UniformIntDistributionTest 43: [ RUN ] UniformIntDistributionTest.Output 43: [ OK ] UniformIntDistributionTest.Output (0 ms) 43: [ RUN ] UniformIntDistributionTest.Logical 43: [ OK ] UniformIntDistributionTest.Logical (0 ms) 43: [ RUN ] UniformIntDistributionTest.Reset 43: [ OK ] UniformIntDistributionTest.Reset (0 ms) 43: [ RUN ] UniformIntDistributionTest.AltParam 43: [ OK ] UniformIntDistributionTest.AltParam (0 ms) 43: [----------] 4 tests from UniformIntDistributionTest (0 ms total) 43: 43: [----------] 5 tests from UniformRealDistributionTest 43: [ RUN ] UniformRealDistributionTest.GenerateCanonical 43: [ OK ] UniformRealDistributionTest.GenerateCanonical (0 ms) 43: [ RUN ] UniformRealDistributionTest.Output 43: [ OK ] UniformRealDistributionTest.Output (0 ms) 43: [ RUN ] UniformRealDistributionTest.Logical 43: [ OK ] UniformRealDistributionTest.Logical (0 ms) 43: [ RUN ] UniformRealDistributionTest.Reset 43: [ OK ] UniformRealDistributionTest.Reset (0 ms) 43: [ RUN ] UniformRealDistributionTest.AltParam 43: [ OK ] UniformRealDistributionTest.AltParam (0 ms) 43: [----------] 5 tests from UniformRealDistributionTest (0 ms total) 43: 43: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test 43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0 43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (0 ms) 43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1 43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (0 ms) 43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2 43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (0 ms) 43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (0 ms) 43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (0 ms) 43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (0 ms) 43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (0 ms) 43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (0 ms) 43: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 43: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (0 ms) 43: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (0 ms total) 43: 43: [----------] Global test environment tear-down 43: [==========] 44 tests from 10 test suites ran. (2 ms total) 43: [ PASSED ] 44 tests. 43/94 Test #43: RandomUnitTests .............................. Passed 0.35 sec test 44 Start 44: RestraintTests 44: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/restraintpotential-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/RestraintTests.xml" 44: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/restraint/tests 44: Test timeout computed to be: 30 44: [==========] Running 1 test from 1 test suite. 44: [----------] Global test environment set-up. 44: [----------] 1 test from RestraintManager 44: [ RUN ] RestraintManager.restraintList 44: [ OK ] RestraintManager.restraintList (0 ms) 44: [----------] 1 test from RestraintManager (0 ms total) 44: 44: [----------] Global test environment tear-down 44: [==========] 1 test from 1 test suite ran. (0 ms total) 44: [ PASSED ] 1 test. 44/94 Test #44: RestraintTests ............................... Passed 0.34 sec test 45 Start 45: TableUnitTests 45: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/table-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/TableUnitTests.xml" 45: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tables/tests 45: Test timeout computed to be: 30 45: [==========] Running 20 tests from 2 test suites. 45: [----------] Global test environment set-up. 45: [----------] 10 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable 45: [ RUN ] SplineTableTest/0.HandlesIncorrectInput 45: [ OK ] SplineTableTest/0.HandlesIncorrectInput (1 ms) 45: [ RUN ] SplineTableTest/0.Sinc 45: [ OK ] SplineTableTest/0.Sinc (0 ms) 45: [ RUN ] SplineTableTest/0.LJ12 45: [ OK ] SplineTableTest/0.LJ12 (15 ms) 45: [ RUN ] SplineTableTest/0.PmeCorrection 45: [ OK ] SplineTableTest/0.PmeCorrection (1 ms) 45: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput 45: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (0 ms) 45: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr 45: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (0 ms) 45: [ RUN ] SplineTableTest/0.TwoFunctions 45: [ OK ] SplineTableTest/0.TwoFunctions (26 ms) 45: [ RUN ] SplineTableTest/0.ThreeFunctions 45: [ OK ] SplineTableTest/0.ThreeFunctions (28 ms) 45: [ RUN ] SplineTableTest/0.Simd 45: [ OK ] SplineTableTest/0.Simd (5 ms) 45: [ RUN ] SplineTableTest/0.SimdTwoFunctions 45: [ OK ] SplineTableTest/0.SimdTwoFunctions (25 ms) 45: [----------] 10 tests from SplineTableTest/0 (106 ms total) 45: 45: [----------] 10 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable 45: [ RUN ] SplineTableTest/1.HandlesIncorrectInput 45: [ OK ] SplineTableTest/1.HandlesIncorrectInput (1 ms) 45: [ RUN ] SplineTableTest/1.Sinc 45: [ OK ] SplineTableTest/1.Sinc (0 ms) 45: [ RUN ] SplineTableTest/1.LJ12 45: [ OK ] SplineTableTest/1.LJ12 (1 ms) 45: [ RUN ] SplineTableTest/1.PmeCorrection 45: [ OK ] SplineTableTest/1.PmeCorrection (1 ms) 45: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput 45: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (0 ms) 45: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr 45: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (0 ms) 45: [ RUN ] SplineTableTest/1.TwoFunctions 45: [ OK ] SplineTableTest/1.TwoFunctions (3 ms) 45: [ RUN ] SplineTableTest/1.ThreeFunctions 45: [ OK ] SplineTableTest/1.ThreeFunctions (3 ms) 45: [ RUN ] SplineTableTest/1.Simd 45: [ OK ] SplineTableTest/1.Simd (1 ms) 45: [ RUN ] SplineTableTest/1.SimdTwoFunctions 45: [ OK ] SplineTableTest/1.SimdTwoFunctions (3 ms) 45: [----------] 10 tests from SplineTableTest/1 (18 ms total) 45: 45: [----------] Global test environment tear-down 45: [==========] 20 tests from 2 test suites ran. (124 ms total) 45: [ PASSED ] 20 tests. 45/94 Test #45: TableUnitTests ............................... Passed 0.46 sec test 46 Start 46: TaskAssignmentUnitTests 46: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/taskassignment-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/TaskAssignmentUnitTests.xml" 46: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/taskassignment/tests 46: Test timeout computed to be: 30 46: [==========] Running 3 tests from 2 test suites. 46: [----------] Global test environment set-up. 46: [----------] 2 tests from UserTaskAssignmentStringHandlingTest 46: [ RUN ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork 46: [ OK ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork (0 ms) 46: [ RUN ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid 46: [ OK ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid (0 ms) 46: [----------] 2 tests from UserTaskAssignmentStringHandlingTest (0 ms total) 46: 46: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest 46: [ RUN ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow 46: [ OK ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow (0 ms) 46: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest (0 ms total) 46: 46: [----------] Global test environment tear-down 46: [==========] 3 tests from 2 test suites ran. (0 ms total) 46: [ PASSED ] 3 tests. 46/94 Test #46: TaskAssignmentUnitTests ...................... Passed 0.33 sec test 47 Start 47: GmxTimingTests 47: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/timing-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/GmxTimingTests.xml" 47: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/timing/tests 47: Test timeout computed to be: 30 47: [==========] Running 6 tests from 1 test suite. 47: [----------] Global test environment set-up. 47: [----------] 6 tests from TimingTest 47: [ RUN ] TimingTest.ElementCountingWorks 47: [ OK ] TimingTest.ElementCountingWorks (0 ms) 47: [ RUN ] TimingTest.ElementNoCountingWorks 47: [ OK ] TimingTest.ElementNoCountingWorks (0 ms) 47: [ RUN ] TimingTest.SubElementCountingWorks 47: [ OK ] TimingTest.SubElementCountingWorks (0 ms) 47: [ RUN ] TimingTest.SubElementNoCountingWorks 47: [ OK ] TimingTest.SubElementNoCountingWorks (0 ms) 47: [ RUN ] TimingTest.RunWallCycle 47: [ OK ] TimingTest.RunWallCycle (1 ms) 47: [ RUN ] TimingTest.RunWallCycleSub 47: [ OK ] TimingTest.RunWallCycleSub (0 ms) 47: [----------] 6 tests from TimingTest (1 ms total) 47: 47: [----------] Global test environment tear-down 47: [==========] 6 tests from 1 test suite ran. (1 ms total) 47: [ PASSED ] 6 tests. 47/94 Test #47: GmxTimingTests ............................... Passed 0.34 sec test 48 Start 48: TopologyTest 48: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/topology-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/TopologyTest.xml" 48: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/topology/tests 48: Test timeout computed to be: 30 48: [==========] Running 153 tests from 10 test suites. 48: [----------] Global test environment set-up. 48: [----------] 3 tests from PdbAtomEntryTest 48: [ RUN ] PdbAtomEntryTest.CanCreateBasicEntry 48: [ OK ] PdbAtomEntryTest.CanCreateBasicEntry (0 ms) 48: [ RUN ] PdbAtomEntryTest.CanCreateEntryWithOccupAndBfac 48: [ OK ] PdbAtomEntryTest.CanCreateEntryWithOccupAndBfac (0 ms) 48: [ RUN ] PdbAtomEntryTest.CanCreateFullEntry 48: [ OK ] PdbAtomEntryTest.CanCreateFullEntry (0 ms) 48: [----------] 3 tests from PdbAtomEntryTest (0 ms total) 48: 48: [----------] 3 tests from ExclusionBlockTest 48: [ RUN ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks 48: [ OK ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks (0 ms) 48: [ RUN ] ExclusionBlockTest.ConvertExclusionBlockToBlocka 48: [ OK ] ExclusionBlockTest.ConvertExclusionBlockToBlocka (0 ms) 48: [ RUN ] ExclusionBlockTest.MergeExclusions 48: [ OK ] ExclusionBlockTest.MergeExclusions (0 ms) 48: [----------] 3 tests from ExclusionBlockTest (0 ms total) 48: 48: [----------] 6 tests from InteractionListTest 48: [ RUN ] InteractionListTest.EmptyWorks 48: [ OK ] InteractionListTest.EmptyWorks (0 ms) 48: [ RUN ] InteractionListTest.CanAddInteractionArray 48: [ OK ] InteractionListTest.CanAddInteractionArray (0 ms) 48: [ RUN ] InteractionListTest.CanAddInteractionArrayMultipleAtoms 48: [ OK ] InteractionListTest.CanAddInteractionArrayMultipleAtoms (0 ms) 48: [ RUN ] InteractionListTest.CanAddInteractionPointer 48: [ OK ] InteractionListTest.CanAddInteractionPointer (0 ms) 48: [ RUN ] InteractionListTest.CanAddListToOtherList 48: [ OK ] InteractionListTest.CanAddListToOtherList (0 ms) 48: [ RUN ] InteractionListTest.ClearingWorks 48: [ OK ] InteractionListTest.ClearingWorks (0 ms) 48: [----------] 6 tests from InteractionListTest (0 ms total) 48: 48: [----------] 3 tests from IndexTest 48: [ RUN ] IndexTest.AnalyseWorksDefaultGroups 48: 48: WARNING: Masses and atomic (Van der Waals) radii will be guessed 48: based on residue and atom names, since they could not be 48: definitively assigned from the information in your input 48: files. These guessed numbers might deviate from the mass 48: and radius of the atom type. Please check the output 48: files if necessary. Note, that this functionality may 48: be removed in a future GROMACS version. Please, consider 48: using another file format for your input. 48: 48: [ OK ] IndexTest.AnalyseWorksDefaultGroups (3 ms) 48: [ RUN ] IndexTest.WriteIndexWorks 48: 48: WARNING: Masses and atomic (Van der Waals) radii will be guessed 48: based on residue and atom names, since they could not be 48: definitively assigned from the information in your input 48: files. These guessed numbers might deviate from the mass 48: and radius of the atom type. Please check the output 48: files if necessary. Note, that this functionality may 48: be removed in a future GROMACS version. Please, consider 48: using another file format for your input. 48: 48: [ OK ] IndexTest.WriteIndexWorks (47 ms) 48: [ RUN ] IndexTest.WriteAndReadIndexWorks 48: 48: WARNING: Masses and atomic (Van der Waals) radii will be guessed 48: based on residue and atom names, since they could not be 48: definitively assigned from the information in your input 48: files. These guessed numbers might deviate from the mass 48: and radius of the atom type. Please check the output 48: files if necessary. Note, that this functionality may 48: be removed in a future GROMACS version. Please, consider 48: using another file format for your input. 48: 48: [ OK ] IndexTest.WriteAndReadIndexWorks (60 ms) 48: [----------] 3 tests from IndexTest (112 ms total) 48: 48: [----------] 4 tests from MtopTest 48: [ RUN ] MtopTest.RangeBasedLoop 48: [ OK ] MtopTest.RangeBasedLoop (0 ms) 48: [ RUN ] MtopTest.Operators 48: [ OK ] MtopTest.Operators (0 ms) 48: [ RUN ] MtopTest.CanFindResidueStartAndEndAtoms 48: [ OK ] MtopTest.CanFindResidueStartAndEndAtoms (0 ms) 48: [ RUN ] MtopTest.CanSortPerturbedInteractionsCorrectly 48: [ OK ] MtopTest.CanSortPerturbedInteractionsCorrectly (0 ms) 48: [----------] 4 tests from MtopTest (0 ms total) 48: 48: [----------] 2 tests from IListRangeTest 48: [ RUN ] IListRangeTest.RangeBasedLoopWorks 48: [ OK ] IListRangeTest.RangeBasedLoopWorks (0 ms) 48: [ RUN ] IListRangeTest.RangeBasedLoopWithIntermolecularInteraction 48: [ OK ] IListRangeTest.RangeBasedLoopWithIntermolecularInteraction (0 ms) 48: [----------] 2 tests from IListRangeTest (0 ms total) 48: 48: [----------] 13 tests from StringTableTest 48: [ RUN ] StringTableTest.AddSingleEntry 48: [ OK ] StringTableTest.AddSingleEntry (36 ms) 48: [ RUN ] StringTableTest.CanAccessWithAt 48: [ OK ] StringTableTest.CanAccessWithAt (0 ms) 48: [ RUN ] StringTableTest.CanAccessWithBracket 48: [ OK ] StringTableTest.CanAccessWithBracket (0 ms) 48: [ RUN ] StringTableTest.ThrowsOutOfRange 48: [ OK ] StringTableTest.ThrowsOutOfRange (0 ms) 48: [ RUN ] StringTableTest.StringCompareIsCorrect 48: [ OK ] StringTableTest.StringCompareIsCorrect (0 ms) 48: [ RUN ] StringTableTest.AddTwoDistinctEntries 48: [ OK ] StringTableTest.AddTwoDistinctEntries (0 ms) 48: [ RUN ] StringTableTest.TryToAddDuplicates 48: [ OK ] StringTableTest.TryToAddDuplicates (0 ms) 48: [ RUN ] StringTableTest.AddLargeNumberOfEntries 48: [ OK ] StringTableTest.AddLargeNumberOfEntries (0 ms) 48: [ RUN ] StringTableTest.NoDuplicatesInLargeTable 48: [ OK ] StringTableTest.NoDuplicatesInLargeTable (0 ms) 48: [ RUN ] StringTableTest.CanWriteToBuffer 48: [ OK ] StringTableTest.CanWriteToBuffer (0 ms) 48: [ RUN ] StringTableTest.Roundtrip 48: [ OK ] StringTableTest.Roundtrip (0 ms) 48: [ RUN ] StringTableTest.RoundtripWithCorrectStringIndices 48: [ OK ] StringTableTest.RoundtripWithCorrectStringIndices (0 ms) 48: [ RUN ] StringTableTest.CanCopyToLegacyTable 48: [ OK ] StringTableTest.CanCopyToLegacyTable (0 ms) 48: [----------] 13 tests from StringTableTest (38 ms total) 48: 48: [----------] 6 tests from LegacySymtabTest 48: [ RUN ] LegacySymtabTest.EmptyOnOpen 48: [ OK ] LegacySymtabTest.EmptyOnOpen (0 ms) 48: [ RUN ] LegacySymtabTest.AddSingleEntry 48: [ OK ] LegacySymtabTest.AddSingleEntry (0 ms) 48: [ RUN ] LegacySymtabTest.AddTwoDistinctEntries 48: [ OK ] LegacySymtabTest.AddTwoDistinctEntries (0 ms) 48: [ RUN ] LegacySymtabTest.TryToAddDuplicates 48: [ OK ] LegacySymtabTest.TryToAddDuplicates (0 ms) 48: [ RUN ] LegacySymtabTest.AddLargeNumberOfEntries 48: [ OK ] LegacySymtabTest.AddLargeNumberOfEntries (0 ms) 48: [ RUN ] LegacySymtabTest.NoDuplicatesInLargeTable 48: [ OK ] LegacySymtabTest.NoDuplicatesInLargeTable (0 ms) 48: [----------] 6 tests from LegacySymtabTest (0 ms total) 48: 48: [----------] 5 tests from TopSortTest 48: [ RUN ] TopSortTest.WorksOnEmptyIdef 48: [ OK ] TopSortTest.WorksOnEmptyIdef (0 ms) 48: [ RUN ] TopSortTest.WorksOnIdefWithNoPerturbedInteraction 48: [ OK ] TopSortTest.WorksOnIdefWithNoPerturbedInteraction (0 ms) 48: [ RUN ] TopSortTest.WorksOnIdefWithPerturbedInteractions 48: [ OK ] TopSortTest.WorksOnIdefWithPerturbedInteractions (0 ms) 48: [ RUN ] TopSortTest.SortsIdefWithPerturbedInteractions 48: [ OK ] TopSortTest.SortsIdefWithPerturbedInteractions (0 ms) 48: [ RUN ] TopSortTest.SortsMoreComplexIdefWithPerturbedInteractions 48: [ OK ] TopSortTest.SortsMoreComplexIdefWithPerturbedInteractions (0 ms) 48: [----------] 5 tests from TopSortTest (0 ms total) 48: 48: [----------] 108 tests from BuildsValidDataStructure/SimulationParticleTest 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/0 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/0 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/1 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/1 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/2 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/2 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/3 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/3 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/4 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/4 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/5 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/5 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/6 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/6 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/7 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/7 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/8 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/8 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/9 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/9 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/10 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/10 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/11 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/11 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/12 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/12 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/13 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/13 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/14 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/14 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/15 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/15 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/16 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/16 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/17 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/17 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/18 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/18 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/19 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/19 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/20 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/20 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/21 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/21 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/22 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/22 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/23 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/23 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/24 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/24 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/25 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/25 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/26 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/26 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/27 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/27 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/28 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/28 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/29 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/29 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/30 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/30 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/31 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/31 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/32 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/32 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/33 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/33 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/34 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/34 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/35 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/35 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/36 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/36 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/37 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/37 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/38 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/38 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/39 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/39 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/40 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/40 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/41 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/41 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/42 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/42 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/43 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/43 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/44 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/44 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/45 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/45 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/46 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/46 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/47 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/47 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/48 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/48 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/49 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/49 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/50 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/50 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/51 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/51 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/52 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/52 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/53 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/53 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/0 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/0 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/1 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/1 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/2 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/2 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/3 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/3 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/4 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/4 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/5 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/5 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/6 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/6 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/7 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/7 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/8 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/8 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/9 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/9 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/10 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/10 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/11 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/11 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/12 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/12 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/13 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/13 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/14 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/14 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/15 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/15 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/16 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/16 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/17 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/17 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/18 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/18 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/19 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/19 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/20 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/20 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/21 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/21 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/22 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/22 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/23 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/23 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/24 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/24 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/25 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/25 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/26 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/26 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/27 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/27 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/28 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/28 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/29 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/29 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/30 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/30 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/31 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/31 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/32 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/32 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/33 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/33 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/34 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/34 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/35 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/35 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/36 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/36 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/37 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/37 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/38 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/38 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/39 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/39 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/40 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/40 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/41 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/41 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/42 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/42 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/43 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/43 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/44 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/44 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/45 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/45 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/46 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/46 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/47 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/47 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/48 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/48 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/49 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/49 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/50 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/50 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/51 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/51 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/52 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/52 (0 ms) 48: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/53 48: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/53 (0 ms) 48: [----------] 108 tests from BuildsValidDataStructure/SimulationParticleTest (9 ms total) 48: 48: [----------] Global test environment tear-down 48: [==========] 153 tests from 10 test suites ran. (161 ms total) 48: [ PASSED ] 153 tests. 48: 48: YOU HAVE 1 DISABLED TEST 48: 48/94 Test #48: TopologyTest ................................. Passed 0.52 sec test 49 Start 49: PullTest 49: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/pull-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/PullTest.xml" 49: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/pulling/tests 49: Test timeout computed to be: 30 49: [==========] Running 10 tests from 1 test suite. 49: [----------] Global test environment set-up. 49: [----------] 10 tests from PullTest 49: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox 49: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (0 ms) 49: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox 49: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms) 49: [ RUN ] PullTest.MaxPullDistanceXyzTricBox 49: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms) 49: [ RUN ] PullTest.MaxPullDistanceXyzLongBox 49: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms) 49: [ RUN ] PullTest.MaxPullDistanceXySkewedBox 49: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms) 49: [ RUN ] PullTest.TransformationCoordSimple 49: [ OK ] PullTest.TransformationCoordSimple (0 ms) 49: [ RUN ] PullTest.TransformationCoordAdvanced 49: [ OK ] PullTest.TransformationCoordAdvanced (0 ms) 49: [ RUN ] PullTest.TransformationCoordTime 49: [ OK ] PullTest.TransformationCoordTime (0 ms) 49: [ RUN ] PullTest.TransformationCoordTimeNotAllowed 49: [ OK ] PullTest.TransformationCoordTimeNotAllowed (0 ms) 49: [ RUN ] PullTest.TransformationCoordDummyExpression 49: [ OK ] PullTest.TransformationCoordDummyExpression (0 ms) 49: [----------] 10 tests from PullTest (0 ms total) 49: 49: [----------] Global test environment tear-down 49: [==========] 10 tests from 1 test suite ran. (0 ms total) 49: [ PASSED ] 10 tests. 49/94 Test #49: PullTest ..................................... Passed 0.40 sec test 50 Start 50: SimdUnitTests 50: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/simd-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/SimdUnitTests.xml" 50: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/simd/tests 50: Test timeout computed to be: 30 50: [==========] Running 288 tests from 22 test suites. 50: [----------] Global test environment set-up. 50: [----------] 9 tests from SimdBootstrapTest 50: [ RUN ] SimdBootstrapTest.loadStore 50: [ OK ] SimdBootstrapTest.loadStore (0 ms) 50: [ RUN ] SimdBootstrapTest.loadU 50: [ OK ] SimdBootstrapTest.loadU (0 ms) 50: [ RUN ] SimdBootstrapTest.storeU 50: [ OK ] SimdBootstrapTest.storeU (0 ms) 50: [ RUN ] SimdBootstrapTest.loadStoreI 50: [ OK ] SimdBootstrapTest.loadStoreI (0 ms) 50: [ RUN ] SimdBootstrapTest.loadUI 50: [ OK ] SimdBootstrapTest.loadUI (0 ms) 50: [ RUN ] SimdBootstrapTest.storeUI 50: [ OK ] SimdBootstrapTest.storeUI (0 ms) 50: [ RUN ] SimdBootstrapTest.simd4LoadStore 50: [ OK ] SimdBootstrapTest.simd4LoadStore (0 ms) 50: [ RUN ] SimdBootstrapTest.simd4LoadU 50: [ OK ] SimdBootstrapTest.simd4LoadU (0 ms) 50: [ RUN ] SimdBootstrapTest.simd4StoreU 50: [ OK ] SimdBootstrapTest.simd4StoreU (0 ms) 50: [----------] 9 tests from SimdBootstrapTest (0 ms total) 50: 50: [----------] 41 tests from SimdScalarTest 50: [ RUN ] SimdScalarTest.load 50: [ OK ] SimdScalarTest.load (0 ms) 50: [ RUN ] SimdScalarTest.loadU 50: [ OK ] SimdScalarTest.loadU (0 ms) 50: [ RUN ] SimdScalarTest.store 50: [ OK ] SimdScalarTest.store (0 ms) 50: [ RUN ] SimdScalarTest.storeU 50: [ OK ] SimdScalarTest.storeU (0 ms) 50: [ RUN ] SimdScalarTest.setZero 50: [ OK ] SimdScalarTest.setZero (0 ms) 50: [ RUN ] SimdScalarTest.andNot 50: [ OK ] SimdScalarTest.andNot (0 ms) 50: [ RUN ] SimdScalarTest.fma 50: [ OK ] SimdScalarTest.fma (0 ms) 50: [ RUN ] SimdScalarTest.fms 50: [ OK ] SimdScalarTest.fms (0 ms) 50: [ RUN ] SimdScalarTest.fnma 50: [ OK ] SimdScalarTest.fnma (0 ms) 50: [ RUN ] SimdScalarTest.fnms 50: [ OK ] SimdScalarTest.fnms (0 ms) 50: [ RUN ] SimdScalarTest.maskAdd 50: [ OK ] SimdScalarTest.maskAdd (0 ms) 50: [ RUN ] SimdScalarTest.maskzMul 50: [ OK ] SimdScalarTest.maskzMul (0 ms) 50: [ RUN ] SimdScalarTest.maskzFma 50: [ OK ] SimdScalarTest.maskzFma (0 ms) 50: [ RUN ] SimdScalarTest.abs 50: [ OK ] SimdScalarTest.abs (0 ms) 50: [ RUN ] SimdScalarTest.max 50: [ OK ] SimdScalarTest.max (0 ms) 50: [ RUN ] SimdScalarTest.min 50: [ OK ] SimdScalarTest.min (0 ms) 50: [ RUN ] SimdScalarTest.round 50: [ OK ] SimdScalarTest.round (0 ms) 50: [ RUN ] SimdScalarTest.trunc 50: [ OK ] SimdScalarTest.trunc (0 ms) 50: [ RUN ] SimdScalarTest.reduce 50: [ OK ] SimdScalarTest.reduce (0 ms) 50: [ RUN ] SimdScalarTest.testBits 50: [ OK ] SimdScalarTest.testBits (0 ms) 50: [ RUN ] SimdScalarTest.anyTrue 50: [ OK ] SimdScalarTest.anyTrue (0 ms) 50: [ RUN ] SimdScalarTest.selectByMask 50: [ OK ] SimdScalarTest.selectByMask (0 ms) 50: [ RUN ] SimdScalarTest.selectByNotMask 50: [ OK ] SimdScalarTest.selectByNotMask (0 ms) 50: [ RUN ] SimdScalarTest.blend 50: [ OK ] SimdScalarTest.blend (0 ms) 50: [ RUN ] SimdScalarTest.cvtR2I 50: [ OK ] SimdScalarTest.cvtR2I (0 ms) 50: [ RUN ] SimdScalarTest.cvttR2I 50: [ OK ] SimdScalarTest.cvttR2I (0 ms) 50: [ RUN ] SimdScalarTest.cvtI2R 50: [ OK ] SimdScalarTest.cvtI2R (0 ms) 50: [ RUN ] SimdScalarTest.cvtF2D 50: [ OK ] SimdScalarTest.cvtF2D (0 ms) 50: [ RUN ] SimdScalarTest.cvtD2D 50: [ OK ] SimdScalarTest.cvtD2D (0 ms) 50: [ RUN ] SimdScalarTest.loadI 50: [ OK ] SimdScalarTest.loadI (0 ms) 50: [ RUN ] SimdScalarTest.loadUI 50: [ OK ] SimdScalarTest.loadUI (0 ms) 50: [ RUN ] SimdScalarTest.storeI 50: [ OK ] SimdScalarTest.storeI (0 ms) 50: [ RUN ] SimdScalarTest.storeUI 50: [ OK ] SimdScalarTest.storeUI (0 ms) 50: [ RUN ] SimdScalarTest.andNotI 50: [ OK ] SimdScalarTest.andNotI (0 ms) 50: [ RUN ] SimdScalarTest.testBitsI 50: [ OK ] SimdScalarTest.testBitsI (0 ms) 50: [ RUN ] SimdScalarTest.selectByMaskI 50: [ OK ] SimdScalarTest.selectByMaskI (0 ms) 50: [ RUN ] SimdScalarTest.selectByNotMaskI 50: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms) 50: [ RUN ] SimdScalarTest.blendI 50: [ OK ] SimdScalarTest.blendI (0 ms) 50: [ RUN ] SimdScalarTest.cvtB2IB 50: [ OK ] SimdScalarTest.cvtB2IB (0 ms) 50: [ RUN ] SimdScalarTest.cvtIB2B 50: [ OK ] SimdScalarTest.cvtIB2B (0 ms) 50: [ RUN ] SimdScalarTest.expandScalarsToTriplets 50: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms) 50: [----------] 41 tests from SimdScalarTest (0 ms total) 50: 50: [----------] 8 tests from SimdScalarUtilTest 50: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose 50: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms) 50: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose 50: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms) 50: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU 50: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms) 50: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU 50: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms) 50: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU 50: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms) 50: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose 50: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms) 50: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose 50: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms) 50: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum 50: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms) 50: [----------] 8 tests from SimdScalarUtilTest (0 ms total) 50: 50: [----------] 37 tests from SimdScalarMathTest 50: [ RUN ] SimdScalarMathTest.copysign 50: [ OK ] SimdScalarMathTest.copysign (0 ms) 50: [ RUN ] SimdScalarMathTest.invsqrtPair 50: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms) 50: [ RUN ] SimdScalarMathTest.inv 50: [ OK ] SimdScalarMathTest.inv (0 ms) 50: [ RUN ] SimdScalarMathTest.maskzInvsqrt 50: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms) 50: [ RUN ] SimdScalarMathTest.log 50: [ OK ] SimdScalarMathTest.log (0 ms) 50: [ RUN ] SimdScalarMathTest.exp2 50: [ OK ] SimdScalarMathTest.exp2 (0 ms) 50: [ RUN ] SimdScalarMathTest.exp 50: [ OK ] SimdScalarMathTest.exp (0 ms) 50: [ RUN ] SimdScalarMathTest.erf 50: [ OK ] SimdScalarMathTest.erf (0 ms) 50: [ RUN ] SimdScalarMathTest.erfc 50: [ OK ] SimdScalarMathTest.erfc (0 ms) 50: [ RUN ] SimdScalarMathTest.sincos 50: [ OK ] SimdScalarMathTest.sincos (0 ms) 50: [ RUN ] SimdScalarMathTest.sin 50: [ OK ] SimdScalarMathTest.sin (0 ms) 50: [ RUN ] SimdScalarMathTest.cos 50: [ OK ] SimdScalarMathTest.cos (0 ms) 50: [ RUN ] SimdScalarMathTest.tan 50: [ OK ] SimdScalarMathTest.tan (0 ms) 50: [ RUN ] SimdScalarMathTest.asin 50: [ OK ] SimdScalarMathTest.asin (0 ms) 50: [ RUN ] SimdScalarMathTest.acos 50: [ OK ] SimdScalarMathTest.acos (0 ms) 50: [ RUN ] SimdScalarMathTest.atan 50: [ OK ] SimdScalarMathTest.atan (0 ms) 50: [ RUN ] SimdScalarMathTest.atan2 50: [ OK ] SimdScalarMathTest.atan2 (0 ms) 50: [ RUN ] SimdScalarMathTest.pmeForceCorrection 50: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms) 50: [ RUN ] SimdScalarMathTest.pmePotentialCorrection 50: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms) 50: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy 50: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.invSingleAccuracy 50: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy 50: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.logSingleAccuracy 50: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy 50: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.expSingleAccuracy 50: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.erfSingleAccuracy 50: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy 50: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy 50: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.sinSingleAccuracy 50: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.cosSingleAccuracy 50: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.tanSingleAccuracy 50: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.asinSingleAccuracy 50: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.acosSingleAccuracy 50: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.atanSingleAccuracy 50: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy 50: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy 50: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms) 50: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy 50: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 50: [----------] 37 tests from SimdScalarMathTest (0 ms total) 50: 50: [----------] 1 test from SimdTest 50: [ RUN ] SimdTest.GmxAligned 50: [ OK ] SimdTest.GmxAligned (0 ms) 50: [----------] 1 test from SimdTest (0 ms total) 50: 50: [----------] 42 tests from SimdFloatingpointTest 50: [ RUN ] SimdFloatingpointTest.setZero 50: [ OK ] SimdFloatingpointTest.setZero (0 ms) 50: [ RUN ] SimdFloatingpointTest.set 50: [ OK ] SimdFloatingpointTest.set (0 ms) 50: [ RUN ] SimdFloatingpointTest.add 50: [ OK ] SimdFloatingpointTest.add (0 ms) 50: [ RUN ] SimdFloatingpointTest.maskAdd 50: [ OK ] SimdFloatingpointTest.maskAdd (0 ms) 50: [ RUN ] SimdFloatingpointTest.sub 50: [ OK ] SimdFloatingpointTest.sub (0 ms) 50: [ RUN ] SimdFloatingpointTest.mul 50: [ OK ] SimdFloatingpointTest.mul (0 ms) 50: [ RUN ] SimdFloatingpointTest.maskzMul 50: [ OK ] SimdFloatingpointTest.maskzMul (0 ms) 50: [ RUN ] SimdFloatingpointTest.fma 50: [ OK ] SimdFloatingpointTest.fma (0 ms) 50: [ RUN ] SimdFloatingpointTest.maskzFma 50: [ OK ] SimdFloatingpointTest.maskzFma (0 ms) 50: [ RUN ] SimdFloatingpointTest.fms 50: [ OK ] SimdFloatingpointTest.fms (0 ms) 50: [ RUN ] SimdFloatingpointTest.fnma 50: [ OK ] SimdFloatingpointTest.fnma (0 ms) 50: [ RUN ] SimdFloatingpointTest.fnms 50: [ OK ] SimdFloatingpointTest.fnms (0 ms) 50: [ RUN ] SimdFloatingpointTest.abs 50: [ OK ] SimdFloatingpointTest.abs (0 ms) 50: [ RUN ] SimdFloatingpointTest.neg 50: [ OK ] SimdFloatingpointTest.neg (0 ms) 50: [ RUN ] SimdFloatingpointTest.and 50: [ OK ] SimdFloatingpointTest.and (0 ms) 50: [ RUN ] SimdFloatingpointTest.or 50: [ OK ] SimdFloatingpointTest.or (0 ms) 50: [ RUN ] SimdFloatingpointTest.xor 50: [ OK ] SimdFloatingpointTest.xor (0 ms) 50: [ RUN ] SimdFloatingpointTest.andNot 50: [ OK ] SimdFloatingpointTest.andNot (0 ms) 50: [ RUN ] SimdFloatingpointTest.max 50: [ OK ] SimdFloatingpointTest.max (0 ms) 50: [ RUN ] SimdFloatingpointTest.min 50: [ OK ] SimdFloatingpointTest.min (0 ms) 50: [ RUN ] SimdFloatingpointTest.round 50: [ OK ] SimdFloatingpointTest.round (0 ms) 50: [ RUN ] SimdFloatingpointTest.roundMode 50: [ OK ] SimdFloatingpointTest.roundMode (0 ms) 50: [ RUN ] SimdFloatingpointTest.trunc 50: [ OK ] SimdFloatingpointTest.trunc (0 ms) 50: [ RUN ] SimdFloatingpointTest.frexp 50: [ OK ] SimdFloatingpointTest.frexp (0 ms) 50: [ RUN ] SimdFloatingpointTest.ldexp 50: [ OK ] SimdFloatingpointTest.ldexp (0 ms) 50: [ RUN ] SimdFloatingpointTest.rsqrt 50: [ OK ] SimdFloatingpointTest.rsqrt (0 ms) 50: [ RUN ] SimdFloatingpointTest.maskzRsqrt 50: [ OK ] SimdFloatingpointTest.maskzRsqrt (0 ms) 50: [ RUN ] SimdFloatingpointTest.rcp 50: [ OK ] SimdFloatingpointTest.rcp (0 ms) 50: [ RUN ] SimdFloatingpointTest.maskzRcp 50: [ OK ] SimdFloatingpointTest.maskzRcp (0 ms) 50: [ RUN ] SimdFloatingpointTest.cmpEqAndSelectByMask 50: [ OK ] SimdFloatingpointTest.cmpEqAndSelectByMask (0 ms) 50: [ RUN ] SimdFloatingpointTest.selectByNotMask 50: [ OK ] SimdFloatingpointTest.selectByNotMask (0 ms) 50: [ RUN ] SimdFloatingpointTest.cmpNe 50: [ OK ] SimdFloatingpointTest.cmpNe (0 ms) 50: [ RUN ] SimdFloatingpointTest.cmpLe 50: [ OK ] SimdFloatingpointTest.cmpLe (0 ms) 50: [ RUN ] SimdFloatingpointTest.cmpLt 50: [ OK ] SimdFloatingpointTest.cmpLt (0 ms) 50: [ RUN ] SimdFloatingpointTest.testBits 50: [ OK ] SimdFloatingpointTest.testBits (0 ms) 50: [ RUN ] SimdFloatingpointTest.andB 50: [ OK ] SimdFloatingpointTest.andB (0 ms) 50: [ RUN ] SimdFloatingpointTest.orB 50: [ OK ] SimdFloatingpointTest.orB (0 ms) 50: [ RUN ] SimdFloatingpointTest.anyTrueB 50: [ OK ] SimdFloatingpointTest.anyTrueB (0 ms) 50: [ RUN ] SimdFloatingpointTest.blend 50: [ OK ] SimdFloatingpointTest.blend (0 ms) 50: [ RUN ] SimdFloatingpointTest.reduce 50: [ OK ] SimdFloatingpointTest.reduce (0 ms) 50: [ RUN ] SimdFloatingpointTest.cvtFloat2Double 50: [ OK ] SimdFloatingpointTest.cvtFloat2Double (0 ms) 50: [ RUN ] SimdFloatingpointTest.cvtDouble2Float 50: [ OK ] SimdFloatingpointTest.cvtDouble2Float (0 ms) 50: [----------] 42 tests from SimdFloatingpointTest (0 ms total) 50: 50: [----------] 16 tests from SimdFloatingpointUtilTest 50: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose4 50: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose4 (0 ms) 50: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose2 50: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose2 (0 ms) 50: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 50: [ OK ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 (0 ms) 50: [ RUN ] SimdFloatingpointUtilTest.transposeScatterStoreU3 50: [ OK ] SimdFloatingpointUtilTest.transposeScatterStoreU3 (0 ms) 50: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3 50: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3 (0 ms) 50: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping 50: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping (0 ms) 50: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3 50: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3 (0 ms) 50: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping 50: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping (0 ms) 50: [ RUN ] SimdFloatingpointUtilTest.expandScalarsToTriplets 50: [ OK ] SimdFloatingpointUtilTest.expandScalarsToTriplets (0 ms) 50: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 50: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 (0 ms) 50: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 50: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 (0 ms) 50: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 50: [ OK ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 (0 ms) 50: [ RUN ] SimdFloatingpointUtilTest.reduceIncr4Sum 50: [ OK ] SimdFloatingpointUtilTest.reduceIncr4Sum (0 ms) 50: [ RUN ] SimdFloatingpointUtilTest.loadUNDuplicate4 50: [ OK ] SimdFloatingpointUtilTest.loadUNDuplicate4 (0 ms) 50: [ RUN ] SimdFloatingpointUtilTest.load4DuplicateN 50: [ OK ] SimdFloatingpointUtilTest.load4DuplicateN (0 ms) 50: [ RUN ] SimdFloatingpointUtilTest.loadU4NOffset 50: [ OK ] SimdFloatingpointUtilTest.loadU4NOffset (0 ms) 50: [----------] 16 tests from SimdFloatingpointUtilTest (0 ms total) 50: 50: [----------] 23 tests from SimdIntegerTest 50: [ RUN ] SimdIntegerTest.setZero 50: [ OK ] SimdIntegerTest.setZero (0 ms) 50: [ RUN ] SimdIntegerTest.set 50: [ OK ] SimdIntegerTest.set (0 ms) 50: [ RUN ] SimdIntegerTest.add 50: [ OK ] SimdIntegerTest.add (0 ms) 50: [ RUN ] SimdIntegerTest.sub 50: [ OK ] SimdIntegerTest.sub (0 ms) 50: [ RUN ] SimdIntegerTest.mul 50: [ OK ] SimdIntegerTest.mul (0 ms) 50: [ RUN ] SimdIntegerTest.and 50: [ OK ] SimdIntegerTest.and (0 ms) 50: [ RUN ] SimdIntegerTest.andNot 50: [ OK ] SimdIntegerTest.andNot (0 ms) 50: [ RUN ] SimdIntegerTest.or 50: [ OK ] SimdIntegerTest.or (0 ms) 50: [ RUN ] SimdIntegerTest.xor 50: [ OK ] SimdIntegerTest.xor (0 ms) 50: [ RUN ] SimdIntegerTest.extract 50: [ OK ] SimdIntegerTest.extract (0 ms) 50: [ RUN ] SimdIntegerTest.cvtR2I 50: [ OK ] SimdIntegerTest.cvtR2I (0 ms) 50: [ RUN ] SimdIntegerTest.cvttR2I 50: [ OK ] SimdIntegerTest.cvttR2I (0 ms) 50: [ RUN ] SimdIntegerTest.cvtI2R 50: [ OK ] SimdIntegerTest.cvtI2R (0 ms) 50: [ RUN ] SimdIntegerTest.cmpEqAndSelectMask 50: [ OK ] SimdIntegerTest.cmpEqAndSelectMask (0 ms) 50: [ RUN ] SimdIntegerTest.cmpEqAndSelectNotMask 50: [ OK ] SimdIntegerTest.cmpEqAndSelectNotMask (0 ms) 50: [ RUN ] SimdIntegerTest.cmpLt 50: [ OK ] SimdIntegerTest.cmpLt (0 ms) 50: [ RUN ] SimdIntegerTest.testBits 50: [ OK ] SimdIntegerTest.testBits (0 ms) 50: [ RUN ] SimdIntegerTest.andB 50: [ OK ] SimdIntegerTest.andB (0 ms) 50: [ RUN ] SimdIntegerTest.orB 50: [ OK ] SimdIntegerTest.orB (0 ms) 50: [ RUN ] SimdIntegerTest.anyTrue 50: [ OK ] SimdIntegerTest.anyTrue (0 ms) 50: [ RUN ] SimdIntegerTest.blend 50: [ OK ] SimdIntegerTest.blend (0 ms) 50: [ RUN ] SimdIntegerTest.cvtB2IB 50: [ OK ] SimdIntegerTest.cvtB2IB (0 ms) 50: [ RUN ] SimdIntegerTest.cvtIB2B 50: [ OK ] SimdIntegerTest.cvtIB2B (0 ms) 50: [----------] 23 tests from SimdIntegerTest (0 ms total) 50: 50: [----------] 56 tests from SimdMathTest 50: [ RUN ] SimdMathTest.generateTestPointsFloat 50: [ OK ] SimdMathTest.generateTestPointsFloat (0 ms) 50: [ RUN ] SimdMathTest.copysign 50: [ OK ] SimdMathTest.copysign (0 ms) 50: [ RUN ] SimdMathTest.invsqrt 50: [ OK ] SimdMathTest.invsqrt (0 ms) 50: [ RUN ] SimdMathTest.maskzInvsqrt 50: [ OK ] SimdMathTest.maskzInvsqrt (0 ms) 50: [ RUN ] SimdMathTest.invsqrtPair 50: [ OK ] SimdMathTest.invsqrtPair (0 ms) 50: [ RUN ] SimdMathTest.sqrt 50: [ OK ] SimdMathTest.sqrt (0 ms) 50: [ RUN ] SimdMathTest.sqrtUnsafe 50: [ OK ] SimdMathTest.sqrtUnsafe (0 ms) 50: [ RUN ] SimdMathTest.inv 50: [ OK ] SimdMathTest.inv (2 ms) 50: [ RUN ] SimdMathTest.maskzInv 50: [ OK ] SimdMathTest.maskzInv (0 ms) 50: [ RUN ] SimdMathTest.cbrt 50: [ OK ] SimdMathTest.cbrt (0 ms) 50: [ RUN ] SimdMathTest.invcbrt 50: [ OK ] SimdMathTest.invcbrt (1 ms) 50: [ RUN ] SimdMathTest.log2 50: [ OK ] SimdMathTest.log2 (0 ms) 50: [ RUN ] SimdMathTest.log 50: [ OK ] SimdMathTest.log (0 ms) 50: [ RUN ] SimdMathTest.exp2 50: [ OK ] SimdMathTest.exp2 (1 ms) 50: [ RUN ] SimdMathTest.exp2Unsafe 50: [ OK ] SimdMathTest.exp2Unsafe (0 ms) 50: [ RUN ] SimdMathTest.exp 50: [ OK ] SimdMathTest.exp (1 ms) 50: [ RUN ] SimdMathTest.expUnsafe 50: [ OK ] SimdMathTest.expUnsafe (0 ms) 50: [ RUN ] SimdMathTest.pow 50: [ OK ] SimdMathTest.pow (0 ms) 50: [ RUN ] SimdMathTest.powUnsafe 50: [ OK ] SimdMathTest.powUnsafe (0 ms) 50: [ RUN ] SimdMathTest.erf 50: [ OK ] SimdMathTest.erf (1 ms) 50: [ RUN ] SimdMathTest.erfc 50: [ OK ] SimdMathTest.erfc (1 ms) 50: [ RUN ] SimdMathTest.sin 50: [ OK ] SimdMathTest.sin (1 ms) 50: [ RUN ] SimdMathTest.cos 50: [ OK ] SimdMathTest.cos (1 ms) 50: [ RUN ] SimdMathTest.tan 50: [ OK ] SimdMathTest.tan (1 ms) 50: [ RUN ] SimdMathTest.asin 50: [ OK ] SimdMathTest.asin (0 ms) 50: [ RUN ] SimdMathTest.acos 50: [ OK ] SimdMathTest.acos (0 ms) 50: [ RUN ] SimdMathTest.atan 50: [ OK ] SimdMathTest.atan (0 ms) 50: [ RUN ] SimdMathTest.atan2 50: [ OK ] SimdMathTest.atan2 (0 ms) 50: [ RUN ] SimdMathTest.pmeForceCorrection 50: [ OK ] SimdMathTest.pmeForceCorrection (0 ms) 50: [ RUN ] SimdMathTest.pmePotentialCorrection 50: [ OK ] SimdMathTest.pmePotentialCorrection (0 ms) 50: [ RUN ] SimdMathTest.invsqrtSingleAccuracy 50: [ OK ] SimdMathTest.invsqrtSingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.invsqrtPairSingleAccuracy 50: [ OK ] SimdMathTest.invsqrtPairSingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.sqrtSingleAccuracy 50: [ OK ] SimdMathTest.sqrtSingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.sqrtSingleAccuracyUnsafe 50: [ OK ] SimdMathTest.sqrtSingleAccuracyUnsafe (0 ms) 50: [ RUN ] SimdMathTest.invSingleAccuracy 50: [ OK ] SimdMathTest.invSingleAccuracy (2 ms) 50: [ RUN ] SimdMathTest.cbrtSingleAccuracy 50: [ OK ] SimdMathTest.cbrtSingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.invcbrtSingleAccuracy 50: [ OK ] SimdMathTest.invcbrtSingleAccuracy (1 ms) 50: [ RUN ] SimdMathTest.log2SingleAccuracy 50: [ OK ] SimdMathTest.log2SingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.logSingleAccuracy 50: [ OK ] SimdMathTest.logSingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.exp2SingleAccuracy 50: [ OK ] SimdMathTest.exp2SingleAccuracy (1 ms) 50: [ RUN ] SimdMathTest.exp2SingleAccuracyUnsafe 50: [ OK ] SimdMathTest.exp2SingleAccuracyUnsafe (0 ms) 50: [ RUN ] SimdMathTest.expSingleAccuracy 50: [ OK ] SimdMathTest.expSingleAccuracy (2 ms) 50: [ RUN ] SimdMathTest.expSingleAccuracyUnsafe 50: [ OK ] SimdMathTest.expSingleAccuracyUnsafe (0 ms) 50: [ RUN ] SimdMathTest.powSingleAccuracy 50: [ OK ] SimdMathTest.powSingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.powSingleAccuracyUnsafe 50: [ OK ] SimdMathTest.powSingleAccuracyUnsafe (0 ms) 50: [ RUN ] SimdMathTest.erfSingleAccuracy 50: [ OK ] SimdMathTest.erfSingleAccuracy (1 ms) 50: [ RUN ] SimdMathTest.erfcSingleAccuracy 50: [ OK ] SimdMathTest.erfcSingleAccuracy (1 ms) 50: [ RUN ] SimdMathTest.sinSingleAccuracy 50: [ OK ] SimdMathTest.sinSingleAccuracy (1 ms) 50: [ RUN ] SimdMathTest.cosSingleAccuracy 50: [ OK ] SimdMathTest.cosSingleAccuracy (1 ms) 50: [ RUN ] SimdMathTest.tanSingleAccuracy 50: [ OK ] SimdMathTest.tanSingleAccuracy (1 ms) 50: [ RUN ] SimdMathTest.asinSingleAccuracy 50: [ OK ] SimdMathTest.asinSingleAccuracy (2 ms) 50: [ RUN ] SimdMathTest.acosSingleAccuracy 50: [ OK ] SimdMathTest.acosSingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.atanSingleAccuracy 50: [ OK ] SimdMathTest.atanSingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.atan2SingleAccuracy 50: [ OK ] SimdMathTest.atan2SingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.pmeForceCorrectionSingleAccuracy 50: [ OK ] SimdMathTest.pmeForceCorrectionSingleAccuracy (0 ms) 50: [ RUN ] SimdMathTest.pmePotentialCorrectionSingleAccuracy 50: [ OK ] SimdMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 50: [----------] 56 tests from SimdMathTest (48 ms total) 50: 50: [----------] 1 test from EmptyArrayRefTest 50: [ RUN ] EmptyArrayRefTest.IsEmpty 50: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 50: [----------] 1 test from EmptyArrayRefTest (0 ms total) 50: 50: [----------] 3 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 50: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 50: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 50: [ RUN ] ArrayRefTest/0.ConstructFromArrayRefWorks 50: [ OK ] ArrayRefTest/0.ConstructFromArrayRefWorks (0 ms) 50: [ RUN ] ArrayRefTest/0.ConstructFromArrayWorks 50: [ OK ] ArrayRefTest/0.ConstructFromArrayWorks (0 ms) 50: [----------] 3 tests from ArrayRefTest/0 (0 ms total) 50: 50: [----------] 3 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 50: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 50: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 50: [ RUN ] ArrayRefTest/1.ConstructFromArrayRefWorks 50: [ OK ] ArrayRefTest/1.ConstructFromArrayRefWorks (0 ms) 50: [ RUN ] ArrayRefTest/1.ConstructFromArrayWorks 50: [ OK ] ArrayRefTest/1.ConstructFromArrayWorks (0 ms) 50: [----------] 3 tests from ArrayRefTest/1 (0 ms total) 50: 50: [----------] 3 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 50: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 50: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 50: [ RUN ] ArrayRefTest/2.ConstructFromArrayRefWorks 50: [ OK ] ArrayRefTest/2.ConstructFromArrayRefWorks (0 ms) 50: [ RUN ] ArrayRefTest/2.ConstructFromArrayWorks 50: [ OK ] ArrayRefTest/2.ConstructFromArrayWorks (0 ms) 50: [----------] 3 tests from ArrayRefTest/2 (0 ms total) 50: 50: [----------] 3 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 50: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 50: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 50: [ RUN ] ArrayRefTest/3.ConstructFromArrayRefWorks 50: [ OK ] ArrayRefTest/3.ConstructFromArrayRefWorks (0 ms) 50: [ RUN ] ArrayRefTest/3.ConstructFromArrayWorks 50: [ OK ] ArrayRefTest/3.ConstructFromArrayWorks (0 ms) 50: [----------] 3 tests from ArrayRefTest/3 (0 ms total) 50: 50: [----------] 1 test from ArrayRefReadWriteTest/0, where TypeParam = gmx::ArrayRef 50: [ RUN ] ArrayRefReadWriteTest/0.Assignment 50: [ OK ] ArrayRefReadWriteTest/0.Assignment (0 ms) 50: [----------] 1 test from ArrayRefReadWriteTest/0 (0 ms total) 50: 50: [----------] 1 test from ArrayRefReadWriteTest/1, where TypeParam = gmx::ArrayRef 50: [ RUN ] ArrayRefReadWriteTest/1.Assignment 50: [ OK ] ArrayRefReadWriteTest/1.Assignment (0 ms) 50: [----------] 1 test from ArrayRefReadWriteTest/1 (0 ms total) 50: 50: [----------] 1 test from ArrayRefArithmeticTest/0, where TypeParam = gmx::ArrayRef 50: [ RUN ] ArrayRefArithmeticTest/0.Basic 50: [ OK ] ArrayRefArithmeticTest/0.Basic (0 ms) 50: [----------] 1 test from ArrayRefArithmeticTest/0 (0 ms total) 50: 50: [----------] 1 test from ArrayRefArithmeticTest/1, where TypeParam = gmx::ArrayRef 50: [ RUN ] ArrayRefArithmeticTest/1.Basic 50: [ OK ] ArrayRefArithmeticTest/1.Basic (0 ms) 50: [----------] 1 test from ArrayRefArithmeticTest/1 (0 ms total) 50: 50: [----------] 3 tests from SimdVectorOperationsTest 50: [ RUN ] SimdVectorOperationsTest.iprod 50: [ OK ] SimdVectorOperationsTest.iprod (0 ms) 50: [ RUN ] SimdVectorOperationsTest.norm2 50: [ OK ] SimdVectorOperationsTest.norm2 (0 ms) 50: [ RUN ] SimdVectorOperationsTest.cprod 50: [ OK ] SimdVectorOperationsTest.cprod (0 ms) 50: [----------] 3 tests from SimdVectorOperationsTest (0 ms total) 50: 50: [----------] 32 tests from Simd4FloatingpointTest 50: [ RUN ] Simd4FloatingpointTest.setZero 50: [ OK ] Simd4FloatingpointTest.setZero (0 ms) 50: [ RUN ] Simd4FloatingpointTest.set 50: [ OK ] Simd4FloatingpointTest.set (0 ms) 50: [ RUN ] Simd4FloatingpointTest.add 50: [ OK ] Simd4FloatingpointTest.add (0 ms) 50: [ RUN ] Simd4FloatingpointTest.sub 50: [ OK ] Simd4FloatingpointTest.sub (0 ms) 50: [ RUN ] Simd4FloatingpointTest.mul 50: [ OK ] Simd4FloatingpointTest.mul (0 ms) 50: [ RUN ] Simd4FloatingpointTest.fma 50: [ OK ] Simd4FloatingpointTest.fma (0 ms) 50: [ RUN ] Simd4FloatingpointTest.fms 50: [ OK ] Simd4FloatingpointTest.fms (0 ms) 50: [ RUN ] Simd4FloatingpointTest.fnma 50: [ OK ] Simd4FloatingpointTest.fnma (0 ms) 50: [ RUN ] Simd4FloatingpointTest.fnms 50: [ OK ] Simd4FloatingpointTest.fnms (0 ms) 50: [ RUN ] Simd4FloatingpointTest.abs 50: [ OK ] Simd4FloatingpointTest.abs (0 ms) 50: [ RUN ] Simd4FloatingpointTest.neg 50: [ OK ] Simd4FloatingpointTest.neg (0 ms) 50: [ RUN ] Simd4FloatingpointTest.and 50: [ OK ] Simd4FloatingpointTest.and (0 ms) 50: [ RUN ] Simd4FloatingpointTest.or 50: [ OK ] Simd4FloatingpointTest.or (0 ms) 50: [ RUN ] Simd4FloatingpointTest.xor 50: [ OK ] Simd4FloatingpointTest.xor (0 ms) 50: [ RUN ] Simd4FloatingpointTest.andNot 50: [ OK ] Simd4FloatingpointTest.andNot (0 ms) 50: [ RUN ] Simd4FloatingpointTest.max 50: [ OK ] Simd4FloatingpointTest.max (0 ms) 50: [ RUN ] Simd4FloatingpointTest.min 50: [ OK ] Simd4FloatingpointTest.min (0 ms) 50: [ RUN ] Simd4FloatingpointTest.round 50: [ OK ] Simd4FloatingpointTest.round (0 ms) 50: [ RUN ] Simd4FloatingpointTest.trunc 50: [ OK ] Simd4FloatingpointTest.trunc (0 ms) 50: [ RUN ] Simd4FloatingpointTest.gmxSimd4RsqrtR 50: [ OK ] Simd4FloatingpointTest.gmxSimd4RsqrtR (0 ms) 50: [ RUN ] Simd4FloatingpointTest.cmpEqAndSelectByMask 50: [ OK ] Simd4FloatingpointTest.cmpEqAndSelectByMask (0 ms) 50: [ RUN ] Simd4FloatingpointTest.selectByNotMask 50: [ OK ] Simd4FloatingpointTest.selectByNotMask (0 ms) 50: [ RUN ] Simd4FloatingpointTest.cmpNe 50: [ OK ] Simd4FloatingpointTest.cmpNe (0 ms) 50: [ RUN ] Simd4FloatingpointTest.cmpLe 50: [ OK ] Simd4FloatingpointTest.cmpLe (0 ms) 50: [ RUN ] Simd4FloatingpointTest.cmpLt 50: [ OK ] Simd4FloatingpointTest.cmpLt (0 ms) 50: [ RUN ] Simd4FloatingpointTest.andB 50: [ OK ] Simd4FloatingpointTest.andB (0 ms) 50: [ RUN ] Simd4FloatingpointTest.orB 50: [ OK ] Simd4FloatingpointTest.orB (0 ms) 50: [ RUN ] Simd4FloatingpointTest.anyTrue 50: [ OK ] Simd4FloatingpointTest.anyTrue (0 ms) 50: [ RUN ] Simd4FloatingpointTest.blend 50: [ OK ] Simd4FloatingpointTest.blend (0 ms) 50: [ RUN ] Simd4FloatingpointTest.reduce 50: [ OK ] Simd4FloatingpointTest.reduce (0 ms) 50: [ RUN ] Simd4FloatingpointTest.dotProduct 50: [ OK ] Simd4FloatingpointTest.dotProduct (0 ms) 50: [ RUN ] Simd4FloatingpointTest.transpose 50: [ OK ] Simd4FloatingpointTest.transpose (0 ms) 50: [----------] 32 tests from Simd4FloatingpointTest (0 ms total) 50: 50: [----------] 2 tests from Simd4MathTest 50: [ RUN ] Simd4MathTest.invsqrt 50: [ OK ] Simd4MathTest.invsqrt (0 ms) 50: [ RUN ] Simd4MathTest.invsqrtSingleAccuracy 50: [ OK ] Simd4MathTest.invsqrtSingleAccuracy (0 ms) 50: [----------] 2 tests from Simd4MathTest (0 ms total) 50: 50: [----------] 1 test from Simd4VectorOperationsTest 50: [ RUN ] Simd4VectorOperationsTest.norm2 50: [ OK ] Simd4VectorOperationsTest.norm2 (0 ms) 50: [----------] 1 test from Simd4VectorOperationsTest (0 ms total) 50: 50: [----------] Global test environment tear-down 50: [==========] 288 tests from 22 test suites ran. (49 ms total) 50: [ PASSED ] 288 tests. 50/94 Test #50: SimdUnitTests ................................ Passed 0.39 sec test 51 Start 51: CompatibilityHelpersTests 51: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/compat-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/CompatibilityHelpersTests.xml" 51: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/compat/tests 51: Test timeout computed to be: 30 51: [==========] Running 9 tests from 6 test suites. 51: [----------] Global test environment set-up. 51: [----------] 4 tests from TemplateMPTest 51: [ RUN ] TemplateMPTest.MpWithIndexInt 51: [ OK ] TemplateMPTest.MpWithIndexInt (0 ms) 51: [ RUN ] TemplateMPTest.MpWithIndexIntBad 51: [ OK ] TemplateMPTest.MpWithIndexIntBad (0 ms) 51: [ RUN ] TemplateMPTest.MpWithIndexBool 51: [ OK ] TemplateMPTest.MpWithIndexBool (0 ms) 51: [ RUN ] TemplateMPTest.MpWithIndexEnum 51: [ OK ] TemplateMPTest.MpWithIndexEnum (0 ms) 51: [----------] 4 tests from TemplateMPTest (0 ms total) 51: 51: [----------] 1 test from NotNullConstruction 51: [ RUN ] NotNullConstruction.Works 51: [ OK ] NotNullConstruction.Works (0 ms) 51: [----------] 1 test from NotNullConstruction (0 ms total) 51: 51: [----------] 1 test from NotNullCasting 51: [ RUN ] NotNullCasting.Works 51: [ OK ] NotNullCasting.Works (0 ms) 51: [----------] 1 test from NotNullCasting (0 ms total) 51: 51: [----------] 1 test from NotNullAssignment 51: [ RUN ] NotNullAssignment.Works 51: [ OK ] NotNullAssignment.Works (0 ms) 51: [----------] 1 test from NotNullAssignment (0 ms total) 51: 51: [----------] 1 test from MakeNotNull 51: [ RUN ] MakeNotNull.Works 51: [ OK ] MakeNotNull.Works (0 ms) 51: [----------] 1 test from MakeNotNull (0 ms total) 51: 51: [----------] 1 test from NotNull 51: [ RUN ] NotNull.WorksInContainers 51: [ OK ] NotNull.WorksInContainers (0 ms) 51: [----------] 1 test from NotNull (0 ms total) 51: 51: [----------] Global test environment tear-down 51: [==========] 9 tests from 6 test suites ran. (0 ms total) 51: [ PASSED ] 9 tests. 51/94 Test #51: CompatibilityHelpersTests .................... Passed 0.33 sec test 52 Start 52: GmxAnaTest 52: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/gmxana-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/GmxAnaTest.xml" 52: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxana/tests 52: Test timeout computed to be: 600 52: [==========] Running 31 tests from 4 test suites. 52: [----------] Global test environment set-up. 52: [----------] 7 tests from Entropy 52: [ RUN ] Entropy.Schlitter_300_NoLinear 52: [ OK ] Entropy.Schlitter_300_NoLinear (0 ms) 52: [ RUN ] Entropy.Schlitter_300_Linear 52: [ OK ] Entropy.Schlitter_300_Linear (0 ms) 52: [ RUN ] Entropy.QuasiHarmonic_300_NoLinear 52: [ OK ] Entropy.QuasiHarmonic_300_NoLinear (0 ms) 52: [ RUN ] Entropy.QuasiHarmonic_200_NoLinear 52: [ OK ] Entropy.QuasiHarmonic_200_NoLinear (0 ms) 52: [ RUN ] Entropy.QuasiHarmonic_200_Linear 52: [ OK ] Entropy.QuasiHarmonic_200_Linear (0 ms) 52: [ RUN ] Entropy.EntropyCompare_200_Linear 52: [ OK ] Entropy.EntropyCompare_200_Linear (0 ms) 52: [ RUN ] Entropy.EntropyCompare_300_Linear 52: [ OK ] Entropy.EntropyCompare_300_Linear (0 ms) 52: [----------] 7 tests from Entropy (0 ms total) 52: 52: [----------] 2 tests from GmxChiTest 52: [ RUN ] GmxChiTest.gmxchiWorksWithAll 52: Analyzing from residue 1 to residue 11 52: 10 residues with dihedrals found 52: 46 dihedrals found 52: Reading frames from gro file 'First 10 residues from 1AKI t= 0.00000 step= 0', 156 atoms. 52: Reading frame 0 time 0.000 Reading frame 1 time 0.020 Reading frame 2 time 0.040 Last frame 2 time 0.040 52: j after resetting (nr. active dihedrals) = 46 52: Printing phiLYS1.xvg Printing phiVAL2.xvg Printing phiPHE3.xvg Printing phiGLY4.xvg Printing phiARG5.xvg Printing phiCYS6.xvg Printing phiGLU7.xvg Printing phiLEU8.xvg Printing phiALA9.xvg Printing phiALA10.xvg Printing psiLYS1.xvg Printing psiVAL2.xvg Printing psiPHE3.xvg Printing psiGLY4.xvg Printing psiARG5.xvg Printing psiCYS6.xvg Printing psiGLU7.xvg Printing psiLEU8.xvg Printing psiALA9.xvg Printing psiALA10.xvg Printing omegaVAL2.xvg Printing omegaPHE3.xvg Printing omegaGLY4.xvg Printing omegaARG5.xvg Printing omegaCYS6.xvg Printing omegaGLU7.xvg Printing omegaLEU8.xvg Printing omegaALA9.xvg Printing omegaALA10.xvg Printing chi1LYS1.xvg Printing chi1VAL2.xvg Printing chi1PHE3.xvg Printing chi1ARG5.xvg Printing chi1CYS6.xvg Printing chi1GLU7.xvg Printing chi1LEU8.xvg Printing chi2LYS1.xvg Printing chi2PHE3.xvg Printing chi2ARG5.xvg Printing chi2GLU7.xvg Printing chi2LEU8.xvg Printing chi3LYS1.xvg Printing chi3ARG5.xvg Printing chi3GLU7.xvg Printing chi4LYS1.xvg Printing chi4ARG5.xvg 52: Now calculating transitions... 52: Total number of transitions: 0 52: Now printing out transitions and OPs... 52: Now printing out rotamer occupancies... 52: Now calculating Chi product trajectories... 52: Printing chiproductLYS1.xvg and histo-chiprodLYS1.xvg Printing chiproductVAL2.xvg and histo-chiprodVAL2.xvg Printing chiproductPHE3.xvg and histo-chiprodPHE3.xvg Printing chiproductARG5.xvg and histo-chiprodARG5.xvg Printing chiproductCYS6.xvg and histo-chiprodCYS6.xvg Printing chiproductGLU7.xvg and histo-chiprodGLU7.xvg Printing chiproductLEU8.xvg and histo-chiprodLEU8.xvg 52: [ OK ] GmxChiTest.gmxchiWorksWithAll (837 ms) 52: [ RUN ] GmxChiTest.gmxchiWorksWithr0AndrN 52: Analyzing from residue 2 to residue 6 52: 5 residues with dihedrals found 52: 23 dihedrals found 52: Reading frames from gro file 'First 10 residues from 1AKI t= 0.00000 step= 0', 156 atoms. 52: Reading frame 0 time 0.000 Reading frame 1 time 0.020 Reading frame 2 time 0.040 Last frame 2 time 0.040 52: j after resetting (nr. active dihedrals) = 23 52: Printing phiVAL2.xvg Printing phiPHE3.xvg Printing phiGLY4.xvg Printing phiARG5.xvg Printing phiCYS6.xvg Printing psiVAL2.xvg Printing psiPHE3.xvg Printing psiGLY4.xvg Printing psiARG5.xvg Printing psiCYS6.xvg Printing omegaVAL2.xvg Printing omegaPHE3.xvg Printing omegaGLY4.xvg Printing omegaARG5.xvg Printing omegaCYS6.xvg Printing chi1VAL2.xvg Printing chi1PHE3.xvg Printing chi1ARG5.xvg Printing chi1CYS6.xvg Printing chi2PHE3.xvg Printing chi2ARG5.xvg Printing chi3ARG5.xvg Printing chi4ARG5.xvg 52: Now calculating transitions... 52: Total number of transitions: 0 52: Now printing out transitions and OPs... 52: Now printing out rotamer occupancies... 52: Now calculating Chi product trajectories... 52: Printing chiproductVAL2.xvg and histo-chiprodVAL2.xvg Printing chiproductPHE3.xvg and histo-chiprodPHE3.xvg Printing chiproductARG5.xvg and histo-chiprodARG5.xvg Printing chiproductCYS6.xvg and histo-chiprodCYS6.xvg 52: [ OK ] GmxChiTest.gmxchiWorksWithr0AndrN (556 ms) 52: [----------] 2 tests from GmxChiTest (1569 ms total) 52: 52: [----------] 10 tests from MindistTest 52: [ RUN ] MindistTest.mindistWorksWithSingleAtoms 52: Group 0 ( atom1) has 1 elements 52: Group 1 ( atom2) has 1 elements 52: Group 2 ( atom3) has 1 elements 52: Group 3 ( atoms12) has 2 elements 52: Group 4 ( atoms23) has 2 elements 52: Group 5 ( atoms123) has 3 elements 52: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 52: Reading frame 0 time 0.000 Last frame 0 time 0.000 52: Selected 0: 'atom1' 52: Selected 1: 'atom2' 52: [ OK ] MindistTest.mindistWorksWithSingleAtoms (55 ms) 52: [ RUN ] MindistTest.mindistWorksWithMultipleAtoms 52: Group 0 ( atom1) has 1 elements 52: Group 1 ( atom2) has 1 elements 52: Group 2 ( atom3) has 1 elements 52: Group 3 ( atoms12) has 2 elements 52: Group 4 ( atoms23) has 2 elements 52: Group 5 ( atoms123) has 3 elements 52: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 52: Reading frame 0 time 0.000 Last frame 0 time 0.000 52: Selected 2: 'atom3' 52: Selected 3: 'atoms12' 52: [ OK ] MindistTest.mindistWorksWithMultipleAtoms (0 ms) 52: [ RUN ] MindistTest.mindistDoesNotPickUpContacts 52: Group 0 ( atom1) has 1 elements 52: Group 1 ( atom2) has 1 elements 52: Group 2 ( atom3) has 1 elements 52: Group 3 ( atoms12) has 2 elements 52: Group 4 ( atoms23) has 2 elements 52: Group 5 ( atoms123) has 3 elements 52: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 52: Reading frame 0 time 0.000 Last frame 0 time 0.000 52: Selected 0: 'atom1' 52: Selected 1: 'atom2' 52: [ OK ] MindistTest.mindistDoesNotPickUpContacts (0 ms) 52: [ RUN ] MindistTest.mindistPicksUpContacts 52: Group 0 ( atom1) has 1 elements 52: Group 1 ( atom2) has 1 elements 52: Group 2 ( atom3) has 1 elements 52: Group 3 ( atoms12) has 2 elements 52: Group 4 ( atoms23) has 2 elements 52: Group 5 ( atoms123) has 3 elements 52: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 52: Reading frame 0 time 0.000 Last frame 0 time 0.000 52: Selected 0: 'atom1' 52: Selected 1: 'atom2' 52: [ OK ] MindistTest.mindistPicksUpContacts (0 ms) 52: [ RUN ] MindistTest.ngWorks 52: Group 0 ( atom1) has 1 elements 52: Group 1 ( atom2) has 1 elements 52: Group 2 ( atom3) has 1 elements 52: Group 3 ( atoms12) has 2 elements 52: Group 4 ( atoms23) has 2 elements 52: Group 5 ( atoms123) has 3 elements 52: Select a group: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 52: Reading frame 0 time 0.000 Last frame 0 time 0.000 52: Selected 0: 'atom1' 52: Selected 1: 'atom2' 52: Selected 2: 'atom3' 52: [ OK ] MindistTest.ngWorks (0 ms) 52: [ RUN ] MindistTest.groupWorks 52: Group 0 ( atom1) has 1 elements 52: Group 1 ( atom2) has 1 elements 52: Group 2 ( atom3) has 1 elements 52: Group 3 ( atoms12) has 2 elements 52: Group 4 ( atoms23) has 2 elements 52: Group 5 ( atoms123) has 3 elements 52: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 52: Reading frame 0 time 0.000 Last frame 0 time 0.000 52: Selected 3: 'atoms12' 52: Selected 2: 'atom3' 52: [ OK ] MindistTest.groupWorks (156 ms) 52: [ RUN ] MindistTest.maxDistWorks 52: Group 0 ( atom1) has 1 elements 52: Group 1 ( atom2) has 1 elements 52: Group 2 ( atom3) has 1 elements 52: Group 3 ( atoms12) has 2 elements 52: Group 4 ( atoms23) has 2 elements 52: Group 5 ( atoms123) has 3 elements 52: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 52: Reading frame 0 time 0.000 Last frame 0 time 0.000 52: Selected 2: 'atom3' 52: Selected 3: 'atoms12' 52: [ OK ] MindistTest.maxDistWorks (0 ms) 52: [ RUN ] MindistTest.noPbcWorks 52: Group 0 ( atom1) has 1 elements 52: Group 1 ( atom2) has 1 elements 52: Group 2 ( atom3) has 1 elements 52: Group 3 ( atoms12) has 2 elements 52: Group 4 ( atoms23) has 2 elements 52: Group 5 ( atoms123) has 3 elements 52: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 52: Reading frame 0 time 0.000 Last frame 0 time 0.000 52: Selected 0: 'atom1' 52: Selected 1: 'atom2' 52: [ OK ] MindistTest.noPbcWorks (0 ms) 52: [ RUN ] MindistTest.resPerTimeWorks 52: Group 0 ( atom1) has 1 elements 52: Group 1 ( atom2) has 1 elements 52: Group 2 ( atom3) has 1 elements 52: Group 3 ( atoms12) has 2 elements 52: Group 4 ( atoms23) has 2 elements 52: Group 5 ( atoms123) has 3 elements 52: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 52: Reading frame 0 time 0.000 Last frame 0 time 0.000 52: Selected 3: 'atoms12' 52: Selected 2: 'atom3' 52: [ OK ] MindistTest.resPerTimeWorks (170 ms) 52: [ RUN ] MindistTest.matrixWorks 52: Group 0 ( atom1) has 1 elements 52: Group 1 ( atom2) has 1 elements 52: Group 2 ( atom3) has 1 elements 52: Group 3 ( atoms12) has 2 elements 52: Group 4 ( atoms23) has 2 elements 52: Group 5 ( atoms123) has 3 elements 52: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 52: Reading frame 0 time 0.000 Last frame 0 time 0.000 52: Selected 5: 'atoms123' 52: Special case: making distance matrix between all atoms in group atoms123 52: [ OK ] MindistTest.matrixWorks (1 ms) 52: [----------] 10 tests from MindistTest (388 ms total) 52: 52: [----------] 12 tests from NoFatalErrorWhenWritingFrom/GmxTraj 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: trr version: GMX_trn_file (single precision) 52: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 (1 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 (0 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 52: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 (0 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 52: Reading frame 1 time 1.000 Last frame 1 time 1.000 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 (0 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 (0 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 (1 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/0 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frame 0 time 0.000 52: WARNING: If there are molecules in the input trajectory file 52: that are broken across periodic boundaries, they 52: cannot be made whole (or treated as whole) without 52: you providing a run input file. 52: 52: Reading frame 1 time 1.000 Last frame 1 time 1.000 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/0 (2 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/1 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frame 0 time 0.000 52: WARNING: If there are molecules in the input trajectory file 52: that are broken across periodic boundaries, they 52: cannot be made whole (or treated as whole) without 52: you providing a run input file. 52: 52: Reading frame 1 time 1.000 Last frame 1 time 1.000 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/1 (2 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/2 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 52: Reading frame 0 time 0.000 52: WARNING: If there are molecules in the input trajectory file 52: that are broken across periodic boundaries, they 52: cannot be made whole (or treated as whole) without 52: you providing a run input file. 52: 52: Reading frame 1 time 1.000 Last frame 1 time 1.000 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/2 (1 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/3 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 52: WARNING: If there are molecules in the input trajectory file 52: that are broken across periodic boundaries, they 52: cannot be made whole (or treated as whole) without 52: you providing a run input file. 52: 52: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 52: Reading frame 1 time 1.000 Last frame 1 time 1.000 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/3 (2 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/4 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frame 0 time 0.000 52: WARNING: If there are molecules in the input trajectory file 52: that are broken across periodic boundaries, they 52: cannot be made whole (or treated as whole) without 52: you providing a run input file. 52: 52: Reading frame 1 time 1.000 Last frame 1 time 1.000 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/4 (160 ms) 52: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/5 52: Group 0 ( System) has 6 elements 52: Group 1 ( Water) has 6 elements 52: Group 2 ( SOL) has 6 elements 52: Select a group: Reading frame 0 time 0.000 52: WARNING: If there are molecules in the input trajectory file 52: that are broken across periodic boundaries, they 52: cannot be made whole (or treated as whole) without 52: you providing a run input file. 52: 52: Reading frame 1 time 1.000 Last frame 1 time 1.000 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: Selected 0: 'System' 52: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/5 (246 ms) 52: [----------] 12 tests from NoFatalErrorWhenWritingFrom/GmxTraj (421 ms total) 52: 52: [----------] Global test environment tear-down 52: [==========] 31 tests from 4 test suites ran. (2379 ms total) 52: [ PASSED ] 31 tests. 52/94 Test #52: GmxAnaTest ................................... Passed 2.72 sec test 53 Start 53: GmxPreprocessTests 53: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/gmxpreprocess-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/GmxPreprocessTests.xml" 53: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests 53: Test timeout computed to be: 1920 53: [==========] Running 257 tests from 16 test suites. 53: [----------] Global test environment set-up. 53: [----------] 1 test from ConvertInteractionsTest 53: [ RUN ] ConvertInteractionsTest.DoingNothingWorks 53: [ OK ] ConvertInteractionsTest.DoingNothingWorks (0 ms) 53: [----------] 1 test from ConvertInteractionsTest (0 ms total) 53: 53: [----------] 4 tests from GenconfTest 53: [ RUN ] GenconfTest.nbox_Works 53: [ OK ] GenconfTest.nbox_Works (2 ms) 53: [ RUN ] GenconfTest.nbox_norenumber_Works 53: [ OK ] GenconfTest.nbox_norenumber_Works (0 ms) 53: [ RUN ] GenconfTest.nbox_dist_Works 53: [ OK ] GenconfTest.nbox_dist_Works (0 ms) 53: [ RUN ] GenconfTest.nbox_rot_Works 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: center of geometry: 1.733667, 1.477000, 0.905167 53: [ OK ] GenconfTest.nbox_rot_Works (0 ms) 53: [----------] 4 tests from GenconfTest (3 ms total) 53: 53: [----------] 2 tests from GenionTest 53: [ RUN ] GenionTest.HighConcentrationIonPlacement 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 53: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet 53: buffer. The cluster pair list does have a buffering effect, but choosing 53: a larger rlist might be necessary for good energy conservation. 53: 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 53: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 53: < 0 53: 53: 53: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: Generating 1-4 interactions: fudge = 0.5 53: Number of degrees of freedom in T-Coupling group rest is 1308.00 53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 53: 53: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 53: You are using a plain Coulomb cut-off, which might produce artifacts. 53: You might want to consider using PME electrostatics. 53: 53: 53: 53: There were 4 NOTEs 53: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 53: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 53: Group 0 ( System) has 653 elements 53: Group 1 ( Water) has 648 elements 53: Group 2 ( SOL) has 648 elements 53: Group 3 ( non-Water) has 5 elements 53: Group 4 ( Other) has 5 elements 53: Group 5 ( METH) has 5 elements 53: Select a group: Number of (3-atomic) solvent molecules: 216 53: Using random seed 1997. 53: Replacing solvent molecule 56 (atom 168) with NA 53: Replacing solvent molecule 120 (atom 360) with NA 53: Replacing solvent molecule 182 (atom 546) with NA 53: Replacing solvent molecule 71 (atom 213) with NA 53: Replacing solvent molecule 189 (atom 567) with CL 53: Replacing solvent molecule 54 (atom 162) with CL 53: Replacing solvent molecule 155 (atom 465) with CL 53: Replacing solvent molecule 99 (atom 297) with CL 53: 53: Setting the LD random seed to -1677985289 53: 53: Generated 331705 of the 331705 non-bonded parameter combinations 53: 53: Generated 331705 of the 331705 1-4 parameter combinations 53: 53: Excluding 2 bonded neighbours molecule type 'SOL' 53: 53: Excluding 3 bonded neighbours molecule type 'methane' 53: 53: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc216_with_methane.gro' 53: Analysing residue names: 53: There are: 216 Water residues 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: This run will generate roughly 0 Mb of data 53: Will try to add 4 NA ions and 4 CL ions. 53: Select a continuous group of solvent molecules 53: Selected 1: 'Water' 53: [ OK ] GenionTest.HighConcentrationIonPlacement (662 ms) 53: [ RUN ] GenionTest.NoIonPlacement 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 53: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet 53: buffer. The cluster pair list does have a buffering effect, but choosing 53: a larger rlist might be necessary for good energy conservation. 53: 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 53: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 53: < 0 53: 53: 53: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: Generating 1-4 interactions: fudge = 0.5 53: Number of degrees of freedom in T-Coupling group rest is 1308.00 53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 53: 53: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 53: You are using a plain Coulomb cut-off, which might produce artifacts. 53: You might want to consider using PME electrostatics. 53: 53: 53: 53: There were 4 NOTEs 53: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 53: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 53: No ions to add, will just copy input configuration. 53: Setting the LD random seed to 1073675751 53: 53: Generated 331705 of the 331705 non-bonded parameter combinations 53: 53: Generated 331705 of the 331705 1-4 parameter combinations 53: 53: Excluding 2 bonded neighbours molecule type 'SOL' 53: 53: Excluding 3 bonded neighbours molecule type 'methane' 53: 53: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc216_with_methane.gro' 53: Analysing residue names: 53: There are: 216 Water residues 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] GenionTest.NoIonPlacement (605 ms) 53: [----------] 2 tests from GenionTest (1268 ms total) 53: 53: [----------] 1 test from GenRestrTest 53: [ RUN ] GenRestrTest.SimpleRestraintsGenerated 53: 53: Reading structure file 53: Group 0 ( System) has 156 elements 53: Group 1 ( Protein) has 156 elements 53: Group 2 ( Protein-H) has 75 elements 53: Group 3 ( C-alpha) has 10 elements 53: Group 4 ( Backbone) has 30 elements 53: Group 5 ( MainChain) has 40 elements 53: Group 6 ( MainChain+Cb) has 49 elements 53: Group 7 ( MainChain+H) has 52 elements 53: Group 8 ( SideChain) has 104 elements 53: Group 9 ( SideChain-H) has 35 elements 53: Select a group: Select group to position restrain 53: Selected 3: 'C-alpha' 53: [ OK ] GenRestrTest.SimpleRestraintsGenerated (1 ms) 53: [----------] 1 test from GenRestrTest (1 ms total) 53: 53: [----------] 9 tests from PreprocessingAtomTypesTest 53: [ RUN ] PreprocessingAtomTypesTest.EmptyOnCreate 53: [ OK ] PreprocessingAtomTypesTest.EmptyOnCreate (0 ms) 53: [ RUN ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid 53: [ OK ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid (0 ms) 53: [ RUN ] PreprocessingAtomTypesTest.AddTypeWorks 53: [ OK ] PreprocessingAtomTypesTest.AddTypeWorks (0 ms) 53: [ RUN ] PreprocessingAtomTypesTest.AddMultipleTypesWorks 53: [ OK ] PreprocessingAtomTypesTest.AddMultipleTypesWorks (0 ms) 53: [ RUN ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry 53: [ OK ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry (0 ms) 53: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFound 53: [ OK ] PreprocessingAtomTypesTest.CorrectNameFound (0 ms) 53: [ RUN ] PreprocessingAtomTypesTest.WrongNameNotFound 53: [ OK ] PreprocessingAtomTypesTest.WrongNameNotFound (0 ms) 53: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber 53: [ OK ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber (0 ms) 53: [ RUN ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber 53: [ OK ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber (0 ms) 53: [----------] 9 tests from PreprocessingAtomTypesTest (0 ms total) 53: 53: [----------] 10 tests from PreprocessingBondAtomTypeTest 53: [ RUN ] PreprocessingBondAtomTypeTest.EmptyOnCreate 53: [ OK ] PreprocessingBondAtomTypeTest.EmptyOnCreate (0 ms) 53: [ RUN ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid 53: [ OK ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid (0 ms) 53: [ RUN ] PreprocessingBondAtomTypeTest.AddTypeWorks 53: [ OK ] PreprocessingBondAtomTypeTest.AddTypeWorks (0 ms) 53: [ RUN ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks 53: [ OK ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks (0 ms) 53: [ RUN ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry 53: [ OK ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry (0 ms) 53: [ RUN ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType 53: [ OK ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType (0 ms) 53: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFound 53: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFound (0 ms) 53: [ RUN ] PreprocessingBondAtomTypeTest.WrongNameNotFound 53: [ OK ] PreprocessingBondAtomTypeTest.WrongNameNotFound (0 ms) 53: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber 53: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber (0 ms) 53: [ RUN ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber 53: [ OK ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber (0 ms) 53: [----------] 10 tests from PreprocessingBondAtomTypeTest (0 ms total) 53: 53: [----------] 3 tests from GromppDirectiveTest 53: [ RUN ] GromppDirectiveTest.edgeCaseAtomTypeNames 53: Ignoring obsolete mdp entry 'title' 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 1 [file directives.top, line 59]: 53: In moleculetype 'A' 2 atoms are not bound by a potential or constraint to 53: any other atom in the same moleculetype. Although technically this might 53: not cause issues in a simulation, this often means that the user forgot 53: to add a bond/potential/constraint or put multiple molecules in the same 53: moleculetype definition by mistake. Run with -v to get information for 53: each atom. 53: 53: Number of degrees of freedom in T-Coupling group rest is 9.00 53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_edgeCaseAtomTypeNames_directives.mdp]: 53: NVE simulation: will use the initial temperature of 300.000 K for 53: determining the Verlet buffer size 53: 53: 53: There were 2 NOTEs 53: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_edgeCaseAtomTypeNames_directives.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 53: Setting the LD random seed to 1044750119 53: 53: Generated 10 of the 10 non-bonded parameter combinations 53: 53: Generated 10 of the 10 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -279281925 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: Analysing residue names: 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 53: 53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] GromppDirectiveTest.edgeCaseAtomTypeNames (5 ms) 53: [ RUN ] GromppDirectiveTest.NoteOnDihedralNotSumToZero 53: Ignoring obsolete mdp entry 'title' 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 1 [file directives.top, line 59]: 53: 1 dihedrals with function type 3 (Ryckaert-Bellemans or Fourier) have 53: coefficients that do not sum to zero. This does not affect the simulation 53: and can be ignored, unless you are comparing potential energy values with 53: other force field ports and/or MD software. 53: First such dihedral in molecule A, involving atoms 0 2 1 3 53: 53: 53: NOTE 2 [file directives.top, line 59]: 53: In moleculetype 'A' 2 atoms are not bound by a potential or constraint to 53: any other atom in the same moleculetype. Although technically this might 53: not cause issues in a simulation, this often means that the user forgot 53: to add a bond/potential/constraint or put multiple molecules in the same 53: moleculetype definition by mistake. Run with -v to get information for 53: each atom. 53: 53: Number of degrees of freedom in T-Coupling group rest is 9.00 53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 53: 53: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_NoteOnDihedralNotSumToZero_directives.mdp]: 53: NVE simulation: will use the initial temperature of 300.000 K for 53: determining the Verlet buffer size 53: 53: 53: There were 3 NOTEs 53: Setting the LD random seed to -336093188 53: 53: Generated 10 of the 10 non-bonded parameter combinations 53: 53: Generated 10 of the 10 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -1094726947 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: Analysing residue names: 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 53: 53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] GromppDirectiveTest.NoteOnDihedralNotSumToZero (17 ms) 53: [ RUN ] GromppDirectiveTest.WarnOnDihedralSumDifferentForFreeEnergy 53: [ OK ] GromppDirectiveTest.WarnOnDihedralSumDifferentForFreeEnergy (0 ms) 53: [----------] 3 tests from GromppDirectiveTest (23 ms total) 53: 53: [----------] 6 tests from InsertMoleculesTest 53: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration 53: Reading solute configuration 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Using random seed 1997 53: Try 1 success (now 8 atoms)! 53: 53: Added 1 molecules (out of 1 requested) 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoExistingConfiguration_out.gro 53: 53: Output configuration contains 8 atoms in 4 residues 53: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration (1 ms) 53: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Using random seed 1997 53: Try 1 success (now 2 atoms)! 53: Try 2 success (now 4 atoms)! 53: Try 3 success (now 6 atoms)! 53: Try 4 success (now 8 atoms)! 53: Try 5 success (now 10 atoms)! 53: 53: Added 5 molecules (out of 5 requested) 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBox_out.gro 53: 53: Output configuration contains 10 atoms in 10 residues 53: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox (2 ms) 53: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBoxConcentration 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Using random seed 1997 53: Try 1 success (now 2 atoms)! 53: Try 2 success (now 4 atoms)! 53: Try 3 success (now 6 atoms)! 53: Try 4 success (now 8 atoms)! 53: Try 5 success (now 10 atoms)! 53: 53: Added 5 molecules (out of 5 requested) 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBoxConcentration_out.gro 53: 53: Output configuration contains 10 atoms in 10 residues 53: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBoxConcentration (1 ms) 53: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox 53: Reading solute configuration 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Using random seed 1997 53: Try 1 success (now 8 atoms)! 53: Try 2 success (now 10 atoms)! 53: 53: Added 2 molecules (out of 2 requested) 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEnlargedBox_out.gro 53: 53: Output configuration contains 10 atoms in 4 residues 53: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox (1 ms) 53: [ RUN ] InsertMoleculesTest.InsertsMoleculesWithReplacement 53: Reading solute configuration 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Using random seed 1997 53: Try 1 success (now 650 atoms)! 53: Try 2 success (now 652 atoms)! 53: Try 3 success (now 654 atoms)! 53: Try 4 success (now 656 atoms)! 53: 53: Added 4 molecules (out of 4 requested) 53: Replaced 8 residues (24 atoms) 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesWithReplacement_out.gro 53: 53: Output configuration contains 632 atoms in 212 residues 53: [ OK ] InsertMoleculesTest.InsertsMoleculesWithReplacement (3 ms) 53: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Using random seed 1997 53: Read 4 positions from file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_5.dat 53: 53: Try 1 success (now 2 atoms)! 53: Try 2 success (now 4 atoms)! 53: Try 3 Try 4 Try 5 Try 6 Try 7 Try 8 Try 9 Try 10 Try 11 Try 12 skipped position (0.990, 2.010, 3.000) 53: Try 13 success (now 6 atoms)! 53: 53: Added 3 molecules (out of 4 requested) 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_out.gro 53: 53: Output configuration contains 6 atoms in 3 residues 53: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions (1 ms) 53: [----------] 6 tests from InsertMoleculesTest (11 ms total) 53: 53: [----------] 3 tests from MassRepartitioning 53: [ RUN ] MassRepartitioning.ValidCaseWorks 53: The smallest mass in the system is 2, setting the minimum mass to 6 53: [ OK ] MassRepartitioning.ValidCaseWorks (0 ms) 53: [ RUN ] MassRepartitioning.UnboundGivesWarning 53: 53: WARNING 1 [file unknown]: 53: The are 1 atoms that have a mass below the mass repartitioning limit but 53: are not bound. These masses cannot be repartitioned. 53: 53: The smallest mass in the system is 2, setting the minimum mass to 6 53: [ OK ] MassRepartitioning.UnboundGivesWarning (0 ms) 53: [ RUN ] MassRepartitioning.LightPartnerGivesError 53: 53: ERROR 1 [file unknown]: 53: Light atoms are bound to at least one atom that has a too low mass for 53: repartitioning 53: 53: The smallest mass in the system is 2, setting the minimum mass to 6 53: [ OK ] MassRepartitioning.LightPartnerGivesError (0 ms) 53: [----------] 3 tests from MassRepartitioning (0 ms total) 53: 53: [----------] 35 tests from GetIrTest 53: [ RUN ] GetIrTest.HandlesDifferentKindsOfMdpLines 53: Ignoring obsolete mdp entry 'title' 53: Replacing old mdp entry 'xtc_grps' by 'compressed-x-grps' 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.HandlesDifferentKindsOfMdpLines (2 ms) 53: [ RUN ] GetIrTest.RejectsNonCommentLineWithNoEquals 53: [ OK ] GetIrTest.RejectsNonCommentLineWithNoEquals (0 ms) 53: [ RUN ] GetIrTest.AcceptsKeyWithoutValue 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsKeyWithoutValue_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.AcceptsKeyWithoutValue (2 ms) 53: [ RUN ] GetIrTest.RejectsValueWithoutKey 53: [ OK ] GetIrTest.RejectsValueWithoutKey (0 ms) 53: [ RUN ] GetIrTest.RejectsEmptyKeyAndEmptyValue 53: [ OK ] GetIrTest.RejectsEmptyKeyAndEmptyValue (0 ms) 53: [ RUN ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsDefineParametersWithValuesIncludingAssignment_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment (2 ms) 53: [ RUN ] GetIrTest.AcceptsEmptyLines 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsEmptyLines_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.AcceptsEmptyLines (2 ms) 53: [ RUN ] GetIrTest.MtsCheckNstcalcenergy 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstcalcenergy_input.mdp]: 53: With MTS, nstcalcenergy = 5 should be a multiple of mts-factor = 2 53: 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstcalcenergy_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.MtsCheckNstcalcenergy (1 ms) 53: [ RUN ] GetIrTest.MtsCheckNstenergy 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 53: With MTS, nstenergy = 5 should be a multiple of mts-factor = 2 53: 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 53: Setting nstcalcenergy (100) equal to nstenergy (5) 53: 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.MtsCheckNstenergy (1 ms) 53: [ RUN ] GetIrTest.MtsCheckNstpcouple 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp, line 7]: 53: Pressure coupling incorrect number of values (I need exactly 1) 53: 53: 53: ERROR 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp, line 7]: 53: Pressure coupling incorrect number of values (I need exactly 1) 53: 53: 53: ERROR 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 53: With multiple time stepping, nstpcouple should be a multiple of 53: mts-factor 53: 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: 53: ERROR 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 53: The Berendsen barostat does not generate any strictly correct ensemble, 53: and should not be used for new production simulations (in our opinion). 53: We recommend using the C-rescale barostat instead. 53: 53: 53: ERROR 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 53: compressibility must be > 0 when using pressure coupling Berendsen 53: 53: 53: [ OK ] GetIrTest.MtsCheckNstpcouple (1 ms) 53: [ RUN ] GetIrTest.MtsCheckNstdhdl 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 53: With MTS, nstdhdl = 5 should be a multiple of mts-factor = 2 53: 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 53: Setting nstcalcenergy (100) equal to nstdhdl (5) 53: 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: 53: ERROR 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 53: Lambda state must be set, either with init-lambda-state or with 53: init-lambda 53: 53: [ OK ] GetIrTest.MtsCheckNstdhdl (1 ms) 53: [ RUN ] GetIrTest.MtsCheckSDNotSupported 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckSDNotSupported_input.mdp]: 53: Multiple time stepping is only supported with integrator md 53: 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckSDNotSupported_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.MtsCheckSDNotSupported (2 ms) 53: [ RUN ] GetIrTest.AcceptsElectricField 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricField_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.AcceptsElectricField (2 ms) 53: [ RUN ] GetIrTest.AcceptsElectricFieldPulsed 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldPulsed_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.AcceptsElectricFieldPulsed (2 ms) 53: [ RUN ] GetIrTest.AcceptsElectricFieldOscillating 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldOscillating_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.AcceptsElectricFieldOscillating (2 ms) 53: [ RUN ] GetIrTest.RejectsDuplicateOldAndNewKeys 53: [ OK ] GetIrTest.RejectsDuplicateOldAndNewKeys (0 ms) 53: [ RUN ] GetIrTest.AcceptsImplicitSolventNo 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsImplicitSolventNo_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.AcceptsImplicitSolventNo (4 ms) 53: [ RUN ] GetIrTest.RejectsImplicitSolventYes 53: [ OK ] GetIrTest.RejectsImplicitSolventYes (0 ms) 53: [ RUN ] GetIrTest.AcceptsMimic 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsMimic_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.AcceptsMimic (3 ms) 53: [ RUN ] GetIrTest.AcceptsTransformationCoord 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsTransformationCoord_input.mdp, line 11]: 53: pull-coord2 has a non-zero force constant and is also referenced in 53: pull-coord1-expression. Make sure that this is intended. In most use 53: cases, the pull coordinates referenced by a transformation coordinate 53: should have their force constant set to zero. 53: 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsTransformationCoord_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.AcceptsTransformationCoord (2 ms) 53: [ RUN ] GetIrTest.InvalidTransformationCoordWithConstraint 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordWithConstraint_input.mdp, line 7]: 53: pull-coord1 cannot have type 'constraint' and geometry 'transformation' 53: 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordWithConstraint_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.InvalidTransformationCoordWithConstraint (2 ms) 53: [ RUN ] GetIrTest.InvalidPullCoordWithConstraintInTransformationExpression 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidPullCoordWithConstraintInTransformationExpression_input.mdp, line 10]: 53: pull-coord2 can not use pull-coord1 in the transformation since this is a 53: constraint 53: 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidPullCoordWithConstraintInTransformationExpression_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.InvalidPullCoordWithConstraintInTransformationExpression (2 ms) 53: [ RUN ] GetIrTest.InvalidTransformationCoordDxValue 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordDxValue_input.mdp, line 7]: 53: pull-coord1-dx cannot be set to zero for pull coordinate of geometry 53: 'transformation' 53: 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordDxValue_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.InvalidTransformationCoordDxValue (1 ms) 53: [ RUN ] GetIrTest.MissingTransformationCoordExpression 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MissingTransformationCoordExpression_input.mdp, line 5]: 53: pull-coord1-expression not set for pull coordinate of geometry 53: 'transformation' 53: 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MissingTransformationCoordExpression_input.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: [ OK ] GetIrTest.MissingTransformationCoordExpression (2 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep 53: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep (1 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep_negativeDelta 53: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep_negativeDelta (1 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep 53: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep (1 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep_negativeDelta 53: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep_negativeDelta (1 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_SC_And_OneStepTooMuch_input.mdp]: 53: With init-lambda = 0 and delta_lambda = 1e-05 and no explicit input, 53: coul-lambdas and vdw-lambdas will be greater than 1 after step 100000 of 53: in total 100001 steps. This is not compatible with using soft-core 53: potentials. 53: 53: 53: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch (1 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta_input.mdp]: 53: With init-lambda = 1 and delta_lambda = -1e-05, the lambda components 53: won't change anymore after step 100000 until the end of the simulation 53: after 100001 steps. 53: 53: 53: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta (1 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta_input.mdp]: 53: With init-lambda = 1 and delta_lambda = -1e-05, the lambda components 53: won't change anymore after step 100000 until the end of the simulation 53: after 100001 steps. 53: 53: 53: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta (1 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_input.mdp]: 53: With init-lambda-state = 0 and delta_lambda = 1e-05, the lambda 53: components won't change anymore after step 100000 until the end of the 53: simulation after 100001 steps. 53: 53: 53: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch (1 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta 53: 53: ERROR 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta_input.mdp]: 53: With init-lambda-state = 2 and delta_lambda = -1e-05, the lambda 53: components won't change anymore after step 100000 until the end of the 53: simulation after 100001 steps. 53: 53: 53: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta (1 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep 53: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep (1 ms) 53: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep_negativeDelta 53: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep_negativeDelta (1 ms) 53: [----------] 35 tests from GetIrTest (67 ms total) 53: 53: [----------] 6 tests from SolvateTest 53: [ RUN ] SolvateTest.cs_box_Works 53: Reading solvent configuration 53: 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Generating solvent configuration 53: Will generate new solvent configuration of 1x1x1 boxes 53: Solvent box contains 270 atoms in 90 residues 53: Removed 129 solvent atoms due to solvent-solvent overlap 53: Sorting configuration 53: Found 1 molecule type: 53: SOL ( 3 atoms): 47 residues 53: Generated solvent containing 141 atoms in 47 residues 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_box_Works_out.gro 53: 53: Output configuration contains 141 atoms in 47 residues 53: Volume : 1.331 (nm^3) 53: Density : 1056.36 (g/l) 53: Number of solvent molecules: 47 53: 53: [ OK ] SolvateTest.cs_box_Works (3 ms) 53: [ RUN ] SolvateTest.cs_cp_Works 53: Reading solute configuration 53: Reading solvent configuration 53: 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Generating solvent configuration 53: Will generate new solvent configuration of 2x2x2 boxes 53: Solvent box contains 3660 atoms in 1220 residues 53: Removed 987 solvent atoms due to solvent-solvent overlap 53: Removed 15 solvent atoms due to solute-solvent overlap 53: Sorting configuration 53: Found 1 molecule type: 53: SOL ( 3 atoms): 886 residues 53: Generated solvent containing 2658 atoms in 886 residues 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_Works_out.gro 53: 53: Output configuration contains 2664 atoms in 888 residues 53: Volume : 27.2709 (nm^3) 53: Density : 974.777 (g/l) 53: Number of solvent molecules: 886 53: 53: [ OK ] SolvateTest.cs_cp_Works (19 ms) 53: [ RUN ] SolvateTest.cs_cp_p_Works 53: Reading solute configuration 53: Reading solvent configuration 53: 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Generating solvent configuration 53: Will generate new solvent configuration of 2x2x2 boxes 53: Solvent box contains 3660 atoms in 1220 residues 53: Removed 987 solvent atoms due to solvent-solvent overlap 53: Removed 15 solvent atoms due to solute-solvent overlap 53: Sorting configuration 53: Found 1 molecule type: 53: SOL ( 3 atoms): 886 residues 53: Generated solvent containing 2658 atoms in 886 residues 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_out.gro 53: 53: Output configuration contains 2664 atoms in 888 residues 53: Volume : 27.2709 (nm^3) 53: Density : 974.777 (g/l) 53: Number of solvent molecules: 886 53: 53: Processing topology 53: Adding line for 886 solvent molecules with resname (SOL) to topology file (/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_spc-and-methanol.top) 53: [ OK ] SolvateTest.cs_cp_p_Works (21 ms) 53: [ RUN ] SolvateTest.shell_Works 53: Reading solute configuration 53: Reading solvent configuration 53: 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Generating solvent configuration 53: Will generate new solvent configuration of 2x2x2 boxes 53: Solvent box contains 3660 atoms in 1220 residues 53: Removed 987 solvent atoms due to solvent-solvent overlap 53: Removed 1902 solvent atoms more than 1.000000 nm from solute. 53: Removed 15 solvent atoms due to solute-solvent overlap 53: Sorting configuration 53: Found 1 molecule type: 53: SOL ( 3 atoms): 252 residues 53: Generated solvent containing 756 atoms in 252 residues 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_shell_Works_out.gro 53: 53: Output configuration contains 762 atoms in 254 residues 53: Volume : 27.2709 (nm^3) 53: Density : 279.3 (g/l) 53: Number of solvent molecules: 252 53: 53: [ OK ] SolvateTest.shell_Works (11 ms) 53: [ RUN ] SolvateTest.update_Topology_Works 53: Reading solute configuration 53: Reading solvent configuration 53: 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Generating solvent configuration 53: Will generate new solvent configuration of 3x3x3 boxes 53: Solvent box contains 14952 atoms in 4984 residues 53: Removed 2787 solvent atoms due to solvent-solvent overlap 53: Removed 30 solvent atoms due to solute-solvent overlap 53: Sorting configuration 53: Found 2 different molecule types: 53: HOH ( 3 atoms): 1876 residues 53: SOL ( 3 atoms): 2169 residues 53: Generated solvent containing 0 atoms in 0 residues 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_out.gro 53: 53: Output configuration contains 12141 atoms in 4047 residues 53: Volume : 125 (nm^3) 53: Density : 968.963 (g/l) 53: Number of solvent molecules: 4045 53: 53: Processing topology 53: Adding line for 1876 solvent molecules with resname (HOH) to topology file (/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 53: Adding line for 2169 solvent molecules with resname (SOL) to topology file (/build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 53: [ OK ] SolvateTest.update_Topology_Works (83 ms) 53: [ RUN ] SolvateTest.cs_pdb_big_box_Works 53: Reading solvent configuration 53: 53: Initialising inter-atomic distances... 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. (1964) 53: DOI: 10.1021/j100785a001 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Generating solvent configuration 53: Will generate new solvent configuration of 2x2x2 boxes 53: Solvent box contains 1218 atoms in 406 residues 53: Removed 555 solvent atoms due to solvent-solvent overlap 53: Sorting configuration 53: Found 1 molecule type: 53: SOL ( 3 atoms): 221 residues 53: Generated solvent containing 663 atoms in 221 residues 53: Writing generated configuration to /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_pdb_big_box_Works_out.gro 53: 53: Output configuration contains 663 atoms in 221 residues 53: Volume : 8 (nm^3) 53: Density : 826.409 (g/l) 53: Number of solvent molecules: 221 53: 53: [ OK ] SolvateTest.cs_pdb_big_box_Works (10 ms) 53: [----------] 6 tests from SolvateTest (151 ms total) 53: 53: [----------] 1 test from TopDirTests 53: [ RUN ] TopDirTests.NamesArrayHasCorrectSize 53: [ OK ] TopDirTests.NamesArrayHasCorrectSize (0 ms) 53: [----------] 1 test from TopDirTests (0 ms total) 53: 53: [----------] 95 tests from InteractionFunctionKind/ConvertInteractionsTest 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Bond 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Bond (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Morse 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Morse (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Cubic_Bonds 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Cubic_Bonds (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Connect_Bonds 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Connect_Bonds (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Harmonic_Pot_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Harmonic_Pot_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/FENE_Bonds 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/FENE_Bonds (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds_NC 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds_NC (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restraint_Pot_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restraint_Pot_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Angle 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Angle (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Angles 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Angles (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Lin__Angle 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Lin__Angle (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond_Cross 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond_Cross (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/BA_Cross 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/BA_Cross (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/U_B 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/U_B (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quartic_Angles 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quartic_Angles (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Angles 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Angles (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Proper_Dih_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Proper_Dih_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ryckaert_Bell_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ryckaert_Bell_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Dih_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Dih_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/CBT_Dih_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/CBT_Dih_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Fourier_Dih_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Fourier_Dih_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Improper_Dih_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Improper_Dih_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Per__Imp__Dih_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Per__Imp__Dih_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Dih_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Dih_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/CMAP_Dih_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/CMAP_Dih_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_2_Pol_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_2_Pol_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_3_Pol_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_3_Pol_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_4_Pol_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_4_Pol_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_Polariz_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_Polariz_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Nonpolar_Sol_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Nonpolar_Sol_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_14 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_14 (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb_14 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb_14 (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_14_q 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_14_q (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_Pairs_NB 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_Pairs_NB (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ__SR_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ__SR_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Buck_ham__SR_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Buck_ham__SR_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/B_ham 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/B_ham (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Disper__corr_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Disper__corr_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb__SR_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb__SR_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/RF_excl_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/RF_excl_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul__recip_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul__recip_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_recip_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_recip_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/DPD 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/DPD (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Polarization 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Polarization (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Water_Pol_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Water_Pol_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Thole_Pol_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Thole_Pol_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Anharm__Pol_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Anharm__Pol_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Position_Rest_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Position_Rest_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Flat_b__P_R_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Flat_b__P_R_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dis__Rest_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dis__Rest_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/D_R_Viol___nm_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/D_R_Viol___nm_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Orient__Rest_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Orient__Rest_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ori__R__RMSD 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ori__R__RMSD (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest__Z 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest__Z (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest__Vi_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest__Vi_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constraint 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constraint (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constr__No_Co_ 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constr__No_Co_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Settle 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Settle (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_1 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_1 (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_2 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_2 (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_2fd 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_2fd (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_3 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_3 (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_3fd 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_3fd (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3fad 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3fad (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3out 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3out (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_4fd 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_4fd (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_4fdn 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_4fdn (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_N 53: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_N (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/COM_Pull_En_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/COM_Pull_En_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dens__fitting 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dens__fitting (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quantum_En_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quantum_En_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/NN_Potential 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/NN_Potential (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Potential 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Potential (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Kinetic_En_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Kinetic_En_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Total_Energy 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Total_Energy (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Conserved_En_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Conserved_En_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Temperature 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Temperature (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__Temp_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__Temp_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pres__DC 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pres__DC (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pressure 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pressure (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dH_dl_constr_ 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dH_dl_constr_ (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVremain_dl 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVremain_dl (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dEkin_dl 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dEkin_dl (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVcoul_dl 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVcoul_dl (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVvdw_dl 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVvdw_dl (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVbonded_dl 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVbonded_dl (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVrestraint_dl 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVrestraint_dl (0 ms) 53: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVtemp_dl 53: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:132: Skipped 53: Skipping interaction type that does not represent a interaction with parameters converted in grompp 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVtemp_dl (0 ms) 53: [----------] 95 tests from InteractionFunctionKind/ConvertInteractionsTest (1 ms total) 53: 53: [----------] 45 tests from SinglePeptideFragments/EditconfTest 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/0 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/0 (4 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/1 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/1 (3 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/2 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/2 (12 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/3 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/3 (2 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/4 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/4 (1 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/5 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/5 (1 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/6 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/6 (2 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/7 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/7 (2 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/8 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/8 (2 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/0 53: 53: Select a group for output: 53: Group 0 ( two_residues) has 23 elements 53: There is one group in the index 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/0 (3 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/1 53: 53: Select a group for output: 53: Group 0 ( two_residues) has 23 elements 53: There is one group in the index 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/1 (3 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/2 53: 53: Select a group for output: 53: Group 0 ( two_residues) has 23 elements 53: There is one group in the index 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/2 (3 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/3 53: 53: Select a group for output: 53: Group 0 ( two_residues) has 23 elements 53: There is one group in the index 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/3 (1 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/4 53: 53: Select a group for output: 53: Group 0 ( two_residues) has 23 elements 53: There is one group in the index 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/4 (1 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/5 53: 53: Select a group for output: 53: Group 0 ( two_residues) has 23 elements 53: There is one group in the index 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/5 (1 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/6 53: 53: Select a group for output: 53: Group 0 ( two_residues) has 23 elements 53: There is one group in the index 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/6 (1 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/7 53: 53: Select a group for output: 53: Group 0 ( two_residues) has 23 elements 53: There is one group in the index 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/7 (1 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/8 53: 53: Select a group for output: 53: Group 0 ( two_residues) has 23 elements 53: There is one group in the index 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/8 (1 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/0 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : 0.212 1.187 3.527 (nm) 53: new center : 4.028 2.819 3.723 (nm) 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/0 (3 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/1 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : 0.212 1.187 3.527 (nm) 53: new center : 4.028 2.819 3.723 (nm) 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/1 (3 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/2 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : 0.212 1.187 3.527 (nm) 53: new center : 4.028 2.819 3.723 (nm) 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/2 (3 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/3 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : 0.212 1.187 3.527 (nm) 53: new center : 4.028 2.819 3.723 (nm) 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/3 (1 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/4 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : 0.212 1.187 3.527 (nm) 53: new center : 4.028 2.819 3.723 (nm) 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/4 (1 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/5 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : 0.212 1.187 3.527 (nm) 53: new center : 4.028 2.819 3.723 (nm) 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/5 (1 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/6 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : 0.212 1.187 3.527 (nm) 53: new center : 4.028 2.819 3.723 (nm) 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/6 (2 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/7 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : 0.212 1.187 3.527 (nm) 53: new center : 4.028 2.819 3.723 (nm) 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/7 (2 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/8 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : 0.212 1.187 3.527 (nm) 53: new center : 4.028 2.819 3.723 (nm) 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/8 (5 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/0 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : -0.814 1.104 2.657 (nm) 53: new center : 3.002 2.736 2.852 (nm) 53: new box vectors : 6.004 5.472 5.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 187.42 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/0 (4 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/1 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : -0.814 1.104 2.657 (nm) 53: new center : 3.002 2.736 2.852 (nm) 53: new box vectors : 6.004 5.472 5.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 187.42 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/1 (4 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/2 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : -0.814 1.104 2.657 (nm) 53: new center : 3.002 2.736 2.852 (nm) 53: new box vectors : 6.004 5.472 5.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 187.42 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/2 (3 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/3 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : -0.814 1.104 2.657 (nm) 53: new center : 3.002 2.736 2.852 (nm) 53: new box vectors : 6.004 5.472 5.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 187.40 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/3 (2 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/4 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : -0.814 1.104 2.657 (nm) 53: new center : 3.002 2.736 2.852 (nm) 53: new box vectors : 6.004 5.472 5.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 187.40 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/4 (2 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/5 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : -0.814 1.104 2.657 (nm) 53: new center : 3.002 2.736 2.852 (nm) 53: new box vectors : 6.004 5.472 5.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 187.40 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/5 (1 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/6 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : -0.814 1.104 2.657 (nm) 53: new center : 3.002 2.736 2.852 (nm) 53: new box vectors : 6.004 5.472 5.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 187.40 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/6 (3 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/7 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : -0.814 1.104 2.657 (nm) 53: new center : 3.002 2.736 2.852 (nm) 53: new box vectors : 6.004 5.472 5.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 187.40 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/7 (2 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/8 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: shift : -0.814 1.104 2.657 (nm) 53: new center : 3.002 2.736 2.852 (nm) 53: new box vectors : 6.004 5.472 5.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 187.40 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/8 (4 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/0 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: new center : 3.816 1.632 0.195 (nm) 53: new box vectors : 5.004 4.472 4.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 105.28 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/0 (3 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/1 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: new center : 3.816 1.632 0.195 (nm) 53: new box vectors : 5.004 4.472 4.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 105.28 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/1 (3 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/2 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: new center : 3.816 1.632 0.195 (nm) 53: new box vectors : 5.004 4.472 4.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 105.28 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/2 (3 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/3 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: new center : 3.816 1.632 0.195 (nm) 53: new box vectors : 5.004 4.472 4.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 105.27 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/3 (1 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/4 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: new center : 3.816 1.632 0.195 (nm) 53: new box vectors : 5.004 4.472 4.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 105.27 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/4 (1 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/5 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: new center : 3.816 1.632 0.195 (nm) 53: new box vectors : 5.004 4.472 4.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 105.27 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/5 (1 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/6 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: new center : 3.816 1.632 0.195 (nm) 53: new box vectors : 5.004 4.472 4.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 105.27 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/6 (2 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/7 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: new center : 3.816 1.632 0.195 (nm) 53: new box vectors : 5.004 4.472 4.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 105.27 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/7 (2 ms) 53: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/8 53: Note that major changes are planned in future for editconf, to improve usability and utility. 53: Read 252 atoms 53: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 53: No velocities found 53: system size : 2.004 1.472 1.704 (nm) 53: center : 3.816 1.632 0.195 (nm) 53: box vectors : 8.056 5.637 7.445 (nm) 53: box angles : 90.00 90.00 90.00 (degrees) 53: box volume : 338.10 (nm^3) 53: new center : 3.816 1.632 0.195 (nm) 53: new box vectors : 5.004 4.472 4.704 (nm) 53: new box angles : 90.00 90.00 90.00 (degrees) 53: new box volume : 105.27 (nm^3) 53: 53: WARNING: No boxtype specified - distance condition applied in each dimension. 53: If the molecule rotates the actual distance will be smaller. You might want 53: to use a cubic box instead, or why not try a dodecahedron today? 53: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/8 (2 ms) 53: [----------] 45 tests from SinglePeptideFragments/EditconfTest (130 ms total) 53: 53: [----------] 16 tests from CorrectVelocity/MaxwellTest 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/0 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/0 (0 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/1 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/1 (0 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/2 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/2 (0 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/3 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/3 (0 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/4 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/4 (0 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/5 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/5 (0 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/6 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/6 (0 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/7 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/7 (0 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/8 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/8 (0 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/9 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/9 (0 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/10 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/10 (0 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/11 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/11 (0 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/12 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/12 (0 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/13 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/13 (0 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/14 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/14 (0 ms) 53: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/15 53: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/15 (0 ms) 53: [----------] 16 tests from CorrectVelocity/MaxwellTest (12 ms total) 53: 53: [----------] 20 tests from CMAPDefinesAndErrors/GromppDirectiveTest 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/0 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/0 (0 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/1 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/1 (0 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/2 53: Ignoring obsolete mdp entry 'title' 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 1 [file directives-cmap.top, line 105]: 53: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 53: any other atom in the same moleculetype. Although technically this might 53: not cause issues in a simulation, this often means that the user forgot 53: to add a bond/potential/constraint or put multiple molecules in the same 53: moleculetype definition by mistake. Run with -v to get information for 53: each atom. 53: 53: Number of degrees of freedom in T-Coupling group rest is 12.00 53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_2_directives-cmap.mdp]: 53: NVE simulation: will use the initial temperature of 300.000 K for 53: determining the Verlet buffer size 53: 53: 53: There were 2 NOTEs 53: Setting the LD random seed to -538841605 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -33619969 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: Analysing residue names: 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 53: 53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/2 (24 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/3 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/3 (0 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/4 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/4 (0 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/5 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/5 (0 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/6 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/6 (0 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/7 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/7 (0 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/8 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/8 (0 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/9 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/9 (0 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/10 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/10 (0 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/11 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/11 (0 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/12 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/12 (0 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/13 53: Ignoring obsolete mdp entry 'title' 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 1 [file directives-cmap.top, line 105]: 53: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 53: any other atom in the same moleculetype. Although technically this might 53: not cause issues in a simulation, this often means that the user forgot 53: to add a bond/potential/constraint or put multiple molecules in the same 53: moleculetype definition by mistake. Run with -v to get information for 53: each atom. 53: 53: Number of degrees of freedom in T-Coupling group rest is 12.00 53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_13_directives-cmap.mdp]: 53: NVE simulation: will use the initial temperature of 300.000 K for 53: determining the Verlet buffer size 53: 53: 53: There were 2 NOTEs 53: Setting the LD random seed to -101204269 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -73859353 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: Analysing residue names: 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 53: 53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/13 (6 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/14 53: Ignoring obsolete mdp entry 'title' 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 1 [file directives-cmap.top, line 105]: 53: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 53: any other atom in the same moleculetype. Although technically this might 53: not cause issues in a simulation, this often means that the user forgot 53: to add a bond/potential/constraint or put multiple molecules in the same 53: moleculetype definition by mistake. Run with -v to get information for 53: each atom. 53: 53: Number of degrees of freedom in T-Coupling group rest is 12.00 53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_14_directives-cmap.mdp]: 53: NVE simulation: will use the initial temperature of 300.000 K for 53: determining the Verlet buffer size 53: 53: 53: There were 2 NOTEs 53: Setting the LD random seed to -325 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to -138412033 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: Analysing residue names: 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 53: 53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/14 (4 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/15 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/15 (0 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/16 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/16 (0 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/17 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/17 (0 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/18 53: Ignoring obsolete mdp entry 'title' 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 1 [file directives-cmap.top, line 105]: 53: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 53: any other atom in the same moleculetype. Although technically this might 53: not cause issues in a simulation, this often means that the user forgot 53: to add a bond/potential/constraint or put multiple molecules in the same 53: moleculetype definition by mistake. Run with -v to get information for 53: each atom. 53: 53: Number of degrees of freedom in T-Coupling group rest is 12.00 53: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 53: 53: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_18_directives-cmap.mdp]: 53: NVE simulation: will use the initial temperature of 300.000 K for 53: determining the Verlet buffer size 53: 53: 53: There were 2 NOTEs 53: Setting the LD random seed to -148310789 53: 53: Generated 3 of the 3 non-bonded parameter combinations 53: 53: Generated 3 of the 3 1-4 parameter combinations 53: 53: Excluding 0 bonded neighbours molecule type 'A' 53: 53: Setting gen_seed to 1828610006 53: 53: Velocities were taken from a Maxwell distribution at 300 K 53: Analysing residue names: 53: There are: 1 Other residues 53: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 53: 53: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/18 (4 ms) 53: [ RUN ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/19 53: [ OK ] CMAPDefinesAndErrors/GromppDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/19 (0 ms) 53: [----------] 20 tests from CMAPDefinesAndErrors/GromppDirectiveTest (42 ms total) 53: 53: [----------] Global test environment tear-down 53: [==========] 257 tests from 16 test suites ran. (1713 ms total) 53: [ PASSED ] 217 tests. 53: [ SKIPPED ] 40 tests, listed below: 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_2_Pol_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_3_Pol_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_4_Pol_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_Polariz_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Nonpolar_Sol_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb_14 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ__SR_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Buck_ham__SR_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/B_ham 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Disper__corr_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb__SR_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/RF_excl_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul__recip_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_recip_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/DPD 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/D_R_Viol___nm_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ori__R__RMSD 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest__Vi_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/COM_Pull_En_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dens__fitting 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quantum_En_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/NN_Potential 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Potential 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Kinetic_En_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Total_Energy 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Conserved_En_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Temperature 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__Temp_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pres__DC 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pressure 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dH_dl_constr_ 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVremain_dl 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dEkin_dl 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVcoul_dl 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVvdw_dl 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVbonded_dl 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVrestraint_dl 53: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVtemp_dl 53/94 Test #53: GmxPreprocessTests ........................... Passed 2.06 sec test 54 Start 54: Pdb2gmx1Test 54: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/pdb2gmx1-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/Pdb2gmx1Test.xml" 54: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests 54: Test timeout computed to be: 1920 54: [==========] Running 30 tests from 1 test suite. 54: [----------] Global test environment set-up. 54: [----------] 30 tests from Oplsaa/Pdb2gmxTest 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Before cleaning: 653 pairs 54: Before cleaning: 663 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 128 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (128 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 252 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 254, now 254 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 663 dihedrals, 51 impropers, 457 angles 54: 650 pairs, 254 bonds and 0 virtual sites 54: 54: Total mass 1846.112 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 54: 54: The Oplsaa force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (32 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 30 donors and 22 acceptors were found. 54: There are 36 hydrogen bonds 54: Will use HISE for residue 29 54: Will use HISE for residue 32 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS27 HIS29 54: SG90 NE2111 54: HIS29 NE2111 0.987 54: HIS32 NE2135 1.590 1.155 54: Before cleaning: 748 pairs 54: Before cleaning: 778 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 149 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (149 atoms, 16 residues) 54: 54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue PHE33 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus PHE-33: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 281 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 290, now 290 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 778 dihedrals, 72 impropers, 516 angles 54: 736 pairs, 290 bonds and 0 virtual sites 54: 54: Total mass 2088.357 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 54: 54: The Oplsaa force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (34 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 22 acceptors were found. 54: There are 26 hydrogen bonds 54: Will use HISE for residue 45 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS45 54: NE295 54: MET46 SD102 1.078 54: Before cleaning: 676 pairs 54: Before cleaning: 696 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 132 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (132 atoms, 16 residues) 54: 54: Identified residue ALA34 as a starting terminus. 54: 54: Identified residue ALA49 as a ending terminus. 54: Start terminus ALA-34: NH3+ 54: End terminus ALA-49: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 261, now 261 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 696 dihedrals, 56 impropers, 472 angles 54: 667 pairs, 261 bonds and 0 virtual sites 54: 54: Total mass 1861.128 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 54: 54: The Oplsaa force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (30 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 21 acceptors were found. 54: There are 30 hydrogen bonds 54: Will use HISE for residue 60 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS60 54: NE285 54: CYS62 SG98 0.803 54: Before cleaning: 603 pairs 54: Before cleaning: 618 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 117 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (117 atoms, 16 residues) 54: 54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue LYS50 as a starting terminus. 54: 54: Identified residue PRO65 as a ending terminus. 54: Start terminus LYS-50: NH3+ 54: End terminus PRO-65: PRO-COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 228 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 232, now 232 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 618 dihedrals, 48 impropers, 419 angles 54: 597 pairs, 232 bonds and 0 virtual sites 54: 54: Total mass 1662.883 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 54: 54: The Oplsaa force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (30 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 89 donors and 98 acceptors were found. 54: There are 129 hydrogen bonds 54: Will use HISE for residue 31 54: Will use HISE for residue 51 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS25 HIS31 HIS51 54: SG14 NE264 NE2226 54: HIS31 NE264 1.921 54: HIS51 NE2226 1.498 2.650 54: CYS80 SG477 0.207 1.984 1.570 54: Linking CYS-25 SG-14 and CYS-80 SG-477... 54: Before cleaning: 2499 pairs 54: Before cleaning: 2524 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 58 488 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 'A' (488 atoms, 58 residues) 54: 54: Identified residue ASN24 as a starting terminus. 54: 54: Identified residue ARG81 as a ending terminus. 54: Start terminus ASN-24: NH3+ 54: End terminus ARG-81: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 58 residues with 936 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 951, now 951 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2524 dihedrals, 208 impropers, 1704 angles 54: 2469 pairs, 951 bonds and 0 virtual sites 54: 54: Total mass 6908.578 a.m.u. 54: 54: Total charge -6.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 54: 54: The Oplsaa force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (85 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Marked 124 virtual sites 54: Added 16 dummy masses 54: Added 26 new constraints 54: Before cleaning: 653 pairs 54: Before cleaning: 663 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 128 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (128 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 252 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 254, now 254 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 663 dihedrals, 51 impropers, 457 angles 54: 650 pairs, 254 bonds and 130 virtual sites 54: 54: Total mass 1846.112 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 54: 54: The Oplsaa force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (31 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 30 donors and 22 acceptors were found. 54: There are 36 hydrogen bonds 54: Will use HISE for residue 29 54: Will use HISE for residue 32 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS27 HIS29 54: SG90 NE2111 54: HIS29 NE2111 0.987 54: HIS32 NE2135 1.590 1.155 54: Marked 132 virtual sites 54: Added 10 dummy masses 54: Added 19 new constraints 54: Before cleaning: 748 pairs 54: Before cleaning: 778 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 149 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (149 atoms, 16 residues) 54: 54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue PHE33 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus PHE-33: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 281 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 290, now 290 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 778 dihedrals, 72 impropers, 516 angles 54: 736 pairs, 290 bonds and 133 virtual sites 54: 54: Total mass 2088.357 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 54: 54: The Oplsaa force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (34 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 22 acceptors were found. 54: There are 26 hydrogen bonds 54: Will use HISE for residue 45 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS45 54: NE295 54: MET46 SD102 1.078 54: Marked 123 virtual sites 54: Added 22 dummy masses 54: Added 35 new constraints 54: Before cleaning: 676 pairs 54: Before cleaning: 696 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 132 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (132 atoms, 16 residues) 54: 54: Identified residue ALA34 as a starting terminus. 54: 54: Identified residue ALA49 as a ending terminus. 54: Start terminus ALA-34: NH3+ 54: End terminus ALA-49: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 261, now 261 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 696 dihedrals, 56 impropers, 472 angles 54: 667 pairs, 261 bonds and 132 virtual sites 54: 54: Total mass 1861.128 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 54: 54: The Oplsaa force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (31 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 21 acceptors were found. 54: There are 30 hydrogen bonds 54: Will use HISE for residue 60 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS60 54: NE285 54: CYS62 SG98 0.803 54: Marked 111 virtual sites 54: Added 18 dummy masses 54: Added 31 new constraints 54: Before cleaning: 603 pairs 54: Before cleaning: 618 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 117 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (117 atoms, 16 residues) 54: 54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue LYS50 as a starting terminus. 54: 54: Identified residue PRO65 as a ending terminus. 54: Start terminus LYS-50: NH3+ 54: End terminus PRO-65: PRO-COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 228 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 232, now 232 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 618 dihedrals, 48 impropers, 419 angles 54: 597 pairs, 232 bonds and 116 virtual sites 54: 54: Total mass 1662.883 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 54: 54: The Oplsaa force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (30 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 89 donors and 98 acceptors were found. 54: There are 129 hydrogen bonds 54: Will use HISE for residue 31 54: Will use HISE for residue 51 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS25 HIS31 HIS51 54: SG14 NE264 NE2226 54: HIS31 NE264 1.921 54: HIS51 NE2226 1.498 2.650 54: CYS80 SG477 0.207 1.984 1.570 54: Linking CYS-25 SG-14 and CYS-80 SG-477... 54: Marked 447 virtual sites 54: Added 58 dummy masses 54: Added 101 new constraints 54: Before cleaning: 2499 pairs 54: Before cleaning: 2524 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 58 488 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 'A' (488 atoms, 58 residues) 54: 54: Identified residue ASN24 as a starting terminus. 54: 54: Identified residue ARG81 as a ending terminus. 54: Start terminus ASN-24: NH3+ 54: End terminus ARG-81: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 58 residues with 936 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 951, now 951 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2524 dihedrals, 208 impropers, 1704 angles 54: 2469 pairs, 951 bonds and 462 virtual sites 54: 54: Total mass 6908.578 a.m.u. 54: 54: Total charge -6.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 54: 54: The Oplsaa force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (89 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Before cleaning: 653 pairs 54: Before cleaning: 663 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 128 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (128 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 252 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 254, now 254 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 663 dihedrals, 51 impropers, 457 angles 54: 650 pairs, 254 bonds and 0 virtual sites 54: 54: Total mass 1846.112 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 54: 54: The Oplsaa force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (270 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 30 donors and 22 acceptors were found. 54: There are 36 hydrogen bonds 54: Will use HISE for residue 29 54: Will use HISE for residue 32 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS27 HIS29 54: SG90 NE2111 54: HIS29 NE2111 0.987 54: HIS32 NE2135 1.590 1.155 54: Before cleaning: 748 pairs 54: Before cleaning: 778 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 149 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (149 atoms, 16 residues) 54: 54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue PHE33 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus PHE-33: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 281 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 290, now 290 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 778 dihedrals, 72 impropers, 516 angles 54: 736 pairs, 290 bonds and 0 virtual sites 54: 54: Total mass 2088.357 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 54: 54: The Oplsaa force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (40 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 22 acceptors were found. 54: There are 26 hydrogen bonds 54: Will use HISE for residue 45 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS45 54: NE295 54: MET46 SD102 1.078 54: Before cleaning: 676 pairs 54: Before cleaning: 696 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 132 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (132 atoms, 16 residues) 54: 54: Identified residue ALA34 as a starting terminus. 54: 54: Identified residue ALA49 as a ending terminus. 54: Start terminus ALA-34: NH3+ 54: End terminus ALA-49: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 261, now 261 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 696 dihedrals, 56 impropers, 472 angles 54: 667 pairs, 261 bonds and 0 virtual sites 54: 54: Total mass 1861.128 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 54: 54: The Oplsaa force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (41 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 21 acceptors were found. 54: There are 30 hydrogen bonds 54: Will use HISE for residue 60 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS60 54: NE285 54: CYS62 SG98 0.803 54: Before cleaning: 603 pairs 54: Before cleaning: 618 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 117 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (117 atoms, 16 residues) 54: 54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue LYS50 as a starting terminus. 54: 54: Identified residue PRO65 as a ending terminus. 54: Start terminus LYS-50: NH3+ 54: End terminus PRO-65: PRO-COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 228 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 232, now 232 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 618 dihedrals, 48 impropers, 419 angles 54: 597 pairs, 232 bonds and 0 virtual sites 54: 54: Total mass 1662.883 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 54: 54: The Oplsaa force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (193 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 89 donors and 98 acceptors were found. 54: There are 129 hydrogen bonds 54: Will use HISE for residue 31 54: Will use HISE for residue 51 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS25 HIS31 HIS51 54: SG14 NE264 NE2226 54: HIS31 NE264 1.921 54: HIS51 NE2226 1.498 2.650 54: CYS80 SG477 0.207 1.984 1.570 54: Linking CYS-25 SG-14 and CYS-80 SG-477... 54: Before cleaning: 2499 pairs 54: Before cleaning: 2524 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 58 488 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 'A' (488 atoms, 58 residues) 54: 54: Identified residue ASN24 as a starting terminus. 54: 54: Identified residue ARG81 as a ending terminus. 54: Start terminus ASN-24: NH3+ 54: End terminus ARG-81: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 58 residues with 936 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 951, now 951 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2524 dihedrals, 208 impropers, 1704 angles 54: 2469 pairs, 951 bonds and 0 virtual sites 54: 54: Total mass 6908.578 a.m.u. 54: 54: Total charge -6.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 54: 54: The Oplsaa force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (139 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Marked 124 virtual sites 54: Added 16 dummy masses 54: Added 26 new constraints 54: Before cleaning: 653 pairs 54: Before cleaning: 663 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 128 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (128 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 252 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 254, now 254 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 663 dihedrals, 51 impropers, 457 angles 54: 650 pairs, 254 bonds and 130 virtual sites 54: 54: Total mass 1846.112 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 54: 54: The Oplsaa force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (36 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 30 donors and 22 acceptors were found. 54: There are 36 hydrogen bonds 54: Will use HISE for residue 29 54: Will use HISE for residue 32 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS27 HIS29 54: SG90 NE2111 54: HIS29 NE2111 0.987 54: HIS32 NE2135 1.590 1.155 54: Marked 132 virtual sites 54: Added 10 dummy masses 54: Added 19 new constraints 54: Before cleaning: 748 pairs 54: Before cleaning: 778 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 149 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (149 atoms, 16 residues) 54: 54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue PHE33 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus PHE-33: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 281 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 290, now 290 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 778 dihedrals, 72 impropers, 516 angles 54: 736 pairs, 290 bonds and 133 virtual sites 54: 54: Total mass 2088.357 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 54: 54: The Oplsaa force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (169 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 22 acceptors were found. 54: There are 26 hydrogen bonds 54: Will use HISE for residue 45 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS45 54: NE295 54: MET46 SD102 1.078 54: Marked 123 virtual sites 54: Added 22 dummy masses 54: Added 35 new constraints 54: Before cleaning: 676 pairs 54: Before cleaning: 696 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 132 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (132 atoms, 16 residues) 54: 54: Identified residue ALA34 as a starting terminus. 54: 54: Identified residue ALA49 as a ending terminus. 54: Start terminus ALA-34: NH3+ 54: End terminus ALA-49: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 261, now 261 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 696 dihedrals, 56 impropers, 472 angles 54: 667 pairs, 261 bonds and 132 virtual sites 54: 54: Total mass 1861.128 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 54: 54: The Oplsaa force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (158 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 21 acceptors were found. 54: There are 30 hydrogen bonds 54: Will use HISE for residue 60 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS60 54: NE285 54: CYS62 SG98 0.803 54: Marked 111 virtual sites 54: Added 18 dummy masses 54: Added 31 new constraints 54: Before cleaning: 603 pairs 54: Before cleaning: 618 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 117 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (117 atoms, 16 residues) 54: 54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue LYS50 as a starting terminus. 54: 54: Identified residue PRO65 as a ending terminus. 54: Start terminus LYS-50: NH3+ 54: End terminus PRO-65: PRO-COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 228 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 232, now 232 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 618 dihedrals, 48 impropers, 419 angles 54: 597 pairs, 232 bonds and 116 virtual sites 54: 54: Total mass 1662.883 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 54: 54: The Oplsaa force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (141 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 89 donors and 98 acceptors were found. 54: There are 129 hydrogen bonds 54: Will use HISE for residue 31 54: Will use HISE for residue 51 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS25 HIS31 HIS51 54: SG14 NE264 NE2226 54: HIS31 NE264 1.921 54: HIS51 NE2226 1.498 2.650 54: CYS80 SG477 0.207 1.984 1.570 54: Linking CYS-25 SG-14 and CYS-80 SG-477... 54: Marked 447 virtual sites 54: Added 58 dummy masses 54: Added 101 new constraints 54: Before cleaning: 2499 pairs 54: Before cleaning: 2524 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 58 488 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 'A' (488 atoms, 58 residues) 54: 54: Identified residue ASN24 as a starting terminus. 54: 54: Identified residue ARG81 as a ending terminus. 54: Start terminus ASN-24: NH3+ 54: End terminus ARG-81: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 58 residues with 936 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 951, now 951 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2524 dihedrals, 208 impropers, 1704 angles 54: 2469 pairs, 951 bonds and 462 virtual sites 54: 54: Total mass 6908.578 a.m.u. 54: 54: Total charge -6.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 54: 54: The Oplsaa force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (243 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Before cleaning: 653 pairs 54: Before cleaning: 663 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 128 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (128 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 252 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 254, now 254 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 663 dihedrals, 51 impropers, 457 angles 54: 650 pairs, 254 bonds and 0 virtual sites 54: 54: Total mass 1846.112 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 54: 54: The Oplsaa force field and the tip5p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (158 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 30 donors and 22 acceptors were found. 54: There are 36 hydrogen bonds 54: Will use HISE for residue 29 54: Will use HISE for residue 32 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS27 HIS29 54: SG90 NE2111 54: HIS29 NE2111 0.987 54: HIS32 NE2135 1.590 1.155 54: Before cleaning: 748 pairs 54: Before cleaning: 778 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 149 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (149 atoms, 16 residues) 54: 54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue PHE33 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus PHE-33: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 281 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 290, now 290 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 778 dihedrals, 72 impropers, 516 angles 54: 736 pairs, 290 bonds and 0 virtual sites 54: 54: Total mass 2088.357 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 54: 54: The Oplsaa force field and the tip5p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (186 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 22 acceptors were found. 54: There are 26 hydrogen bonds 54: Will use HISE for residue 45 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS45 54: NE295 54: MET46 SD102 1.078 54: Before cleaning: 676 pairs 54: Before cleaning: 696 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 132 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (132 atoms, 16 residues) 54: 54: Identified residue ALA34 as a starting terminus. 54: 54: Identified residue ALA49 as a ending terminus. 54: Start terminus ALA-34: NH3+ 54: End terminus ALA-49: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 261, now 261 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 696 dihedrals, 56 impropers, 472 angles 54: 667 pairs, 261 bonds and 0 virtual sites 54: 54: Total mass 1861.128 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 54: 54: The Oplsaa force field and the tip5p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (132 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 21 acceptors were found. 54: There are 30 hydrogen bonds 54: Will use HISE for residue 60 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS60 54: NE285 54: CYS62 SG98 0.803 54: Before cleaning: 603 pairs 54: Before cleaning: 618 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 117 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (117 atoms, 16 residues) 54: 54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue LYS50 as a starting terminus. 54: 54: Identified residue PRO65 as a ending terminus. 54: Start terminus LYS-50: NH3+ 54: End terminus PRO-65: PRO-COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 228 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 232, now 232 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 618 dihedrals, 48 impropers, 419 angles 54: 597 pairs, 232 bonds and 0 virtual sites 54: 54: Total mass 1662.883 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 54: 54: The Oplsaa force field and the tip5p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (283 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 89 donors and 98 acceptors were found. 54: There are 129 hydrogen bonds 54: Will use HISE for residue 31 54: Will use HISE for residue 51 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS25 HIS31 HIS51 54: SG14 NE264 NE2226 54: HIS31 NE264 1.921 54: HIS51 NE2226 1.498 2.650 54: CYS80 SG477 0.207 1.984 1.570 54: Linking CYS-25 SG-14 and CYS-80 SG-477... 54: Before cleaning: 2499 pairs 54: Before cleaning: 2524 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 58 488 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 'A' (488 atoms, 58 residues) 54: 54: Identified residue ASN24 as a starting terminus. 54: 54: Identified residue ARG81 as a ending terminus. 54: Start terminus ASN-24: NH3+ 54: End terminus ARG-81: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 58 residues with 936 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 951, now 951 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2524 dihedrals, 208 impropers, 1704 angles 54: 2469 pairs, 951 bonds and 0 virtual sites 54: 54: Total mass 6908.578 a.m.u. 54: 54: Total charge -6.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 54: 54: The Oplsaa force field and the tip5p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (422 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Marked 124 virtual sites 54: Added 16 dummy masses 54: Added 26 new constraints 54: Before cleaning: 653 pairs 54: Before cleaning: 663 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 128 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (128 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 252 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 254, now 254 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 663 dihedrals, 51 impropers, 457 angles 54: 650 pairs, 254 bonds and 130 virtual sites 54: 54: Total mass 1846.112 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 54: 54: The Oplsaa force field and the tip5p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (381 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 30 donors and 22 acceptors were found. 54: There are 36 hydrogen bonds 54: Will use HISE for residue 29 54: Will use HISE for residue 32 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS27 HIS29 54: SG90 NE2111 54: HIS29 NE2111 0.987 54: HIS32 NE2135 1.590 1.155 54: Marked 132 virtual sites 54: Added 10 dummy masses 54: Added 19 new constraints 54: Before cleaning: 748 pairs 54: Before cleaning: 778 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 149 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (149 atoms, 16 residues) 54: 54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue PHE33 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus PHE-33: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 281 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 290, now 290 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 778 dihedrals, 72 impropers, 516 angles 54: 736 pairs, 290 bonds and 133 virtual sites 54: 54: Total mass 2088.357 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 54: 54: The Oplsaa force field and the tip5p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (324 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 22 acceptors were found. 54: There are 26 hydrogen bonds 54: Will use HISE for residue 45 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS45 54: NE295 54: MET46 SD102 1.078 54: Marked 123 virtual sites 54: Added 22 dummy masses 54: Added 35 new constraints 54: Before cleaning: 676 pairs 54: Before cleaning: 696 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 132 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (132 atoms, 16 residues) 54: 54: Identified residue ALA34 as a starting terminus. 54: 54: Identified residue ALA49 as a ending terminus. 54: Start terminus ALA-34: NH3+ 54: End terminus ALA-49: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 261, now 261 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 696 dihedrals, 56 impropers, 472 angles 54: 667 pairs, 261 bonds and 132 virtual sites 54: 54: Total mass 1861.128 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 54: 54: The Oplsaa force field and the tip5p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (37 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 21 acceptors were found. 54: There are 30 hydrogen bonds 54: Will use HISE for residue 60 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS60 54: NE285 54: CYS62 SG98 0.803 54: Marked 111 virtual sites 54: Added 18 dummy masses 54: Added 31 new constraints 54: Before cleaning: 603 pairs 54: Before cleaning: 618 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 117 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 (117 atoms, 16 residues) 54: 54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue LYS50 as a starting terminus. 54: 54: Identified residue PRO65 as a ending terminus. 54: Start terminus LYS-50: NH3+ 54: End terminus PRO-65: PRO-COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 228 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 232, now 232 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 618 dihedrals, 48 impropers, 419 angles 54: 597 pairs, 232 bonds and 116 virtual sites 54: 54: Total mass 1662.883 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 54: 54: The Oplsaa force field and the tip5p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (34 ms) 54: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/oplsaa.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 89 donors and 98 acceptors were found. 54: There are 129 hydrogen bonds 54: Will use HISE for residue 31 54: Will use HISE for residue 51 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS25 HIS31 HIS51 54: SG14 NE264 NE2226 54: HIS31 NE264 1.921 54: HIS51 NE2226 1.498 2.650 54: CYS80 SG477 0.207 1.984 1.570 54: Linking CYS-25 SG-14 and CYS-80 SG-477... 54: Marked 447 virtual sites 54: Added 58 dummy masses 54: Added 101 new constraints 54: Before cleaning: 2499 pairs 54: Before cleaning: 2524 dihedrals 54: Using the Oplsaa force field in directory oplsaa.ff 54: 54: going to rename oplsaa.ff/aminoacids.r2b 54: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 58 488 54: 54: All occupancies are one 54: 54: Reading residue database... (Oplsaa) 54: 54: Processing chain 1 'A' (488 atoms, 58 residues) 54: 54: Identified residue ASN24 as a starting terminus. 54: 54: Identified residue ARG81 as a ending terminus. 54: Start terminus ASN-24: NH3+ 54: End terminus ARG-81: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 58 residues with 936 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 951, now 951 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2524 dihedrals, 208 impropers, 1704 angles 54: 2469 pairs, 951 bonds and 462 virtual sites 54: 54: Total mass 6908.578 a.m.u. 54: 54: Total charge -6.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 54: 54: The Oplsaa force field and the tip5p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (198 ms) 54: [----------] 30 tests from Oplsaa/Pdb2gmxTest (4030 ms total) 54: 54: [----------] Global test environment tear-down 54: [==========] 30 tests from 1 test suite ran. (4030 ms total) 54: [ PASSED ] 30 tests. 54/94 Test #54: Pdb2gmx1Test ................................. Passed 4.39 sec test 55 Start 55: Pdb2gmx2Test 55: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/pdb2gmx2-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/Pdb2gmx2Test.xml" 55: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests 55: Test timeout computed to be: 1920 55: [==========] Running 40 tests from 2 test suites. 55: [----------] Global test environment set-up. 55: [----------] 20 tests from G43a1/Pdb2gmxTest 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 25 donors and 23 acceptors were found. 55: There are 41 hydrogen bonds 55: Will use HISE for residue 8 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS3 HIS8 55: SG9 NE251 55: HIS8 NE251 1.055 55: MET12 SD83 0.763 0.990 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 267 pairs 55: Before cleaning: 305 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 55: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 128 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (128 atoms, 16 residues) 55: 55: Identified residue ALA2 as a starting terminus. 55: 55: Identified residue SER17 as a ending terminus. 55: Start terminus ALA-2: NH3+ 55: End terminus SER-17: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 165 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 172, now 167 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 90 dihedrals, 77 impropers, 241 angles 55: 267 pairs, 167 bonds and 0 virtual sites 55: 55: Total mass 1846.116 a.m.u. 55: 55: Total charge 0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 55: 55: The Gromos43a1 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (47 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 30 donors and 22 acceptors were found. 55: There are 36 hydrogen bonds 55: Will use HISE for residue 29 55: Will use HISE for residue 32 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS27 HIS29 55: SG90 NE2111 55: HIS29 NE2111 0.987 55: HIS32 NE2135 1.590 1.155 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 273 pairs 55: Before cleaning: 429 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 55: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 149 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (149 atoms, 16 residues) 55: 55: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue THR18 as a starting terminus. 55: 55: Identified residue PHE33 as a ending terminus. 55: Start terminus THR-18: NH3+ 55: End terminus PHE-33: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 202 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 216, now 211 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 93 dihedrals, 134 impropers, 316 angles 55: 273 pairs, 211 bonds and 0 virtual sites 55: 55: Total mass 2088.361 a.m.u. 55: 55: Total charge 1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 55: 55: The Gromos43a1 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (61 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 22 acceptors were found. 55: There are 26 hydrogen bonds 55: Will use HISE for residue 45 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS45 55: NE295 55: MET46 SD102 1.078 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 242 pairs 55: Before cleaning: 349 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 55: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 132 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (132 atoms, 16 residues) 55: 55: Identified residue ALA34 as a starting terminus. 55: 55: Identified residue ALA49 as a ending terminus. 55: Start terminus ALA-34: NH3+ 55: End terminus ALA-49: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 168 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 179, now 174 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 81 dihedrals, 102 impropers, 260 angles 55: 242 pairs, 174 bonds and 0 virtual sites 55: 55: Total mass 1861.132 a.m.u. 55: 55: Total charge -1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 55: 55: The Gromos43a1 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (52 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 21 acceptors were found. 55: There are 30 hydrogen bonds 55: Will use HISE for residue 60 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS60 55: NE285 55: CYS62 SG98 0.803 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 232 pairs 55: Before cleaning: 299 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 55: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 117 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (117 atoms, 16 residues) 55: 55: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue LYS50 as a starting terminus. 55: 55: Identified residue PRO65 as a ending terminus. 55: Start terminus LYS-50: NH3+ 55: End terminus PRO-65: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 150 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 159, now 154 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 78 dihedrals, 80 impropers, 227 angles 55: 232 pairs, 154 bonds and 0 virtual sites 55: 55: Total mass 1662.887 a.m.u. 55: 55: Total charge 0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 55: 55: The Gromos43a1 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (39 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 89 donors and 98 acceptors were found. 55: There are 129 hydrogen bonds 55: Will use HISE for residue 31 55: Will use HISE for residue 51 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS25 HIS31 HIS51 55: SG14 NE264 NE2226 55: HIS31 NE264 1.921 55: HIS51 NE2226 1.498 2.650 55: CYS80 SG477 0.207 1.984 1.570 55: Linking CYS-25 SG-14 and CYS-80 SG-477... 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 972 pairs 55: Before cleaning: 1256 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 55: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 55: 55: chain #res #atoms 55: 55: 1 'A' 58 488 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 'A' (488 atoms, 58 residues) 55: 55: Identified residue ASN24 as a starting terminus. 55: 55: Identified residue ARG81 as a ending terminus. 55: Start terminus ASN-24: NH3+ 55: End terminus ARG-81: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 58 residues with 635 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 655, now 650 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 321 dihedrals, 350 impropers, 955 angles 55: 972 pairs, 650 bonds and 0 virtual sites 55: 55: Total mass 6908.582 a.m.u. 55: 55: Total charge -6.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 55: 55: The Gromos43a1 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (82 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 25 donors and 23 acceptors were found. 55: There are 41 hydrogen bonds 55: Will use HISE for residue 8 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS3 HIS8 55: SG9 NE251 55: HIS8 NE251 1.055 55: MET12 SD83 0.763 0.990 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 37 virtual sites 55: Added 4 dummy masses 55: Added 8 new constraints 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 267 pairs 55: Before cleaning: 305 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 55: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 128 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (128 atoms, 16 residues) 55: 55: Identified residue ALA2 as a starting terminus. 55: 55: Identified residue SER17 as a ending terminus. 55: Start terminus ALA-2: NH3+ 55: End terminus SER-17: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 165 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 172, now 167 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 90 dihedrals, 77 impropers, 241 angles 55: 267 pairs, 167 bonds and 37 virtual sites 55: 55: Total mass 1846.116 a.m.u. 55: 55: Total charge 0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 55: 55: The Gromos43a1 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (45 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 30 donors and 22 acceptors were found. 55: There are 36 hydrogen bonds 55: Will use HISE for residue 29 55: Will use HISE for residue 32 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS27 HIS29 55: SG90 NE2111 55: HIS29 NE2111 0.987 55: HIS32 NE2135 1.590 1.155 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 53 virtual sites 55: Added 4 dummy masses 55: Added 10 new constraints 55: 55: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 273 pairs 55: Before cleaning: 429 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 55: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 149 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (149 atoms, 16 residues) 55: 55: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue THR18 as a starting terminus. 55: 55: Identified residue PHE33 as a ending terminus. 55: Start terminus THR-18: NH3+ 55: End terminus PHE-33: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 202 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 216, now 211 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 93 dihedrals, 134 impropers, 316 angles 55: 273 pairs, 211 bonds and 51 virtual sites 55: 55: Total mass 2088.361 a.m.u. 55: 55: Total charge 1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 55: 55: The Gromos43a1 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (46 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 22 acceptors were found. 55: There are 26 hydrogen bonds 55: Will use HISE for residue 45 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS45 55: NE295 55: MET46 SD102 1.078 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 36 virtual sites 55: Added 4 dummy masses 55: Added 8 new constraints 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 242 pairs 55: Before cleaning: 349 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 55: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 132 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (132 atoms, 16 residues) 55: 55: Identified residue ALA34 as a starting terminus. 55: 55: Identified residue ALA49 as a ending terminus. 55: Start terminus ALA-34: NH3+ 55: End terminus ALA-49: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 168 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 179, now 174 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 81 dihedrals, 102 impropers, 260 angles 55: 242 pairs, 174 bonds and 36 virtual sites 55: 55: Total mass 1861.132 a.m.u. 55: 55: Total charge -1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 55: 55: The Gromos43a1 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (41 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 21 acceptors were found. 55: There are 30 hydrogen bonds 55: Will use HISE for residue 60 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS60 55: NE285 55: CYS62 SG98 0.803 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 33 virtual sites 55: Added 4 dummy masses 55: Added 10 new constraints 55: 55: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 232 pairs 55: Before cleaning: 299 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 55: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 117 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (117 atoms, 16 residues) 55: 55: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue LYS50 as a starting terminus. 55: 55: Identified residue PRO65 as a ending terminus. 55: Start terminus LYS-50: NH3+ 55: End terminus PRO-65: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 150 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 159, now 154 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 78 dihedrals, 80 impropers, 227 angles 55: 232 pairs, 154 bonds and 31 virtual sites 55: 55: Total mass 1662.887 a.m.u. 55: 55: Total charge 0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 55: 55: The Gromos43a1 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (43 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 89 donors and 98 acceptors were found. 55: There are 129 hydrogen bonds 55: Will use HISE for residue 31 55: Will use HISE for residue 51 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS25 HIS31 HIS51 55: SG14 NE264 NE2226 55: HIS31 NE264 1.921 55: HIS51 NE2226 1.498 2.650 55: CYS80 SG477 0.207 1.984 1.570 55: Linking CYS-25 SG-14 and CYS-80 SG-477... 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 146 virtual sites 55: Added 10 dummy masses 55: Added 29 new constraints 55: 55: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 972 pairs 55: Before cleaning: 1256 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 55: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 55: 55: chain #res #atoms 55: 55: 1 'A' 58 488 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 'A' (488 atoms, 58 residues) 55: 55: Identified residue ASN24 as a starting terminus. 55: 55: Identified residue ARG81 as a ending terminus. 55: Start terminus ASN-24: NH3+ 55: End terminus ARG-81: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 58 residues with 635 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 655, now 650 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 321 dihedrals, 350 impropers, 955 angles 55: 972 pairs, 650 bonds and 137 virtual sites 55: 55: Total mass 6908.582 a.m.u. 55: 55: Total charge -6.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 55: 55: The Gromos43a1 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (84 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 25 donors and 23 acceptors were found. 55: There are 41 hydrogen bonds 55: Will use HISE for residue 8 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS3 HIS8 55: SG9 NE251 55: HIS8 NE251 1.055 55: MET12 SD83 0.763 0.990 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 267 pairs 55: Before cleaning: 305 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 55: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 128 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (128 atoms, 16 residues) 55: 55: Identified residue ALA2 as a starting terminus. 55: 55: Identified residue SER17 as a ending terminus. 55: Start terminus ALA-2: NH3+ 55: End terminus SER-17: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 165 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 172, now 167 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 90 dihedrals, 77 impropers, 241 angles 55: 267 pairs, 167 bonds and 0 virtual sites 55: 55: Total mass 1846.116 a.m.u. 55: 55: Total charge 0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 55: 55: The Gromos43a1 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (37 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 30 donors and 22 acceptors were found. 55: There are 36 hydrogen bonds 55: Will use HISE for residue 29 55: Will use HISE for residue 32 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS27 HIS29 55: SG90 NE2111 55: HIS29 NE2111 0.987 55: HIS32 NE2135 1.590 1.155 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 273 pairs 55: Before cleaning: 429 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 55: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 149 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (149 atoms, 16 residues) 55: 55: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue THR18 as a starting terminus. 55: 55: Identified residue PHE33 as a ending terminus. 55: Start terminus THR-18: NH3+ 55: End terminus PHE-33: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 202 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 216, now 211 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 93 dihedrals, 134 impropers, 316 angles 55: 273 pairs, 211 bonds and 0 virtual sites 55: 55: Total mass 2088.361 a.m.u. 55: 55: Total charge 1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 55: 55: The Gromos43a1 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (40 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 22 acceptors were found. 55: There are 26 hydrogen bonds 55: Will use HISE for residue 45 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS45 55: NE295 55: MET46 SD102 1.078 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 242 pairs 55: Before cleaning: 349 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 55: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 132 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (132 atoms, 16 residues) 55: 55: Identified residue ALA34 as a starting terminus. 55: 55: Identified residue ALA49 as a ending terminus. 55: Start terminus ALA-34: NH3+ 55: End terminus ALA-49: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 168 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 179, now 174 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 81 dihedrals, 102 impropers, 260 angles 55: 242 pairs, 174 bonds and 0 virtual sites 55: 55: Total mass 1861.132 a.m.u. 55: 55: Total charge -1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 55: 55: The Gromos43a1 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (40 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 21 acceptors were found. 55: There are 30 hydrogen bonds 55: Will use HISE for residue 60 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS60 55: NE285 55: CYS62 SG98 0.803 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 232 pairs 55: Before cleaning: 299 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 55: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 117 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (117 atoms, 16 residues) 55: 55: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue LYS50 as a starting terminus. 55: 55: Identified residue PRO65 as a ending terminus. 55: Start terminus LYS-50: NH3+ 55: End terminus PRO-65: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 150 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 159, now 154 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 78 dihedrals, 80 impropers, 227 angles 55: 232 pairs, 154 bonds and 0 virtual sites 55: 55: Total mass 1662.887 a.m.u. 55: 55: Total charge 0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 55: 55: The Gromos43a1 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (38 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 89 donors and 98 acceptors were found. 55: There are 129 hydrogen bonds 55: Will use HISE for residue 31 55: Will use HISE for residue 51 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS25 HIS31 HIS51 55: SG14 NE264 NE2226 55: HIS31 NE264 1.921 55: HIS51 NE2226 1.498 2.650 55: CYS80 SG477 0.207 1.984 1.570 55: Linking CYS-25 SG-14 and CYS-80 SG-477... 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 972 pairs 55: Before cleaning: 1256 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 55: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 55: 55: chain #res #atoms 55: 55: 1 'A' 58 488 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 'A' (488 atoms, 58 residues) 55: 55: Identified residue ASN24 as a starting terminus. 55: 55: Identified residue ARG81 as a ending terminus. 55: Start terminus ASN-24: NH3+ 55: End terminus ARG-81: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 58 residues with 635 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 655, now 650 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 321 dihedrals, 350 impropers, 955 angles 55: 972 pairs, 650 bonds and 0 virtual sites 55: 55: Total mass 6908.582 a.m.u. 55: 55: Total charge -6.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 55: 55: The Gromos43a1 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (75 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 25 donors and 23 acceptors were found. 55: There are 41 hydrogen bonds 55: Will use HISE for residue 8 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS3 HIS8 55: SG9 NE251 55: HIS8 NE251 1.055 55: MET12 SD83 0.763 0.990 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 37 virtual sites 55: Added 4 dummy masses 55: Added 8 new constraints 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 267 pairs 55: Before cleaning: 305 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 55: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 128 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (128 atoms, 16 residues) 55: 55: Identified residue ALA2 as a starting terminus. 55: 55: Identified residue SER17 as a ending terminus. 55: Start terminus ALA-2: NH3+ 55: End terminus SER-17: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 165 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 172, now 167 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 90 dihedrals, 77 impropers, 241 angles 55: 267 pairs, 167 bonds and 37 virtual sites 55: 55: Total mass 1846.116 a.m.u. 55: 55: Total charge 0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 55: 55: The Gromos43a1 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (49 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 30 donors and 22 acceptors were found. 55: There are 36 hydrogen bonds 55: Will use HISE for residue 29 55: Will use HISE for residue 32 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS27 HIS29 55: SG90 NE2111 55: HIS29 NE2111 0.987 55: HIS32 NE2135 1.590 1.155 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 53 virtual sites 55: Added 4 dummy masses 55: Added 10 new constraints 55: 55: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 273 pairs 55: Before cleaning: 429 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 55: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 149 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (149 atoms, 16 residues) 55: 55: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue THR18 as a starting terminus. 55: 55: Identified residue PHE33 as a ending terminus. 55: Start terminus THR-18: NH3+ 55: End terminus PHE-33: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 202 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 216, now 211 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 93 dihedrals, 134 impropers, 316 angles 55: 273 pairs, 211 bonds and 51 virtual sites 55: 55: Total mass 2088.361 a.m.u. 55: 55: Total charge 1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 55: 55: The Gromos43a1 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (45 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 22 acceptors were found. 55: There are 26 hydrogen bonds 55: Will use HISE for residue 45 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS45 55: NE295 55: MET46 SD102 1.078 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 36 virtual sites 55: Added 4 dummy masses 55: Added 8 new constraints 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 242 pairs 55: Before cleaning: 349 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 55: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 132 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (132 atoms, 16 residues) 55: 55: Identified residue ALA34 as a starting terminus. 55: 55: Identified residue ALA49 as a ending terminus. 55: Start terminus ALA-34: NH3+ 55: End terminus ALA-49: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 168 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 179, now 174 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 81 dihedrals, 102 impropers, 260 angles 55: 242 pairs, 174 bonds and 36 virtual sites 55: 55: Total mass 1861.132 a.m.u. 55: 55: Total charge -1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 55: 55: The Gromos43a1 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (41 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 21 acceptors were found. 55: There are 30 hydrogen bonds 55: Will use HISE for residue 60 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS60 55: NE285 55: CYS62 SG98 0.803 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 33 virtual sites 55: Added 4 dummy masses 55: Added 10 new constraints 55: 55: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 232 pairs 55: Before cleaning: 299 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 55: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 117 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 (117 atoms, 16 residues) 55: 55: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue LYS50 as a starting terminus. 55: 55: Identified residue PRO65 as a ending terminus. 55: Start terminus LYS-50: NH3+ 55: End terminus PRO-65: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 150 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 159, now 154 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 78 dihedrals, 80 impropers, 227 angles 55: 232 pairs, 154 bonds and 31 virtual sites 55: 55: Total mass 1662.887 a.m.u. 55: 55: Total charge 0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 55: 55: The Gromos43a1 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (41 ms) 55: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.rtp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos43a1.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 89 donors and 98 acceptors were found. 55: There are 129 hydrogen bonds 55: Will use HISE for residue 31 55: Will use HISE for residue 51 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS25 HIS31 HIS51 55: SG14 NE264 NE2226 55: HIS31 NE264 1.921 55: HIS51 NE2226 1.498 2.650 55: CYS80 SG477 0.207 1.984 1.570 55: Linking CYS-25 SG-14 and CYS-80 SG-477... 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 146 virtual sites 55: Added 10 dummy masses 55: Added 29 new constraints 55: 55: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 972 pairs 55: Before cleaning: 1256 dihedrals 55: Using the Gromos43a1 force field in directory gromos43a1.ff 55: 55: going to rename gromos43a1.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 55: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 55: 55: chain #res #atoms 55: 55: 1 'A' 58 488 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos43a1) 55: 55: Processing chain 1 'A' (488 atoms, 58 residues) 55: 55: Identified residue ASN24 as a starting terminus. 55: 55: Identified residue ARG81 as a ending terminus. 55: Start terminus ASN-24: NH3+ 55: End terminus ARG-81: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 58 residues with 635 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 655, now 650 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 321 dihedrals, 350 impropers, 955 angles 55: 972 pairs, 650 bonds and 137 virtual sites 55: 55: Total mass 6908.582 a.m.u. 55: 55: Total charge -6.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 55: 55: The Gromos43a1 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (77 ms) 55: [----------] 20 tests from G43a1/Pdb2gmxTest (1034 ms total) 55: 55: [----------] 20 tests from G53a6/Pdb2gmxTest 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 25 donors and 23 acceptors were found. 55: There are 41 hydrogen bonds 55: Will use HISE for residue 8 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS3 HIS8 55: SG9 NE251 55: HIS8 NE251 1.055 55: MET12 SD83 0.763 0.990 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 267 pairs 55: Before cleaning: 312 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 55: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 128 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (128 atoms, 16 residues) 55: 55: Identified residue ALA2 as a starting terminus. 55: 55: Identified residue SER17 as a ending terminus. 55: Start terminus ALA-2: NH3+ 55: End terminus SER-17: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 167 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 174, now 169 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 90 dihedrals, 79 impropers, 245 angles 55: 267 pairs, 169 bonds and 0 virtual sites 55: 55: Total mass 1846.116 a.m.u. 55: 55: Total charge -0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 55: 55: The Gromos53a6 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (44 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 30 donors and 22 acceptors were found. 55: There are 36 hydrogen bonds 55: Will use HISE for residue 29 55: Will use HISE for residue 32 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS27 HIS29 55: SG90 NE2111 55: HIS29 NE2111 0.987 55: HIS32 NE2135 1.590 1.155 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 273 pairs 55: Before cleaning: 443 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 55: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 149 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (149 atoms, 16 residues) 55: 55: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue THR18 as a starting terminus. 55: 55: Identified residue PHE33 as a ending terminus. 55: Start terminus THR-18: NH3+ 55: End terminus PHE-33: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 206 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 220, now 215 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 93 dihedrals, 138 impropers, 324 angles 55: 273 pairs, 215 bonds and 0 virtual sites 55: 55: Total mass 2088.361 a.m.u. 55: 55: Total charge 1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 55: 55: The Gromos53a6 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (73 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 22 acceptors were found. 55: There are 26 hydrogen bonds 55: Will use HISE for residue 45 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS45 55: NE295 55: MET46 SD102 1.078 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 242 pairs 55: Before cleaning: 356 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 55: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 132 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (132 atoms, 16 residues) 55: 55: Identified residue ALA34 as a starting terminus. 55: 55: Identified residue ALA49 as a ending terminus. 55: Start terminus ALA-34: NH3+ 55: End terminus ALA-49: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 170 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 181, now 176 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 81 dihedrals, 104 impropers, 264 angles 55: 242 pairs, 176 bonds and 0 virtual sites 55: 55: Total mass 1861.132 a.m.u. 55: 55: Total charge -1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 55: 55: The Gromos53a6 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (46 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 21 acceptors were found. 55: There are 30 hydrogen bonds 55: Will use HISE for residue 60 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS60 55: NE285 55: CYS62 SG98 0.803 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 232 pairs 55: Before cleaning: 306 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 55: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 117 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (117 atoms, 16 residues) 55: 55: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue LYS50 as a starting terminus. 55: 55: Identified residue PRO65 as a ending terminus. 55: Start terminus LYS-50: NH3+ 55: End terminus PRO-65: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 152 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 161, now 156 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 78 dihedrals, 82 impropers, 231 angles 55: 232 pairs, 156 bonds and 0 virtual sites 55: 55: Total mass 1662.887 a.m.u. 55: 55: Total charge -0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 55: 55: The Gromos53a6 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (42 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 89 donors and 98 acceptors were found. 55: There are 129 hydrogen bonds 55: Will use HISE for residue 31 55: Will use HISE for residue 51 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS25 HIS31 HIS51 55: SG14 NE264 NE2226 55: HIS31 NE264 1.921 55: HIS51 NE2226 1.498 2.650 55: CYS80 SG477 0.207 1.984 1.570 55: Linking CYS-25 SG-14 and CYS-80 SG-477... 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 972 pairs 55: Before cleaning: 1270 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 55: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 55: 55: chain #res #atoms 55: 55: 1 'A' 58 488 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 'A' (488 atoms, 58 residues) 55: 55: Identified residue ASN24 as a starting terminus. 55: 55: Identified residue ARG81 as a ending terminus. 55: Start terminus ASN-24: NH3+ 55: End terminus ARG-81: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 58 residues with 639 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 659, now 654 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 321 dihedrals, 354 impropers, 963 angles 55: 972 pairs, 654 bonds and 0 virtual sites 55: 55: Total mass 6908.582 a.m.u. 55: 55: Total charge -6.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 55: 55: The Gromos53a6 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (74 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 25 donors and 23 acceptors were found. 55: There are 41 hydrogen bonds 55: Will use HISE for residue 8 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS3 HIS8 55: SG9 NE251 55: HIS8 NE251 1.055 55: MET12 SD83 0.763 0.990 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 39 virtual sites 55: Added 4 dummy masses 55: Added 8 new constraints 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 267 pairs 55: Before cleaning: 312 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 55: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 128 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (128 atoms, 16 residues) 55: 55: Identified residue ALA2 as a starting terminus. 55: 55: Identified residue SER17 as a ending terminus. 55: Start terminus ALA-2: NH3+ 55: End terminus SER-17: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 167 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 174, now 169 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 90 dihedrals, 79 impropers, 245 angles 55: 267 pairs, 169 bonds and 39 virtual sites 55: 55: Total mass 1846.116 a.m.u. 55: 55: Total charge -0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 55: 55: The Gromos53a6 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (45 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 30 donors and 22 acceptors were found. 55: There are 36 hydrogen bonds 55: Will use HISE for residue 29 55: Will use HISE for residue 32 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS27 HIS29 55: SG90 NE2111 55: HIS29 NE2111 0.987 55: HIS32 NE2135 1.590 1.155 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 57 virtual sites 55: Added 4 dummy masses 55: Added 10 new constraints 55: 55: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 273 pairs 55: Before cleaning: 443 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 55: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 149 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (149 atoms, 16 residues) 55: 55: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue THR18 as a starting terminus. 55: 55: Identified residue PHE33 as a ending terminus. 55: Start terminus THR-18: NH3+ 55: End terminus PHE-33: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 206 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 220, now 215 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 93 dihedrals, 138 impropers, 324 angles 55: 273 pairs, 215 bonds and 55 virtual sites 55: 55: Total mass 2088.361 a.m.u. 55: 55: Total charge 1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 55: 55: The Gromos53a6 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (50 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 22 acceptors were found. 55: There are 26 hydrogen bonds 55: Will use HISE for residue 45 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS45 55: NE295 55: MET46 SD102 1.078 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 38 virtual sites 55: Added 4 dummy masses 55: Added 8 new constraints 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 242 pairs 55: Before cleaning: 356 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 55: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 132 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (132 atoms, 16 residues) 55: 55: Identified residue ALA34 as a starting terminus. 55: 55: Identified residue ALA49 as a ending terminus. 55: Start terminus ALA-34: NH3+ 55: End terminus ALA-49: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 170 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 181, now 176 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 81 dihedrals, 104 impropers, 264 angles 55: 242 pairs, 176 bonds and 38 virtual sites 55: 55: Total mass 1861.132 a.m.u. 55: 55: Total charge -1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 55: 55: The Gromos53a6 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (60 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 21 acceptors were found. 55: There are 30 hydrogen bonds 55: Will use HISE for residue 60 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS60 55: NE285 55: CYS62 SG98 0.803 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 35 virtual sites 55: Added 4 dummy masses 55: Added 10 new constraints 55: 55: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 232 pairs 55: Before cleaning: 306 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 55: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 117 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (117 atoms, 16 residues) 55: 55: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue LYS50 as a starting terminus. 55: 55: Identified residue PRO65 as a ending terminus. 55: Start terminus LYS-50: NH3+ 55: End terminus PRO-65: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 152 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 161, now 156 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 78 dihedrals, 82 impropers, 231 angles 55: 232 pairs, 156 bonds and 33 virtual sites 55: 55: Total mass 1662.887 a.m.u. 55: 55: Total charge -0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 55: 55: The Gromos53a6 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (42 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 89 donors and 98 acceptors were found. 55: There are 129 hydrogen bonds 55: Will use HISE for residue 31 55: Will use HISE for residue 51 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS25 HIS31 HIS51 55: SG14 NE264 NE2226 55: HIS31 NE264 1.921 55: HIS51 NE2226 1.498 2.650 55: CYS80 SG477 0.207 1.984 1.570 55: Linking CYS-25 SG-14 and CYS-80 SG-477... 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 150 virtual sites 55: Added 10 dummy masses 55: Added 29 new constraints 55: 55: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 972 pairs 55: Before cleaning: 1270 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 55: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 55: 55: chain #res #atoms 55: 55: 1 'A' 58 488 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 'A' (488 atoms, 58 residues) 55: 55: Identified residue ASN24 as a starting terminus. 55: 55: Identified residue ARG81 as a ending terminus. 55: Start terminus ASN-24: NH3+ 55: End terminus ARG-81: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 58 residues with 639 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 659, now 654 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 321 dihedrals, 354 impropers, 963 angles 55: 972 pairs, 654 bonds and 141 virtual sites 55: 55: Total mass 6908.582 a.m.u. 55: 55: Total charge -6.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 55: 55: The Gromos53a6 force field and the spc water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (84 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 25 donors and 23 acceptors were found. 55: There are 41 hydrogen bonds 55: Will use HISE for residue 8 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS3 HIS8 55: SG9 NE251 55: HIS8 NE251 1.055 55: MET12 SD83 0.763 0.990 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 267 pairs 55: Before cleaning: 312 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 55: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 128 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (128 atoms, 16 residues) 55: 55: Identified residue ALA2 as a starting terminus. 55: 55: Identified residue SER17 as a ending terminus. 55: Start terminus ALA-2: NH3+ 55: End terminus SER-17: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 167 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 174, now 169 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 90 dihedrals, 79 impropers, 245 angles 55: 267 pairs, 169 bonds and 0 virtual sites 55: 55: Total mass 1846.116 a.m.u. 55: 55: Total charge -0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 55: 55: The Gromos53a6 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (43 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 30 donors and 22 acceptors were found. 55: There are 36 hydrogen bonds 55: Will use HISE for residue 29 55: Will use HISE for residue 32 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS27 HIS29 55: SG90 NE2111 55: HIS29 NE2111 0.987 55: HIS32 NE2135 1.590 1.155 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 273 pairs 55: Before cleaning: 443 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 55: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 149 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (149 atoms, 16 residues) 55: 55: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue THR18 as a starting terminus. 55: 55: Identified residue PHE33 as a ending terminus. 55: Start terminus THR-18: NH3+ 55: End terminus PHE-33: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 206 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 220, now 215 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 93 dihedrals, 138 impropers, 324 angles 55: 273 pairs, 215 bonds and 0 virtual sites 55: 55: Total mass 2088.361 a.m.u. 55: 55: Total charge 1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 55: 55: The Gromos53a6 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (45 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 22 acceptors were found. 55: There are 26 hydrogen bonds 55: Will use HISE for residue 45 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS45 55: NE295 55: MET46 SD102 1.078 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 242 pairs 55: Before cleaning: 356 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 55: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 132 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (132 atoms, 16 residues) 55: 55: Identified residue ALA34 as a starting terminus. 55: 55: Identified residue ALA49 as a ending terminus. 55: Start terminus ALA-34: NH3+ 55: End terminus ALA-49: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 170 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 181, now 176 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 81 dihedrals, 104 impropers, 264 angles 55: 242 pairs, 176 bonds and 0 virtual sites 55: 55: Total mass 1861.132 a.m.u. 55: 55: Total charge -1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 55: 55: The Gromos53a6 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (42 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 21 acceptors were found. 55: There are 30 hydrogen bonds 55: Will use HISE for residue 60 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS60 55: NE285 55: CYS62 SG98 0.803 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 232 pairs 55: Before cleaning: 306 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 55: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 117 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (117 atoms, 16 residues) 55: 55: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue LYS50 as a starting terminus. 55: 55: Identified residue PRO65 as a ending terminus. 55: Start terminus LYS-50: NH3+ 55: End terminus PRO-65: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 152 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 161, now 156 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 78 dihedrals, 82 impropers, 231 angles 55: 232 pairs, 156 bonds and 0 virtual sites 55: 55: Total mass 1662.887 a.m.u. 55: 55: Total charge -0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 55: 55: The Gromos53a6 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (41 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 89 donors and 98 acceptors were found. 55: There are 129 hydrogen bonds 55: Will use HISE for residue 31 55: Will use HISE for residue 51 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS25 HIS31 HIS51 55: SG14 NE264 NE2226 55: HIS31 NE264 1.921 55: HIS51 NE2226 1.498 2.650 55: CYS80 SG477 0.207 1.984 1.570 55: Linking CYS-25 SG-14 and CYS-80 SG-477... 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 972 pairs 55: Before cleaning: 1270 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 55: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 55: 55: chain #res #atoms 55: 55: 1 'A' 58 488 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 'A' (488 atoms, 58 residues) 55: 55: Identified residue ASN24 as a starting terminus. 55: 55: Identified residue ARG81 as a ending terminus. 55: Start terminus ASN-24: NH3+ 55: End terminus ARG-81: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 58 residues with 639 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 659, now 654 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 321 dihedrals, 354 impropers, 963 angles 55: 972 pairs, 654 bonds and 0 virtual sites 55: 55: Total mass 6908.582 a.m.u. 55: 55: Total charge -6.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 55: 55: The Gromos53a6 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (72 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 25 donors and 23 acceptors were found. 55: There are 41 hydrogen bonds 55: Will use HISE for residue 8 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS3 HIS8 55: SG9 NE251 55: HIS8 NE251 1.055 55: MET12 SD83 0.763 0.990 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 39 virtual sites 55: Added 4 dummy masses 55: Added 8 new constraints 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 267 pairs 55: Before cleaning: 312 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 55: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 128 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (128 atoms, 16 residues) 55: 55: Identified residue ALA2 as a starting terminus. 55: 55: Identified residue SER17 as a ending terminus. 55: Start terminus ALA-2: NH3+ 55: End terminus SER-17: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 167 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 174, now 169 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 90 dihedrals, 79 impropers, 245 angles 55: 267 pairs, 169 bonds and 39 virtual sites 55: 55: Total mass 1846.116 a.m.u. 55: 55: Total charge -0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 55: 55: The Gromos53a6 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (45 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 30 donors and 22 acceptors were found. 55: There are 36 hydrogen bonds 55: Will use HISE for residue 29 55: Will use HISE for residue 32 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS27 HIS29 55: SG90 NE2111 55: HIS29 NE2111 0.987 55: HIS32 NE2135 1.590 1.155 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 57 virtual sites 55: Added 4 dummy masses 55: Added 10 new constraints 55: 55: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 273 pairs 55: Before cleaning: 443 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 55: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 149 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (149 atoms, 16 residues) 55: 55: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue THR18 as a starting terminus. 55: 55: Identified residue PHE33 as a ending terminus. 55: Start terminus THR-18: NH3+ 55: End terminus PHE-33: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 206 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 220, now 215 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 93 dihedrals, 138 impropers, 324 angles 55: 273 pairs, 215 bonds and 55 virtual sites 55: 55: Total mass 2088.361 a.m.u. 55: 55: Total charge 1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 55: 55: The Gromos53a6 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (74 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 22 acceptors were found. 55: There are 26 hydrogen bonds 55: Will use HISE for residue 45 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS45 55: NE295 55: MET46 SD102 1.078 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 38 virtual sites 55: Added 4 dummy masses 55: Added 8 new constraints 55: 55: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 242 pairs 55: Before cleaning: 356 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 55: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 132 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (132 atoms, 16 residues) 55: 55: Identified residue ALA34 as a starting terminus. 55: 55: Identified residue ALA49 as a ending terminus. 55: Start terminus ALA-34: NH3+ 55: End terminus ALA-49: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 170 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 181, now 176 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 81 dihedrals, 104 impropers, 264 angles 55: 242 pairs, 176 bonds and 38 virtual sites 55: 55: Total mass 1861.132 a.m.u. 55: 55: Total charge -1.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 55: 55: The Gromos53a6 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (47 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 22 donors and 21 acceptors were found. 55: There are 30 hydrogen bonds 55: Will use HISE for residue 60 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: HIS60 55: NE285 55: CYS62 SG98 0.803 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 35 virtual sites 55: Added 4 dummy masses 55: Added 10 new constraints 55: 55: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 232 pairs 55: Before cleaning: 306 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 55: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 55: 55: chain #res #atoms 55: 55: 1 ' ' 16 117 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 (117 atoms, 16 residues) 55: 55: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 55: 55: Identified residue LYS50 as a starting terminus. 55: 55: Identified residue PRO65 as a ending terminus. 55: Start terminus LYS-50: NH3+ 55: End terminus PRO-65: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 16 residues with 152 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 161, now 156 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 78 dihedrals, 82 impropers, 231 angles 55: 232 pairs, 156 bonds and 33 virtual sites 55: 55: Total mass 1662.887 a.m.u. 55: 55: Total charge -0.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 55: 55: The Gromos53a6 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (45 ms) 55: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.r2b 55: All occupancies are one 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/atomtypes.atp 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.rtp 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.hdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.n.tdb 55: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/gromos53a6.ff/aminoacids.c.tdb 55: Analysing hydrogen-bonding network for automated assignment of histidine 55: protonation. 89 donors and 98 acceptors were found. 55: There are 129 hydrogen bonds 55: Will use HISE for residue 31 55: Will use HISE for residue 51 55: 9 out of 9 lines of specbond.dat converted successfully 55: Special Atom Distance matrix: 55: CYS25 HIS31 HIS51 55: SG14 NE264 NE2226 55: HIS31 NE264 1.921 55: HIS51 NE2226 1.498 2.650 55: CYS80 SG477 0.207 1.984 1.570 55: Linking CYS-25 SG-14 and CYS-80 SG-477... 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: 55: WARNING: Duplicate line found in or between hackblock and rtp entries 55: 55: Marked 150 virtual sites 55: Added 10 dummy masses 55: Added 29 new constraints 55: 55: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom H used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: 55: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 55: to an entry in the topology database, but the atom O used in 55: an interaction of type angle in that entry is not found in the 55: input file. Perhaps your atom and/or residue naming needs to be 55: fixed. 55: 55: 55: Before cleaning: 972 pairs 55: Before cleaning: 1270 dihedrals 55: Using the Gromos53a6 force field in directory gromos53a6.ff 55: 55: going to rename gromos53a6.ff/aminoacids.r2b 55: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 55: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 55: 55: Analyzing pdb file 55: Splitting chemical chains based on TER records or chain id changing. 55: 55: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 55: 55: chain #res #atoms 55: 55: 1 'A' 58 488 55: 55: All occupancies are one 55: 55: Reading residue database... (Gromos53a6) 55: 55: Using default: not generating all possible dihedrals 55: 55: Using default: excluding 3 bonded neighbors 55: 55: Using default: generating 1,4 H--H interactions 55: 55: Using default: removing proper dihedrals found on the same bond as a proper dihedral 55: 55: Processing chain 1 'A' (488 atoms, 58 residues) 55: 55: Identified residue ASN24 as a starting terminus. 55: 55: Identified residue ARG81 as a ending terminus. 55: Start terminus ASN-24: NH3+ 55: End terminus ARG-81: COO- 55: 55: Checking for duplicate atoms.... 55: 55: Generating any missing hydrogen atoms and/or adding termini. 55: 55: Now there are 58 residues with 639 atoms 55: 55: Making bonds... 55: 55: Number of bonds was 659, now 654 55: 55: Generating angles, dihedrals and pairs... 55: 55: Making cmap torsions... 55: 55: There are 321 dihedrals, 354 impropers, 963 angles 55: 972 pairs, 654 bonds and 141 virtual sites 55: 55: Total mass 6908.582 a.m.u. 55: 55: Total charge -6.000 e 55: 55: Writing topology 55: 55: Writing coordinate file... 55: 55: --------- PLEASE NOTE ------------ 55: 55: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 55: 55: The Gromos53a6 force field and the spce water model are used. 55: 55: --------- ETON ESAELP ------------ 55: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (83 ms) 55: [----------] 20 tests from G53a6/Pdb2gmxTest (1107 ms total) 55: 55: [----------] Global test environment tear-down 55: [==========] 40 tests from 2 test suites ran. (2141 ms total) 55: [ PASSED ] 40 tests. 55/94 Test #55: Pdb2gmx2Test ................................. Passed 2.49 sec test 56 Start 56: Pdb2gmx3Test 56: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/pdb2gmx3-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/Pdb2gmx3Test.xml" 56: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/gmxpreprocess/tests 56: Test timeout computed to be: 1920 56: [==========] Running 39 tests from 6 test suites. 56: [----------] Global test environment set-up. 56: [----------] 10 tests from Amber/Pdb2gmxTest 56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 25 donors and 23 acceptors were found. 56: There are 41 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 HIS8 56: SG9 NE251 56: HIS8 NE251 1.055 56: MET12 SD83 0.763 0.990 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 56: Before cleaning: 653 pairs 56: Before cleaning: 691 dihedrals 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 128 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 (128 atoms, 16 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 252 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 255, now 254 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 691 dihedrals, 51 impropers, 457 angles 56: 650 pairs, 254 bonds and 0 virtual sites 56: 56: Total mass 1846.132 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 56: 56: The Amber99sb-ildn force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (56 ms) 56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 30 donors and 22 acceptors were found. 56: There are 36 hydrogen bonds 56: Will use HISE for residue 29 56: Will use HISE for residue 32 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS27 HIS29 56: SG90 NE2111 56: HIS29 NE2111 0.987 56: HIS32 NE2135 1.590 1.155 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 56: Before cleaning: 748 pairs 56: Before cleaning: 788 dihedrals 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 56: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 149 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 (149 atoms, 16 residues) 56: 56: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 56: 56: Identified residue THR18 as a starting terminus. 56: 56: Identified residue PHE33 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 281 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 291, now 290 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 788 dihedrals, 72 impropers, 516 angles 56: 736 pairs, 290 bonds and 0 virtual sites 56: 56: Total mass 2088.366 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 56: 56: The Amber99sb-ildn force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (89 ms) 56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 22 donors and 22 acceptors were found. 56: There are 26 hydrogen bonds 56: Will use HISE for residue 45 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS45 56: NE295 56: MET46 SD102 1.078 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 56: Before cleaning: 676 pairs 56: Before cleaning: 727 dihedrals 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 56: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 132 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 (132 atoms, 16 residues) 56: 56: Identified residue ALA34 as a starting terminus. 56: 56: Identified residue ALA49 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 255 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 262, now 261 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 727 dihedrals, 56 impropers, 472 angles 56: 667 pairs, 261 bonds and 0 virtual sites 56: 56: Total mass 1861.124 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 56: 56: The Amber99sb-ildn force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (60 ms) 56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 22 donors and 21 acceptors were found. 56: There are 30 hydrogen bonds 56: Will use HISE for residue 60 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS60 56: NE285 56: CYS62 SG98 0.803 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 56: Before cleaning: 603 pairs 56: Before cleaning: 634 dihedrals 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 56: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 117 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 (117 atoms, 16 residues) 56: 56: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 56: 56: Identified residue LYS50 as a starting terminus. 56: 56: Identified residue PRO65 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 228 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 233, now 232 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 634 dihedrals, 48 impropers, 419 angles 56: 597 pairs, 232 bonds and 0 virtual sites 56: 56: Total mass 1662.888 a.m.u. 56: 56: Total charge -0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 56: 56: The Amber99sb-ildn force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (47 ms) 56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 89 donors and 98 acceptors were found. 56: There are 129 hydrogen bonds 56: Will use HISE for residue 31 56: Will use HISE for residue 51 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS25 HIS31 HIS51 56: SG14 NE264 NE2226 56: HIS31 NE264 1.921 56: HIS51 NE2226 1.498 2.650 56: CYS80 SG477 0.207 1.984 1.570 56: Linking CYS-25 SG-14 and CYS-80 SG-477... 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 56: Before cleaning: 2499 pairs 56: Before cleaning: 2631 dihedrals 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 56: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 58 488 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 'A' (488 atoms, 58 residues) 56: 56: Identified residue ASN24 as a starting terminus. 56: 56: Identified residue ARG81 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 58 residues with 936 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 952, now 951 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 2631 dihedrals, 208 impropers, 1704 angles 56: 2469 pairs, 951 bonds and 0 virtual sites 56: 56: Total mass 6908.576 a.m.u. 56: 56: Total charge -6.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 56: 56: The Amber99sb-ildn force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (135 ms) 56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 25 donors and 23 acceptors were found. 56: There are 41 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 HIS8 56: SG9 NE251 56: HIS8 NE251 1.055 56: MET12 SD83 0.763 0.990 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 56: Marked 124 virtual sites 56: Added 16 dummy masses 56: Added 26 new constraints 56: Before cleaning: 653 pairs 56: Before cleaning: 691 dihedrals 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 128 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 (128 atoms, 16 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 252 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 255, now 254 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 691 dihedrals, 51 impropers, 457 angles 56: 650 pairs, 254 bonds and 130 virtual sites 56: 56: Total mass 1846.132 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 56: 56: The Amber99sb-ildn force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (59 ms) 56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 30 donors and 22 acceptors were found. 56: There are 36 hydrogen bonds 56: Will use HISE for residue 29 56: Will use HISE for residue 32 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS27 HIS29 56: SG90 NE2111 56: HIS29 NE2111 0.987 56: HIS32 NE2135 1.590 1.155 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 56: Marked 132 virtual sites 56: Added 10 dummy masses 56: Added 19 new constraints 56: Before cleaning: 748 pairs 56: Before cleaning: 788 dihedrals 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 56: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 149 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 (149 atoms, 16 residues) 56: 56: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 56: 56: Identified residue THR18 as a starting terminus. 56: 56: Identified residue PHE33 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 281 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 291, now 290 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 788 dihedrals, 72 impropers, 516 angles 56: 736 pairs, 290 bonds and 133 virtual sites 56: 56: Total mass 2088.366 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 56: 56: The Amber99sb-ildn force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (102 ms) 56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 22 donors and 22 acceptors were found. 56: There are 26 hydrogen bonds 56: Will use HISE for residue 45 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS45 56: NE295 56: MET46 SD102 1.078 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 56: Marked 123 virtual sites 56: Added 22 dummy masses 56: Added 35 new constraints 56: Before cleaning: 676 pairs 56: Before cleaning: 727 dihedrals 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 56: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 132 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 (132 atoms, 16 residues) 56: 56: Identified residue ALA34 as a starting terminus. 56: 56: Identified residue ALA49 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 255 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 262, now 261 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 727 dihedrals, 56 impropers, 472 angles 56: 667 pairs, 261 bonds and 132 virtual sites 56: 56: Total mass 1861.124 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 56: 56: The Amber99sb-ildn force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (60 ms) 56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 22 donors and 21 acceptors were found. 56: There are 30 hydrogen bonds 56: Will use HISE for residue 60 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS60 56: NE285 56: CYS62 SG98 0.803 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 56: Marked 111 virtual sites 56: Added 18 dummy masses 56: Added 31 new constraints 56: Before cleaning: 603 pairs 56: Before cleaning: 634 dihedrals 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 56: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 117 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 (117 atoms, 16 residues) 56: 56: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 56: 56: Identified residue LYS50 as a starting terminus. 56: 56: Identified residue PRO65 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 228 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 233, now 232 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 634 dihedrals, 48 impropers, 419 angles 56: 597 pairs, 232 bonds and 116 virtual sites 56: 56: Total mass 1662.888 a.m.u. 56: 56: Total charge -0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 56: 56: The Amber99sb-ildn force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (63 ms) 56: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 89 donors and 98 acceptors were found. 56: There are 129 hydrogen bonds 56: Will use HISE for residue 31 56: Will use HISE for residue 51 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS25 HIS31 HIS51 56: SG14 NE264 NE2226 56: HIS31 NE264 1.921 56: HIS51 NE2226 1.498 2.650 56: CYS80 SG477 0.207 1.984 1.570 56: Linking CYS-25 SG-14 and CYS-80 SG-477... 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 56: Marked 447 virtual sites 56: Added 58 dummy masses 56: Added 101 new constraints 56: Before cleaning: 2499 pairs 56: Before cleaning: 2631 dihedrals 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 56: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 58 488 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 'A' (488 atoms, 58 residues) 56: 56: Identified residue ASN24 as a starting terminus. 56: 56: Identified residue ARG81 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 58 residues with 936 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 952, now 951 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 2631 dihedrals, 208 impropers, 1704 angles 56: 2469 pairs, 951 bonds and 462 virtual sites 56: 56: Total mass 6908.576 a.m.u. 56: 56: Total charge -6.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 56: 56: The Amber99sb-ildn force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (186 ms) 56: [----------] 10 tests from Amber/Pdb2gmxTest (863 ms total) 56: 56: [----------] 1 test from AmberTip4p/Pdb2gmxTest 56: [ RUN ] AmberTip4p/Pdb2gmxTest.Runs/ff_amber99sbildn_tip4p_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/amber99sb-ildn.ff/rna.arn 56: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 56: 56: going to rename amber99sb-ildn.ff/aminoacids.r2b 56: 56: going to rename amber99sb-ildn.ff/dna.r2b 56: 56: going to rename amber99sb-ildn.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/tip4p.pdb... 56: Read 'TIP4p ice to test that MW is handled correctly', 4 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 0 chains and 1 blocks of water and 2 residues with 4 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 2 4 (only water) 56: 56: All occupancies are one 56: 56: Reading residue database... (Amber99sb-ildn) 56: 56: Processing chain 1 (4 atoms, 2 residues) 56: 56: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 2 residues with 8 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 4, now 4 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 0 dihedrals, 0 impropers, 2 angles 56: 0 pairs, 4 bonds and 0 virtual sites 56: 56: Total mass 36.032 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/tip4p.pdb. 56: 56: The Amber99sb-ildn force field and the tip4p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] AmberTip4p/Pdb2gmxTest.Runs/ff_amber99sbildn_tip4p_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full (27 ms) 56: [----------] 1 test from AmberTip4p/Pdb2gmxTest (27 ms total) 56: 56: [----------] 12 tests from Charmm/Pdb2gmxTest 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 25 donors and 23 acceptors were found. 56: There are 41 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 HIS8 56: SG9 NE251 56: HIS8 NE251 1.055 56: MET12 SD83 0.763 0.990 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 653 pairs 56: Before cleaning: 663 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 128 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 (128 atoms, 16 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 252 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 254, now 254 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 14 cmap torsion pairs 56: 56: There are 663 dihedrals, 48 impropers, 457 angles 56: 650 pairs, 254 bonds and 0 virtual sites 56: 56: Total mass 1846.115 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (54 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 30 donors and 22 acceptors were found. 56: There are 36 hydrogen bonds 56: Will use HISE for residue 29 56: Will use HISE for residue 32 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS27 HIS29 56: SG90 NE2111 56: HIS29 NE2111 0.987 56: HIS32 NE2135 1.590 1.155 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 748 pairs 56: Before cleaning: 778 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 56: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 149 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 (149 atoms, 16 residues) 56: 56: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 56: 56: Identified residue THR18 as a starting terminus. 56: 56: Identified residue PHE33 as a ending terminus. 56: Start terminus THR-18: NH3+ 56: End terminus PHE-33: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 281 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 290, now 290 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 14 cmap torsion pairs 56: 56: There are 778 dihedrals, 49 impropers, 516 angles 56: 736 pairs, 290 bonds and 0 virtual sites 56: 56: Total mass 2088.361 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (65 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 22 donors and 22 acceptors were found. 56: There are 26 hydrogen bonds 56: Will use HISE for residue 45 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS45 56: NE295 56: MET46 SD102 1.078 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 676 pairs 56: Before cleaning: 696 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 56: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 132 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 (132 atoms, 16 residues) 56: 56: Identified residue ALA34 as a starting terminus. 56: 56: Identified residue ALA49 as a ending terminus. 56: Start terminus ALA-34: NH3+ 56: End terminus ALA-49: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 255 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 261, now 261 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 14 cmap torsion pairs 56: 56: There are 696 dihedrals, 39 impropers, 472 angles 56: 667 pairs, 261 bonds and 0 virtual sites 56: 56: Total mass 1861.130 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (66 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 22 donors and 21 acceptors were found. 56: There are 30 hydrogen bonds 56: Will use HISE for residue 60 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS60 56: NE285 56: CYS62 SG98 0.803 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 603 pairs 56: Before cleaning: 618 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 56: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 117 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 (117 atoms, 16 residues) 56: 56: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 56: 56: Identified residue LYS50 as a starting terminus. 56: 56: Identified residue PRO65 as a ending terminus. 56: Start terminus LYS-50: NH3+ 56: End terminus PRO-65: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 228 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 232, now 232 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 14 cmap torsion pairs 56: 56: There are 618 dihedrals, 38 impropers, 419 angles 56: 597 pairs, 232 bonds and 0 virtual sites 56: 56: Total mass 1662.885 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (56 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 89 donors and 98 acceptors were found. 56: There are 129 hydrogen bonds 56: Will use HISE for residue 31 56: Will use HISE for residue 51 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS25 HIS31 HIS51 56: SG14 NE264 NE2226 56: HIS31 NE264 1.921 56: HIS51 NE2226 1.498 2.650 56: CYS80 SG477 0.207 1.984 1.570 56: Linking CYS-25 SG-14 and CYS-80 SG-477... 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 2499 pairs 56: Before cleaning: 2524 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 56: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 58 488 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (488 atoms, 58 residues) 56: 56: Identified residue ASN24 as a starting terminus. 56: 56: Identified residue ARG81 as a ending terminus. 56: Start terminus ASN-24: NH3+ 56: End terminus ARG-81: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 58 residues with 936 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 951, now 951 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 56 cmap torsion pairs 56: 56: There are 2524 dihedrals, 149 impropers, 1704 angles 56: 2469 pairs, 951 bonds and 0 virtual sites 56: 56: Total mass 6908.566 a.m.u. 56: 56: Total charge -6.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (116 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_monomerpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 39 pairs 56: Before cleaning: 39 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/monomer.pdb... 56: Read 'GLU', 9 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 1 residues with 9 atoms 56: 56: chain #res #atoms 56: 56: 1 'X' 1 9 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'X' (9 atoms, 1 residues) 56: 56: Identified residue GLU1 as a starting terminus. 56: 56: Identified residue GLU1 as a ending terminus. 56: Start terminus GLU-1: NH3+ 56: End terminus GLU-1: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 1 residues with 18 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 17, now 17 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 39 dihedrals, 2 impropers, 30 angles 56: 39 pairs, 17 bonds and 0 virtual sites 56: 56: Total mass 146.123 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/monomer.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_monomerpdb_format_gro_match_file (54 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 25 donors and 23 acceptors were found. 56: There are 41 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 HIS8 56: SG9 NE251 56: HIS8 NE251 1.055 56: MET12 SD83 0.763 0.990 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Marked 124 virtual sites 56: Added 16 dummy masses 56: Added 26 new constraints 56: Before cleaning: 653 pairs 56: Before cleaning: 663 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 128 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 (128 atoms, 16 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 252 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 254, now 254 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 14 cmap torsion pairs 56: 56: There are 663 dihedrals, 48 impropers, 457 angles 56: 650 pairs, 254 bonds and 130 virtual sites 56: 56: Total mass 1846.115 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/A.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (55 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 30 donors and 22 acceptors were found. 56: There are 36 hydrogen bonds 56: Will use HISE for residue 29 56: Will use HISE for residue 32 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS27 HIS29 56: SG90 NE2111 56: HIS29 NE2111 0.987 56: HIS32 NE2135 1.590 1.155 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Marked 132 virtual sites 56: Added 10 dummy masses 56: Added 19 new constraints 56: Before cleaning: 748 pairs 56: Before cleaning: 778 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb... 56: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 149 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 (149 atoms, 16 residues) 56: 56: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 56: 56: Identified residue THR18 as a starting terminus. 56: 56: Identified residue PHE33 as a ending terminus. 56: Start terminus THR-18: NH3+ 56: End terminus PHE-33: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 281 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 290, now 290 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 14 cmap torsion pairs 56: 56: There are 778 dihedrals, 49 impropers, 516 angles 56: 736 pairs, 290 bonds and 133 virtual sites 56: 56: Total mass 2088.361 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/B.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (52 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 22 donors and 22 acceptors were found. 56: There are 26 hydrogen bonds 56: Will use HISE for residue 45 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS45 56: NE295 56: MET46 SD102 1.078 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Marked 123 virtual sites 56: Added 22 dummy masses 56: Added 35 new constraints 56: Before cleaning: 676 pairs 56: Before cleaning: 696 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb... 56: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 132 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 (132 atoms, 16 residues) 56: 56: Identified residue ALA34 as a starting terminus. 56: 56: Identified residue ALA49 as a ending terminus. 56: Start terminus ALA-34: NH3+ 56: End terminus ALA-49: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 255 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 261, now 261 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 14 cmap torsion pairs 56: 56: There are 696 dihedrals, 39 impropers, 472 angles 56: 667 pairs, 261 bonds and 132 virtual sites 56: 56: Total mass 1861.130 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/C.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (57 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 22 donors and 21 acceptors were found. 56: There are 30 hydrogen bonds 56: Will use HISE for residue 60 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS60 56: NE285 56: CYS62 SG98 0.803 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Marked 111 virtual sites 56: Added 18 dummy masses 56: Added 31 new constraints 56: Before cleaning: 603 pairs 56: Before cleaning: 618 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb... 56: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 56: 56: chain #res #atoms 56: 56: 1 ' ' 16 117 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 (117 atoms, 16 residues) 56: 56: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 56: 56: Identified residue LYS50 as a starting terminus. 56: 56: Identified residue PRO65 as a ending terminus. 56: Start terminus LYS-50: NH3+ 56: End terminus PRO-65: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 228 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 232, now 232 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 14 cmap torsion pairs 56: 56: There are 618 dihedrals, 38 impropers, 419 angles 56: 597 pairs, 232 bonds and 116 virtual sites 56: 56: Total mass 1662.885 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/D.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (50 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 89 donors and 98 acceptors were found. 56: There are 129 hydrogen bonds 56: Will use HISE for residue 31 56: Will use HISE for residue 51 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS25 HIS31 HIS51 56: SG14 NE264 NE2226 56: HIS31 NE264 1.921 56: HIS51 NE2226 1.498 2.650 56: CYS80 SG477 0.207 1.984 1.570 56: Linking CYS-25 SG-14 and CYS-80 SG-477... 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Marked 447 virtual sites 56: Added 58 dummy masses 56: Added 101 new constraints 56: Before cleaning: 2499 pairs 56: Before cleaning: 2524 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb... 56: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 58 488 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (488 atoms, 58 residues) 56: 56: Identified residue ASN24 as a starting terminus. 56: 56: Identified residue ARG81 as a ending terminus. 56: Start terminus ASN-24: NH3+ 56: End terminus ARG-81: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 58 residues with 936 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 951, now 951 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 56 cmap torsion pairs 56: 56: There are 2524 dihedrals, 149 impropers, 1704 angles 56: 2469 pairs, 951 bonds and 462 virtual sites 56: 56: Total mass 6908.566 a.m.u. 56: 56: Total charge -6.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/E.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (148 ms) 56: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_monomerpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Marked 8 virtual sites 56: Added 2 dummy masses 56: Added 3 new constraints 56: Before cleaning: 39 pairs 56: Before cleaning: 39 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/monomer.pdb... 56: Read 'GLU', 9 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 1 residues with 9 atoms 56: 56: chain #res #atoms 56: 56: 1 'X' 1 9 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'X' (9 atoms, 1 residues) 56: 56: Identified residue GLU1 as a starting terminus. 56: 56: Identified residue GLU1 as a ending terminus. 56: Start terminus GLU-1: NH3+ 56: End terminus GLU-1: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 1 residues with 18 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 17, now 17 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 39 dihedrals, 2 impropers, 30 angles 56: 39 pairs, 17 bonds and 9 virtual sites 56: 56: Total mass 146.123 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/monomer.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_monomerpdb_format_gro_match_file (54 ms) 56: [----------] 12 tests from Charmm/Pdb2gmxTest (833 ms total) 56: 56: [----------] 8 tests from ChainSep/Pdb2gmxTest 56: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_all_chainTerpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 25 donors and 23 acceptors were found. 56: There are 41 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 HIS8 56: SG9 NE251 56: HIS8 NE251 1.055 56: MET12 SD83 0.763 0.990 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 651 pairs 56: Before cleaning: 661 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on changing chain id only (ignoring TER records). 56: 56: Merged chains into joint molecule definitions at 2 places. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 16 127 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (127 atoms, 16 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue GLU5 as a ending terminus. 56: 56: Identified residue PHE6 as a starting terminus. 56: 56: Identified residue MET12 as a ending terminus. 56: 56: Identified residue ASN13 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus GLU-5: COO- 56: Start terminus PHE-6: NH3+ 56: End terminus MET-12: COO- 56: Start terminus ASN-13: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 258 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 258, now 258 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 10 cmap torsion pairs 56: 56: There are 661 dihedrals, 46 impropers, 463 angles 56: 648 pairs, 258 bonds and 0 virtual sites 56: 56: Total mass 1882.146 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_all_chainTerpdb_format_gro_match_file (41 ms) 56: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_chainTerpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 123 pairs 56: Before cleaning: 123 dihedrals 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 10 donors and 7 acceptors were found. 56: There are 7 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: HIS8 56: NE223 56: MET12 SD55 0.990 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 317 pairs 56: Before cleaning: 322 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 211 pairs 56: Before cleaning: 216 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on changing chain id only (ignoring TER records). 56: 56: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 4 28 56: 56: 2 'B' 7 58 56: 56: 3 'C' 5 41 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (28 atoms, 4 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue GLU5 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus GLU-5: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 4 residues with 51 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 50, now 50 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 2 cmap torsion pairs 56: 56: There are 123 dihedrals, 9 impropers, 88 angles 56: 123 pairs, 50 bonds and 0 virtual sites 56: 56: Total mass 434.421 a.m.u. 56: 56: Total charge -2.000 e 56: 56: Writing topology 56: 56: Processing chain 2 'B' (58 atoms, 7 residues) 56: 56: Identified residue PHE6 as a starting terminus. 56: 56: Identified residue MET12 as a ending terminus. 56: Start terminus PHE-6: NH3+ 56: End terminus MET-12: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 7 residues with 124 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 125, now 125 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 5 cmap torsion pairs 56: 56: There are 322 dihedrals, 19 impropers, 227 angles 56: 314 pairs, 125 bonds and 0 virtual sites 56: 56: Total mass 846.083 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Processing chain 3 'C' (41 atoms, 5 residues) 56: 56: Identified residue ASN13 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ASN-13: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 5 residues with 83 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 83, now 83 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 3 cmap torsion pairs 56: 56: There are 216 dihedrals, 18 impropers, 148 angles 56: 211 pairs, 83 bonds and 0 virtual sites 56: 56: Total mass 601.643 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Including chain 1 in system: 51 atoms 4 residues 56: 56: Including chain 2 in system: 124 atoms 7 residues 56: 56: Including chain 3 in system: 83 atoms 5 residues 56: 56: Now there are 258 atoms and 16 residues 56: 56: Total mass in system 1882.146 a.m.u. 56: 56: Total charge in system 0.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_chainTerpdb_format_gro_match_file (42 ms) 56: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_all_chainTerpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 25 donors and 23 acceptors were found. 56: There are 41 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 HIS8 56: SG9 NE251 56: HIS8 NE251 1.055 56: MET12 SD83 0.763 0.990 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 651 pairs 56: Before cleaning: 661 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records only (ignoring chain id). 56: 56: Merged chains into joint molecule definitions at 2 places. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 16 127 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (127 atoms, 16 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue ILE9 as a ending terminus. 56: 56: Identified residue LYS10 as a starting terminus. 56: 56: Identified residue MET12 as a ending terminus. 56: 56: Identified residue ASN13 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus ILE-9: COO- 56: Start terminus LYS-10: NH3+ 56: End terminus MET-12: COO- 56: Start terminus ASN-13: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 258 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 258, now 258 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 10 cmap torsion pairs 56: 56: There are 661 dihedrals, 46 impropers, 463 angles 56: 648 pairs, 258 bonds and 0 virtual sites 56: 56: Total mass 1882.146 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_all_chainTerpdb_format_gro_match_file (47 ms) 56: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_chainTerpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 10 donors and 12 acceptors were found. 56: There are 13 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 56: SG9 56: HIS8 NE251 1.055 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 288 pairs 56: Before cleaning: 293 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 152 pairs 56: Before cleaning: 152 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 211 pairs 56: Before cleaning: 216 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records only (ignoring chain id). 56: 56: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 8 61 56: 56: 2 'B' 3 25 56: 56: 3 'C' 5 41 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (61 atoms, 8 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue ILE9 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus ILE-9: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 8 residues with 114 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 115, now 115 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 6 cmap torsion pairs 56: 56: There are 293 dihedrals, 23 impropers, 203 angles 56: 285 pairs, 115 bonds and 0 virtual sites 56: 56: Total mass 888.952 a.m.u. 56: 56: Total charge -2.000 e 56: 56: Writing topology 56: 56: Processing chain 2 'B' (25 atoms, 3 residues) 56: 56: Identified residue LYS10 as a starting terminus. 56: 56: Identified residue MET12 as a ending terminus. 56: Start terminus LYS-10: NH3+ 56: End terminus MET-12: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 3 residues with 61 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 60, now 60 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 1 cmap torsion pairs 56: 56: There are 152 dihedrals, 5 impropers, 112 angles 56: 152 pairs, 60 bonds and 0 virtual sites 56: 56: Total mass 391.552 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Processing chain 3 'C' (41 atoms, 5 residues) 56: 56: Identified residue ASN13 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ASN-13: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 5 residues with 83 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 83, now 83 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 3 cmap torsion pairs 56: 56: There are 216 dihedrals, 18 impropers, 148 angles 56: 211 pairs, 83 bonds and 0 virtual sites 56: 56: Total mass 601.643 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Including chain 1 in system: 114 atoms 8 residues 56: 56: Including chain 2 in system: 61 atoms 3 residues 56: 56: Including chain 3 in system: 83 atoms 5 residues 56: 56: Now there are 258 atoms and 16 residues 56: 56: Total mass in system 1882.146 a.m.u. 56: 56: Total charge in system 0.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_chainTerpdb_format_gro_match_file (40 ms) 56: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_chainTerpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 25 donors and 23 acceptors were found. 56: There are 41 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 HIS8 56: SG9 NE251 56: HIS8 NE251 1.055 56: MET12 SD83 0.763 0.990 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 650 pairs 56: Before cleaning: 660 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: Merged chains into joint molecule definitions at 3 places. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 16 127 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (127 atoms, 16 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue GLU5 as a ending terminus. 56: 56: Identified residue PHE6 as a starting terminus. 56: 56: Identified residue ILE9 as a ending terminus. 56: 56: Identified residue LYS10 as a starting terminus. 56: 56: Identified residue MET12 as a ending terminus. 56: 56: Identified residue ASN13 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus GLU-5: COO- 56: Start terminus PHE-6: NH3+ 56: End terminus ILE-9: COO- 56: Start terminus LYS-10: NH3+ 56: End terminus MET-12: COO- 56: Start terminus ASN-13: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 261 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 260, now 260 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 8 cmap torsion pairs 56: 56: There are 660 dihedrals, 45 impropers, 466 angles 56: 647 pairs, 260 bonds and 0 virtual sites 56: 56: Total mass 1900.162 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_chainTerpdb_format_gro_match_file (42 ms) 56: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_chainTerpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 56: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 56: 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 123 pairs 56: Before cleaning: 123 dihedrals 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 6 donors and 4 acceptors were found. 56: There are 3 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 164 pairs 56: Before cleaning: 169 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 152 pairs 56: Before cleaning: 152 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 211 pairs 56: Before cleaning: 216 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 56: 56: There are 4 chains and 0 blocks of water and 16 residues with 127 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 4 28 56: 56: 2 'B' 4 33 56: 56: 3 'B' 3 25 56: 56: 4 'C' 5 41 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (28 atoms, 4 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue GLU5 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus GLU-5: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 4 residues with 51 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 50, now 50 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 2 cmap torsion pairs 56: 56: There are 123 dihedrals, 9 impropers, 88 angles 56: 123 pairs, 50 bonds and 0 virtual sites 56: 56: Total mass 434.421 a.m.u. 56: 56: Total charge -2.000 e 56: 56: Writing topology 56: 56: Processing chain 2 'B' (33 atoms, 4 residues) 56: 56: Identified residue PHE6 as a starting terminus. 56: 56: Identified residue ILE9 as a ending terminus. 56: Start terminus PHE-6: NH3+ 56: End terminus ILE-9: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 4 residues with 66 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 67, now 67 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 2 cmap torsion pairs 56: 56: There are 169 dihedrals, 13 impropers, 118 angles 56: 161 pairs, 67 bonds and 0 virtual sites 56: 56: Total mass 472.547 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Processing chain 3 'B' (25 atoms, 3 residues) 56: 56: Identified residue LYS10 as a starting terminus. 56: 56: Identified residue MET12 as a ending terminus. 56: Start terminus LYS-10: NH3+ 56: End terminus MET-12: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 3 residues with 61 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 60, now 60 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 1 cmap torsion pairs 56: 56: There are 152 dihedrals, 5 impropers, 112 angles 56: 152 pairs, 60 bonds and 0 virtual sites 56: 56: Total mass 391.552 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Processing chain 4 'C' (41 atoms, 5 residues) 56: 56: Identified residue ASN13 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ASN-13: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 5 residues with 83 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 83, now 83 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 3 cmap torsion pairs 56: 56: There are 216 dihedrals, 18 impropers, 148 angles 56: 211 pairs, 83 bonds and 0 virtual sites 56: 56: Total mass 601.643 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Including chain 1 in system: 51 atoms 4 residues 56: 56: Including chain 2 in system: 66 atoms 4 residues 56: 56: Including chain 3 in system: 61 atoms 3 residues 56: 56: Including chain 4 in system: 83 atoms 5 residues 56: 56: Now there are 261 atoms and 16 residues 56: 56: Total mass in system 1900.162 a.m.u. 56: 56: Total charge in system 0.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_chainTerpdb_format_gro_match_file (45 ms) 56: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_all_chainTerpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 25 donors and 23 acceptors were found. 56: There are 41 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 HIS8 56: SG9 NE251 56: HIS8 NE251 1.055 56: MET12 SD83 0.763 0.990 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 652 pairs 56: Before cleaning: 662 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records and chain id changing. 56: 56: Merged chains into joint molecule definitions at 1 places. 56: 56: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 16 127 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (127 atoms, 16 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue MET12 as a ending terminus. 56: 56: Identified residue ASN13 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus MET-12: COO- 56: Start terminus ASN-13: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 255 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 256, now 256 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 12 cmap torsion pairs 56: 56: There are 662 dihedrals, 47 impropers, 460 angles 56: 649 pairs, 256 bonds and 0 virtual sites 56: 56: Total mass 1864.131 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_all_chainTerpdb_format_gro_match_file (46 ms) 56: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_chainTerpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 56: Analysing hydrogen-bonding network for automated assignment of histidine 56: protonation. 14 donors and 15 acceptors were found. 56: There are 20 hydrogen bonds 56: Will use HISE for residue 8 56: 9 out of 9 lines of specbond.dat converted successfully 56: Special Atom Distance matrix: 56: CYS3 HIS8 56: SG9 NE251 56: HIS8 NE251 1.055 56: MET12 SD83 0.763 0.990 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 441 pairs 56: Before cleaning: 446 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 211 pairs 56: Before cleaning: 216 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 56: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records and chain id changing. 56: 56: There are 2 chains and 0 blocks of water and 16 residues with 127 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 11 86 56: 56: 2 'C' 5 41 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (86 atoms, 11 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue MET12 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus MET-12: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 11 residues with 172 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 173, now 173 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 9 cmap torsion pairs 56: 56: There are 446 dihedrals, 29 impropers, 312 angles 56: 438 pairs, 173 bonds and 0 virtual sites 56: 56: Total mass 1262.488 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Processing chain 2 'C' (41 atoms, 5 residues) 56: 56: Identified residue ASN13 as a starting terminus. 56: 56: Identified residue SER17 as a ending terminus. 56: Start terminus ASN-13: NH3+ 56: End terminus SER-17: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 5 residues with 83 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 83, now 83 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 3 cmap torsion pairs 56: 56: There are 216 dihedrals, 18 impropers, 148 angles 56: 211 pairs, 83 bonds and 0 virtual sites 56: 56: Total mass 601.643 a.m.u. 56: 56: Total charge 1.000 e 56: 56: Writing topology 56: 56: Including chain 1 in system: 172 atoms 11 residues 56: 56: Including chain 2 in system: 83 atoms 5 residues 56: 56: Now there are 255 atoms and 16 residues 56: 56: Total mass in system 1864.131 a.m.u. 56: 56: Total charge in system 0.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_chainTerpdb_format_gro_match_file (44 ms) 56: [----------] 8 tests from ChainSep/Pdb2gmxTest (349 ms total) 56: 56: [----------] 4 tests from ChainChanges/Pdb2gmxTest 56: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_fragmentspdb_format_pdb_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 83 pairs 56: Before cleaning: 83 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 145 pairs 56: Before cleaning: 150 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/fragments.pdb... 56: Read 'Fragments of peptides and ions', 47 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on changing chain id only (ignoring TER records). 56: 56: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 3 19 56: 56: 2 'B' 3 28 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (19 atoms, 3 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue ASP4 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus ASP-4: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 3 residues with 36 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 35, now 35 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 1 cmap torsion pairs 56: 56: There are 83 dihedrals, 6 impropers, 61 angles 56: 83 pairs, 35 bonds and 0 virtual sites 56: 56: Total mass 306.314 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Processing chain 2 'B' (28 atoms, 3 residues) 56: 56: Identified residue THR18 as a starting terminus. 56: 56: Identified residue TRP20 as a ending terminus. 56: Start terminus THR-18: NH3+ 56: End terminus TRP-20: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 3 residues with 57 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 58, now 58 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 1 cmap torsion pairs 56: 56: There are 150 dihedrals, 5 impropers, 103 angles 56: 142 pairs, 58 bonds and 0 virtual sites 56: 56: Total mass 404.468 a.m.u. 56: 56: Total charge -0.000 e 56: 56: Writing topology 56: 56: Including chain 1 in system: 36 atoms 3 residues 56: 56: Including chain 2 in system: 57 atoms 3 residues 56: 56: Now there are 93 atoms and 6 residues 56: 56: Total mass in system 710.782 a.m.u. 56: 56: Total charge in system -1.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/fragments.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_fragmentspdb_format_pdb_match_file (35 ms) 56: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_fragmentspdb_format_pdb_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 83 pairs 56: Before cleaning: 83 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 145 pairs 56: Before cleaning: 150 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/fragments.pdb... 56: Read 'Fragments of peptides and ions', 47 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records only (ignoring chain id). 56: 56: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 3 19 56: 56: 2 'B' 3 28 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (19 atoms, 3 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue ASP4 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus ASP-4: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 3 residues with 36 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 35, now 35 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 1 cmap torsion pairs 56: 56: There are 83 dihedrals, 6 impropers, 61 angles 56: 83 pairs, 35 bonds and 0 virtual sites 56: 56: Total mass 306.314 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Processing chain 2 'B' (28 atoms, 3 residues) 56: 56: Identified residue THR18 as a starting terminus. 56: 56: Identified residue TRP20 as a ending terminus. 56: Start terminus THR-18: NH3+ 56: End terminus TRP-20: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 3 residues with 57 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 58, now 58 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 1 cmap torsion pairs 56: 56: There are 150 dihedrals, 5 impropers, 103 angles 56: 142 pairs, 58 bonds and 0 virtual sites 56: 56: Total mass 404.468 a.m.u. 56: 56: Total charge -0.000 e 56: 56: Writing topology 56: 56: Including chain 1 in system: 36 atoms 3 residues 56: 56: Including chain 2 in system: 57 atoms 3 residues 56: 56: Now there are 93 atoms and 6 residues 56: 56: Total mass in system 710.782 a.m.u. 56: 56: Total charge in system -1.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/fragments.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_fragmentspdb_format_pdb_match_file (42 ms) 56: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_fragmentspdb_format_pdb_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 83 pairs 56: Before cleaning: 83 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 145 pairs 56: Before cleaning: 150 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/fragments.pdb... 56: Read 'Fragments of peptides and ions', 47 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 3 19 56: 56: 2 'B' 3 28 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (19 atoms, 3 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue ASP4 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus ASP-4: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 3 residues with 36 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 35, now 35 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 1 cmap torsion pairs 56: 56: There are 83 dihedrals, 6 impropers, 61 angles 56: 83 pairs, 35 bonds and 0 virtual sites 56: 56: Total mass 306.314 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Processing chain 2 'B' (28 atoms, 3 residues) 56: 56: Identified residue THR18 as a starting terminus. 56: 56: Identified residue TRP20 as a ending terminus. 56: Start terminus THR-18: NH3+ 56: End terminus TRP-20: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 3 residues with 57 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 58, now 58 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 1 cmap torsion pairs 56: 56: There are 150 dihedrals, 5 impropers, 103 angles 56: 142 pairs, 58 bonds and 0 virtual sites 56: 56: Total mass 404.468 a.m.u. 56: 56: Total charge -0.000 e 56: 56: Writing topology 56: 56: Including chain 1 in system: 36 atoms 3 residues 56: 56: Including chain 2 in system: 57 atoms 3 residues 56: 56: Now there are 93 atoms and 6 residues 56: 56: Total mass in system 710.782 a.m.u. 56: 56: Total charge in system -1.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/fragments.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_fragmentspdb_format_pdb_match_file (42 ms) 56: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_fragmentspdb_format_pdb_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 83 pairs 56: Before cleaning: 83 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 145 pairs 56: Before cleaning: 150 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/fragments.pdb... 56: Read 'Fragments of peptides and ions', 47 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records and chain id changing. 56: 56: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 3 19 56: 56: 2 'B' 3 28 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (19 atoms, 3 residues) 56: 56: Identified residue ALA2 as a starting terminus. 56: 56: Identified residue ASP4 as a ending terminus. 56: Start terminus ALA-2: NH3+ 56: End terminus ASP-4: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 3 residues with 36 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 35, now 35 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 1 cmap torsion pairs 56: 56: There are 83 dihedrals, 6 impropers, 61 angles 56: 83 pairs, 35 bonds and 0 virtual sites 56: 56: Total mass 306.314 a.m.u. 56: 56: Total charge -1.000 e 56: 56: Writing topology 56: 56: Processing chain 2 'B' (28 atoms, 3 residues) 56: 56: Identified residue THR18 as a starting terminus. 56: 56: Identified residue TRP20 as a ending terminus. 56: Start terminus THR-18: NH3+ 56: End terminus TRP-20: COO- 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 3 residues with 57 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 58, now 58 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 1 cmap torsion pairs 56: 56: There are 150 dihedrals, 5 impropers, 103 angles 56: 142 pairs, 58 bonds and 0 virtual sites 56: 56: Total mass 404.468 a.m.u. 56: 56: Total charge -0.000 e 56: 56: Writing topology 56: 56: Including chain 1 in system: 36 atoms 3 residues 56: 56: Including chain 2 in system: 57 atoms 3 residues 56: 56: Now there are 93 atoms and 6 residues 56: 56: Total mass in system 710.782 a.m.u. 56: 56: Total charge in system -1.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/fragments.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_fragmentspdb_format_pdb_match_file (38 ms) 56: [----------] 4 tests from ChainChanges/Pdb2gmxTest (158 ms total) 56: 56: [----------] 4 tests from Cyclic/Pdb2gmxTest 56: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycrnapdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 56: WARNING: all CONECT records are ignored 56: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 56: 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 6040 pairs 56: Before cleaning: 6605 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 6040 pairs 56: Before cleaning: 6605 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb... 56: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 56: 56: Moved all the water blocks to the end 56: 56: There are 3 chains and 2 blocks of water and 175 residues with 3087 atoms 56: 56: chain #res #atoms 56: 56: 1 'P' 71 1527 56: 56: 2 'Q' 71 1527 56: 56: 3 'Q' 7 7 56: 56: 4 ' ' 10 10 (only water) 56: 56: 5 ' ' 16 16 (only water) 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'P' (1527 atoms, 71 residues) 56: 56: Identified residue G1 as a starting terminus. 56: 56: Identified residue U71 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 71 residues with 2297 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 2481, now 2481 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 6605 dihedrals, 183 impropers, 4434 angles 56: 5827 pairs, 2481 bonds and 0 virtual sites 56: 56: Total mass 22984.514 a.m.u. 56: 56: Total charge -71.000 e 56: 56: Writing topology 56: 56: Processing chain 2 'Q' (1527 atoms, 71 residues) 56: 56: Identified residue G1 as a starting terminus. 56: 56: Identified residue U71 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 71 residues with 2297 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: Number of bonds was 2481, now 2481 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 6605 dihedrals, 183 impropers, 4434 angles 56: 5827 pairs, 2481 bonds and 0 virtual sites 56: 56: Total mass 22984.514 a.m.u. 56: 56: Total charge -71.000 e 56: 56: Writing topology 56: 56: Processing chain 3 'Q' (7 atoms, 7 residues) 56: 56: Residue MG72 has type 'Ion', assuming it is not linked into a chain. 56: 56: Residue MG73 has type 'Ion', assuming it is not linked into a chain. 56: 56: Residue MG74 has type 'Ion', assuming it is not linked into a chain. 56: 56: Residue MG75 has type 'Ion', assuming it is not linked into a chain. 56: 56: Residue MG76 has type 'Ion', assuming it is not linked into a chain. 56: 56: Disabling further notes about ions. 56: 56: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 7 residues with 7 atoms 56: Chain time... 56: 56: Making bonds... 56: 56: No bonds 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 0 dihedrals, 0 impropers, 0 angles 56: 0 pairs, 0 bonds and 0 virtual sites 56: 56: Total mass 170.135 a.m.u. 56: 56: Total charge 14.000 e 56: 56: Writing topology 56: 56: Processing chain 4 (10 atoms, 10 residues) 56: 56: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 10 residues with 30 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 30, now 30 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 0 dihedrals, 0 impropers, 30 angles 56: 0 pairs, 30 bonds and 0 virtual sites 56: 56: Total mass 180.154 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Processing chain 5 (16 atoms, 16 residues) 56: 56: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 48 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 48, now 48 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 0 dihedrals, 0 impropers, 48 angles 56: 0 pairs, 48 bonds and 0 virtual sites 56: 56: Total mass 288.246 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Including chain 1 in system: 2297 atoms 71 residues 56: 56: Including chain 2 in system: 2297 atoms 71 residues 56: 56: Including chain 3 in system: 7 atoms 7 residues 56: 56: Including chain 4 in system: 30 atoms 10 residues 56: 56: Including chain 5 in system: 48 atoms 16 residues 56: 56: Now there are 4679 atoms and 175 residues 56: 56: Total mass in system 46607.562 a.m.u. 56: 56: Total charge in system -128.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycrnapdb_format_gro_match_file (385 ms) 56: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycprotpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 2325 pairs 56: Before cleaning: 2325 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb... 56: Read 'CARNOCYCLIN-A', 413 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 60 413 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (413 atoms, 60 residues) 56: 56: Identified residue LEU1 as a starting terminus. 56: 56: Identified residue LEU60 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 60 residues with 878 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 880, now 880 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 60 cmap torsion pairs 56: 56: There are 2325 dihedrals, 137 impropers, 1614 angles 56: 2319 pairs, 880 bonds and 0 virtual sites 56: 56: Total mass 5866.087 a.m.u. 56: 56: Total charge 4.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycprotpdb_format_gro_match_file (236 ms) 56: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycrnapdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 56: WARNING: all CONECT records are ignored 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 12080 pairs 56: Before cleaning: 13210 dihedrals 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb... 56: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: Moved all the water blocks to the end 56: 56: Merged chains into joint molecule definitions at 2 places. 56: 56: There are 1 chains and 2 blocks of water and 175 residues with 3087 atoms 56: 56: chain #res #atoms 56: 56: 1 'P' 149 3061 56: 56: 2 ' ' 10 10 (only water) 56: 56: 3 ' ' 16 16 (only water) 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'P' (3061 atoms, 149 residues) 56: 56: Identified residue G1 as a starting terminus. 56: 56: Identified residue U71 as a ending terminus. 56: 56: Identified residue G1 as a starting terminus. 56: 56: Identified residue U71 as a ending terminus. 56: 56: Residue MG72 has type 'Ion', assuming it is not linked into a chain. 56: 56: Residue MG73 has type 'Ion', assuming it is not linked into a chain. 56: 56: Residue MG74 has type 'Ion', assuming it is not linked into a chain. 56: 56: Residue MG75 has type 'Ion', assuming it is not linked into a chain. 56: 56: Residue MG76 has type 'Ion', assuming it is not linked into a chain. 56: 56: Disabling further notes about ions. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 149 residues with 4601 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 4962, now 4962 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 13210 dihedrals, 366 impropers, 8868 angles 56: 11654 pairs, 4962 bonds and 0 virtual sites 56: 56: Total mass 46139.162 a.m.u. 56: 56: Total charge -128.000 e 56: 56: Writing topology 56: 56: Processing chain 2 (10 atoms, 10 residues) 56: 56: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 10 residues with 30 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 30, now 30 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 0 dihedrals, 0 impropers, 30 angles 56: 0 pairs, 30 bonds and 0 virtual sites 56: 56: Total mass 180.154 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Processing chain 3 (16 atoms, 16 residues) 56: 56: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 16 residues with 48 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 48, now 48 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 0 dihedrals, 0 impropers, 48 angles 56: 0 pairs, 48 bonds and 0 virtual sites 56: 56: Total mass 288.246 a.m.u. 56: 56: Total charge 0.000 e 56: 56: Including chain 1 in system: 4601 atoms 149 residues 56: 56: Including chain 2 in system: 30 atoms 10 residues 56: 56: Including chain 3 in system: 48 atoms 16 residues 56: 56: Now there are 4679 atoms and 175 residues 56: 56: Total mass in system 46607.562 a.m.u. 56: 56: Total charge in system -128.000 e 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycrnapdb_format_gro_match_file (508 ms) 56: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycprotpdb_format_gro_match_file 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.r2b 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.r2b 56: All occupancies are one 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/atomtypes.atp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.rtp 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/lipids.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.hdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.n.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.c.tdb 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.c.tdb 56: 9 out of 9 lines of specbond.dat converted successfully 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/aminoacids.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/dna.arn 56: Opening force field file /build/reproducible-path/gromacs-2025.0/share/top/charmm27.ff/rna.arn 56: Before cleaning: 2325 pairs 56: Before cleaning: 2325 dihedrals 56: Using the Charmm27 force field in directory charmm27.ff 56: 56: going to rename charmm27.ff/aminoacids.r2b 56: 56: going to rename charmm27.ff/rna.r2b 56: Reading /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb... 56: Read 'CARNOCYCLIN-A', 413 atoms 56: 56: Analyzing pdb file 56: Splitting chemical chains based on TER records or chain id changing. 56: 56: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms 56: 56: chain #res #atoms 56: 56: 1 'A' 60 413 56: 56: All occupancies are one 56: 56: Reading residue database... (Charmm27) 56: 56: Processing chain 1 'A' (413 atoms, 60 residues) 56: 56: Identified residue LEU1 as a starting terminus. 56: 56: Identified residue LEU60 as a ending terminus. 56: 56: Checking for duplicate atoms.... 56: 56: Generating any missing hydrogen atoms and/or adding termini. 56: 56: Now there are 60 residues with 878 atoms 56: 56: Making bonds... 56: 56: Number of bonds was 880, now 880 56: 56: Generating angles, dihedrals and pairs... 56: 56: Making cmap torsions... 56: 56: There are 60 cmap torsion pairs 56: 56: There are 2325 dihedrals, 137 impropers, 1614 angles 56: 2319 pairs, 880 bonds and 0 virtual sites 56: 56: Total mass 5866.087 a.m.u. 56: 56: Total charge 4.000 e 56: 56: Writing topology 56: 56: Writing coordinate file... 56: 56: --------- PLEASE NOTE ------------ 56: 56: You have successfully generated a topology from: /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb. 56: 56: The Charmm27 force field and the tip3p water model are used. 56: 56: --------- ETON ESAELP ------------ 56: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycprotpdb_format_gro_match_file (106 ms) 56: [----------] 4 tests from Cyclic/Pdb2gmxTest (1236 ms total) 56: 56: [----------] Global test environment tear-down 56: [==========] 39 tests from 6 test suites ran. (3469 ms total) 56: [ PASSED ] 39 tests. 56/94 Test #56: Pdb2gmx3Test ................................. Passed 3.83 sec test 57 Start 57: CorrelationsTest 57: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/correlations-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/CorrelationsTest.xml" 57: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/correlationfunctions/tests 57: Test timeout computed to be: 30 57: [==========] Running 21 tests from 3 test suites. 57: [----------] Global test environment set-up. 57: [----------] 10 tests from AutocorrTest 57: [ RUN ] AutocorrTest.EacNormal 57: [ OK ] AutocorrTest.EacNormal (72 ms) 57: [ RUN ] AutocorrTest.EacNoNormalize 57: [ OK ] AutocorrTest.EacNoNormalize (47 ms) 57: [ RUN ] AutocorrTest.EacCos 57: [ OK ] AutocorrTest.EacCos (93 ms) 57: [ RUN ] AutocorrTest.EacVector 57: [ OK ] AutocorrTest.EacVector (145 ms) 57: [ RUN ] AutocorrTest.EacRcross 57: [ OK ] AutocorrTest.EacRcross (1 ms) 57: [ RUN ] AutocorrTest.EacP0 57: [ OK ] AutocorrTest.EacP0 (145 ms) 57: [ RUN ] AutocorrTest.EacP1 57: [ OK ] AutocorrTest.EacP1 (137 ms) 57: [ RUN ] AutocorrTest.EacP2 57: [ OK ] AutocorrTest.EacP2 (266 ms) 57: [ RUN ] AutocorrTest.EacP3 57: [ OK ] AutocorrTest.EacP3 (3 ms) 57: [ RUN ] AutocorrTest.EacP4 57: [ OK ] AutocorrTest.EacP4 (140 ms) 57: [----------] 10 tests from AutocorrTest (1057 ms total) 57: 57: [----------] 10 tests from ExpfitTest 57: [ RUN ] ExpfitTest.EffnEXP1 57: [ OK ] ExpfitTest.EffnEXP1 (0 ms) 57: [ RUN ] ExpfitTest.EffnEXP2 57: [ OK ] ExpfitTest.EffnEXP2 (0 ms) 57: [ RUN ] ExpfitTest.EffnEXPEXP 57: [ OK ] ExpfitTest.EffnEXPEXP (1 ms) 57: [ RUN ] ExpfitTest.EffnEXP5 57: [ OK ] ExpfitTest.EffnEXP5 (4 ms) 57: [ RUN ] ExpfitTest.EffnEXP7 57: [ OK ] ExpfitTest.EffnEXP7 (3 ms) 57: [ RUN ] ExpfitTest.EffnEXP9 57: [ OK ] ExpfitTest.EffnEXP9 (17 ms) 57: [ RUN ] ExpfitTest.EffnERF 57: [ OK ] ExpfitTest.EffnERF (2 ms) 57: [ RUN ] ExpfitTest.EffnERREST 57: [ OK ] ExpfitTest.EffnERREST (2 ms) 57: [ RUN ] ExpfitTest.EffnVAC 57: [ OK ] ExpfitTest.EffnVAC (6 ms) 57: [ RUN ] ExpfitTest.EffnPRES 57: [ OK ] ExpfitTest.EffnPRES (16 ms) 57: [----------] 10 tests from ExpfitTest (56 ms total) 57: 57: [----------] 1 test from ManyAutocorrelationTest 57: [ RUN ] ManyAutocorrelationTest.Empty 57: [ OK ] ManyAutocorrelationTest.Empty (0 ms) 57: [----------] 1 test from ManyAutocorrelationTest (0 ms total) 57: 57: [----------] Global test environment tear-down 57: [==========] 21 tests from 3 test suites ran. (1119 ms total) 57: [ PASSED ] 21 tests. 57/94 Test #57: CorrelationsTest ............................. Passed 1.49 sec test 58 Start 58: AnalysisDataUnitTests 58: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/analysisdata-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/AnalysisDataUnitTests.xml" 58: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/analysisdata/tests 58: Test timeout computed to be: 30 58: [==========] Running 69 tests from 14 test suites. 58: [----------] Global test environment set-up. 58: [----------] 3 tests from AnalysisDataInitializationTest 58: [ RUN ] AnalysisDataInitializationTest.BasicInitialization 58: [ OK ] AnalysisDataInitializationTest.BasicInitialization (0 ms) 58: [ RUN ] AnalysisDataInitializationTest.ChecksMultiColumnModules 58: [ OK ] AnalysisDataInitializationTest.ChecksMultiColumnModules (0 ms) 58: [ RUN ] AnalysisDataInitializationTest.ChecksMultipointModules 58: [ OK ] AnalysisDataInitializationTest.ChecksMultipointModules (0 ms) 58: [----------] 3 tests from AnalysisDataInitializationTest (0 ms total) 58: 58: [----------] 8 tests from AnalysisDataCommonTest/0, where TypeParam = gmx::test::(anonymous namespace)::SimpleInputData 58: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectly (0 ms) 58: [ RUN ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly (0 ms) 58: [ RUN ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly 58: [ OK ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly (0 ms) 58: [ RUN ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly (0 ms) 58: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames 58: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 58: [ RUN ] AnalysisDataCommonTest/0.FullStorageWorks 58: [ OK ] AnalysisDataCommonTest/0.FullStorageWorks (0 ms) 58: [ RUN ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData 58: [ OK ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData (0 ms) 58: [ RUN ] AnalysisDataCommonTest/0.LimitedStorageWorks 58: [ OK ] AnalysisDataCommonTest/0.LimitedStorageWorks (0 ms) 58: [----------] 8 tests from AnalysisDataCommonTest/0 (1 ms total) 58: 58: [----------] 8 tests from AnalysisDataCommonTest/1, where TypeParam = gmx::test::(anonymous namespace)::DataSetsInputData 58: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectly (0 ms) 58: [ RUN ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly (0 ms) 58: [ RUN ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly 58: [ OK ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly (0 ms) 58: [ RUN ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly (0 ms) 58: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames 58: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 58: [ RUN ] AnalysisDataCommonTest/1.FullStorageWorks 58: [ OK ] AnalysisDataCommonTest/1.FullStorageWorks (0 ms) 58: [ RUN ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData 58: [ OK ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData (0 ms) 58: [ RUN ] AnalysisDataCommonTest/1.LimitedStorageWorks 58: [ OK ] AnalysisDataCommonTest/1.LimitedStorageWorks (0 ms) 58: [----------] 8 tests from AnalysisDataCommonTest/1 (2 ms total) 58: 58: [----------] 8 tests from AnalysisDataCommonTest/2, where TypeParam = gmx::test::(anonymous namespace)::MultipointInputData 58: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectly (0 ms) 58: [ RUN ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly (0 ms) 58: [ RUN ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly 58: [ OK ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly (0 ms) 58: [ RUN ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly (0 ms) 58: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames 58: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 58: [ RUN ] AnalysisDataCommonTest/2.FullStorageWorks 58: [ OK ] AnalysisDataCommonTest/2.FullStorageWorks (0 ms) 58: [ RUN ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData 58: [ OK ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData (0 ms) 58: [ RUN ] AnalysisDataCommonTest/2.LimitedStorageWorks 58: [ OK ] AnalysisDataCommonTest/2.LimitedStorageWorks (0 ms) 58: [----------] 8 tests from AnalysisDataCommonTest/2 (2 ms total) 58: 58: [----------] 8 tests from AnalysisDataCommonTest/3, where TypeParam = gmx::test::(anonymous namespace)::MultipointDataSetsInputData 58: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectly (0 ms) 58: [ RUN ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly (0 ms) 58: [ RUN ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly 58: [ OK ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly (0 ms) 58: [ RUN ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly 58: [ OK ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly (0 ms) 58: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames 58: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 58: [ RUN ] AnalysisDataCommonTest/3.FullStorageWorks 58: [ OK ] AnalysisDataCommonTest/3.FullStorageWorks (0 ms) 58: [ RUN ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData 58: [ OK ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData (0 ms) 58: [ RUN ] AnalysisDataCommonTest/3.LimitedStorageWorks 58: [ OK ] AnalysisDataCommonTest/3.LimitedStorageWorks (0 ms) 58: [----------] 8 tests from AnalysisDataCommonTest/3 (2 ms total) 58: 58: [----------] 4 tests from AnalysisArrayDataTest 58: [ RUN ] AnalysisArrayDataTest.CallsModuleCorrectly 58: [ OK ] AnalysisArrayDataTest.CallsModuleCorrectly (0 ms) 58: [ RUN ] AnalysisArrayDataTest.StorageWorks 58: [ OK ] AnalysisArrayDataTest.StorageWorks (0 ms) 58: [ RUN ] AnalysisArrayDataTest.CanSetXAxis 58: [ OK ] AnalysisArrayDataTest.CanSetXAxis (0 ms) 58: [ RUN ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount 58: [ OK ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount (0 ms) 58: [----------] 4 tests from AnalysisArrayDataTest (0 ms total) 58: 58: [----------] 6 tests from AverageModuleTest 58: [ RUN ] AverageModuleTest.BasicTest 58: [ OK ] AverageModuleTest.BasicTest (0 ms) 58: [ RUN ] AverageModuleTest.HandlesMultipointData 58: [ OK ] AverageModuleTest.HandlesMultipointData (0 ms) 58: [ RUN ] AverageModuleTest.HandlesMultipleDataSets 58: [ OK ] AverageModuleTest.HandlesMultipleDataSets (0 ms) 58: [ RUN ] AverageModuleTest.HandlesDataSetAveraging 58: [ OK ] AverageModuleTest.HandlesDataSetAveraging (0 ms) 58: [ RUN ] AverageModuleTest.CanCustomizeXAxis 58: [ OK ] AverageModuleTest.CanCustomizeXAxis (0 ms) 58: [ RUN ] AverageModuleTest.CanCustomizeNonUniformXAxis 58: [ OK ] AverageModuleTest.CanCustomizeNonUniformXAxis (0 ms) 58: [----------] 6 tests from AverageModuleTest (3 ms total) 58: 58: [----------] 2 tests from FrameAverageModuleTest 58: [ RUN ] FrameAverageModuleTest.BasicTest 58: [ OK ] FrameAverageModuleTest.BasicTest (0 ms) 58: [ RUN ] FrameAverageModuleTest.HandlesMultipleDataSets 58: [ OK ] FrameAverageModuleTest.HandlesMultipleDataSets (0 ms) 58: [----------] 2 tests from FrameAverageModuleTest (0 ms total) 58: 58: [----------] 7 tests from AnalysisHistogramSettingsTest 58: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBins 58: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBins (0 ms) 58: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins 58: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins (0 ms) 58: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount 58: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount (0 ms) 58: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth 58: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth (0 ms) 58: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins 58: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins (0 ms) 58: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins 58: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins (0 ms) 58: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange 58: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange (0 ms) 58: [----------] 7 tests from AnalysisHistogramSettingsTest (0 ms total) 58: 58: [----------] 2 tests from SimpleHistogramModuleTest 58: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectly 58: [ OK ] SimpleHistogramModuleTest.ComputesCorrectly (0 ms) 58: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll 58: [ OK ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll (0 ms) 58: [----------] 2 tests from SimpleHistogramModuleTest (1 ms total) 58: 58: [----------] 3 tests from WeightedHistogramModuleTest 58: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectly 58: [ OK ] WeightedHistogramModuleTest.ComputesCorrectly (0 ms) 58: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll 58: [ OK ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll (0 ms) 58: [ RUN ] WeightedHistogramModuleTest.HandlesMultipleDataSets 58: [ OK ] WeightedHistogramModuleTest.HandlesMultipleDataSets (0 ms) 58: [----------] 3 tests from WeightedHistogramModuleTest (2 ms total) 58: 58: [----------] 3 tests from BinAverageModuleTest 58: [ RUN ] BinAverageModuleTest.ComputesCorrectly 58: [ OK ] BinAverageModuleTest.ComputesCorrectly (0 ms) 58: [ RUN ] BinAverageModuleTest.ComputesCorrectlyWithAll 58: [ OK ] BinAverageModuleTest.ComputesCorrectlyWithAll (0 ms) 58: [ RUN ] BinAverageModuleTest.HandlesMultipleDataSets 58: [ OK ] BinAverageModuleTest.HandlesMultipleDataSets (0 ms) 58: [----------] 3 tests from BinAverageModuleTest (1 ms total) 58: 58: [----------] 4 tests from AbstractAverageHistogramTest 58: [ RUN ] AbstractAverageHistogramTest.ClonesCorrectly 58: [ OK ] AbstractAverageHistogramTest.ClonesCorrectly (0 ms) 58: [ RUN ] AbstractAverageHistogramTest.ComputesCumulativeHistogram 58: [ OK ] AbstractAverageHistogramTest.ComputesCumulativeHistogram (0 ms) 58: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth 58: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth (0 ms) 58: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins 58: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins (0 ms) 58: [----------] 4 tests from AbstractAverageHistogramTest (2 ms total) 58: 58: [----------] 3 tests from LifetimeModuleTest 58: [ RUN ] LifetimeModuleTest.BasicTest 58: [ OK ] LifetimeModuleTest.BasicTest (0 ms) 58: [ RUN ] LifetimeModuleTest.CumulativeTest 58: [ OK ] LifetimeModuleTest.CumulativeTest (0 ms) 58: [ RUN ] LifetimeModuleTest.HandlesMultipleDataSets 58: [ OK ] LifetimeModuleTest.HandlesMultipleDataSets (0 ms) 58: [----------] 3 tests from LifetimeModuleTest (1 ms total) 58: 58: [----------] Global test environment tear-down 58: [==========] 69 tests from 14 test suites ran. (24 ms total) 58: [ PASSED ] 69 tests. 58/94 Test #58: AnalysisDataUnitTests ........................ Passed 0.39 sec test 59 Start 59: CoordinateIOTests 59: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/coordinateio-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/CoordinateIOTests.xml" 59: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/coordinateio/tests 59: Test timeout computed to be: 30 59: [==========] Running 67 tests from 20 test suites. 59: [----------] Global test environment set-up. 59: [----------] 1 test from OutputSelectorDeathTest 59: [ RUN ] OutputSelectorDeathTest.RejectsBadSelection 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] OutputSelectorDeathTest.RejectsBadSelection (3 ms) 59: [----------] 1 test from OutputSelectorDeathTest (3 ms total) 59: 59: [----------] 5 tests from TrajectoryFrameWriterTest 59: [ RUN ] TrajectoryFrameWriterTest.RejectsWrongFiletype 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] TrajectoryFrameWriterTest.RejectsWrongFiletype (3 ms) 59: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms (1 ms) 59: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms (1 ms) 59: [ RUN ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms (3 ms) 59: [ RUN ] TrajectoryFrameWriterTest.TNGOutputWorks 59: [ OK ] TrajectoryFrameWriterTest.TNGOutputWorks (0 ms) 59: [----------] 5 tests from TrajectoryFrameWriterTest (10 ms total) 59: 59: [----------] 5 tests from OutputAdapterContainer 59: [ RUN ] OutputAdapterContainer.MakeEmpty 59: [ OK ] OutputAdapterContainer.MakeEmpty (0 ms) 59: [ RUN ] OutputAdapterContainer.AddAdapter 59: [ OK ] OutputAdapterContainer.AddAdapter (0 ms) 59: [ RUN ] OutputAdapterContainer.RejectBadAdapter 59: [ OK ] OutputAdapterContainer.RejectBadAdapter (0 ms) 59: [ RUN ] OutputAdapterContainer.RejectDuplicateAdapter 59: [ OK ] OutputAdapterContainer.RejectDuplicateAdapter (0 ms) 59: [ RUN ] OutputAdapterContainer.AcceptMultipleAdapters 59: [ OK ] OutputAdapterContainer.AcceptMultipleAdapters (0 ms) 59: [----------] 5 tests from OutputAdapterContainer (0 ms total) 59: 59: [----------] 3 tests from RegisterFrameConverterTest 59: [ RUN ] RegisterFrameConverterTest.NoConverterWorks 59: [ OK ] RegisterFrameConverterTest.NoConverterWorks (0 ms) 59: [ RUN ] RegisterFrameConverterTest.RegistrationWorks 59: [ OK ] RegisterFrameConverterTest.RegistrationWorks (0 ms) 59: [ RUN ] RegisterFrameConverterTest.NewConverterCanInvalidateGuarantees 59: [ OK ] RegisterFrameConverterTest.NewConverterCanInvalidateGuarantees (0 ms) 59: [----------] 3 tests from RegisterFrameConverterTest (0 ms total) 59: 59: [----------] 5 tests from FlagTest 59: [ RUN ] FlagTest.CanSetSimpleFlag 59: [ OK ] FlagTest.CanSetSimpleFlag (0 ms) 59: [ RUN ] FlagTest.CanAddNewBox 59: [ OK ] FlagTest.CanAddNewBox (0 ms) 59: [ RUN ] FlagTest.SetsImplicitPrecisionChange 59: [ OK ] FlagTest.SetsImplicitPrecisionChange (0 ms) 59: [ RUN ] FlagTest.SetsImplicitStartTimeChange 59: [ OK ] FlagTest.SetsImplicitStartTimeChange (0 ms) 59: [ RUN ] FlagTest.SetsImplicitTimeStepChange 59: [ OK ] FlagTest.SetsImplicitTimeStepChange (0 ms) 59: [----------] 5 tests from FlagTest (0 ms total) 59: 59: [----------] 5 tests from SetAtomsTest 59: [ RUN ] SetAtomsTest.RemovesExistingAtoms 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] SetAtomsTest.RemovesExistingAtoms (1 ms) 59: [ RUN ] SetAtomsTest.AddsNewAtoms 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] SetAtomsTest.AddsNewAtoms (1 ms) 59: [ RUN ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable (1 ms) 59: [ RUN ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable (1 ms) 59: [ RUN ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible (1 ms) 59: [----------] 5 tests from SetAtomsTest (8 ms total) 59: 59: [----------] 2 tests from SetBothTimeTest 59: [ RUN ] SetBothTimeTest.StartTimeZeroWorks 59: [ OK ] SetBothTimeTest.StartTimeZeroWorks (0 ms) 59: [ RUN ] SetBothTimeTest.SetStartTimeNonZeroWorks 59: [ OK ] SetBothTimeTest.SetStartTimeNonZeroWorks (0 ms) 59: [----------] 2 tests from SetBothTimeTest (0 ms total) 59: 59: [----------] 2 tests from SetStartTimeTest 59: [ RUN ] SetStartTimeTest.WorksWithNonZeroStart 59: [ OK ] SetStartTimeTest.WorksWithNonZeroStart (0 ms) 59: [ RUN ] SetStartTimeTest.WorksWithZeroStart 59: [ OK ] SetStartTimeTest.WorksWithZeroStart (0 ms) 59: [----------] 2 tests from SetStartTimeTest (0 ms total) 59: 59: [----------] 1 test from SetTimeStepTest 59: [ RUN ] SetTimeStepTest.SetTimeStepWorks 59: [ OK ] SetTimeStepTest.SetTimeStepWorks (0 ms) 59: [----------] 1 test from SetTimeStepTest (0 ms total) 59: 59: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest 59: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 (2 ms) 59: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 (1 ms) 59: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 (1 ms) 59: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 (1 ms) 59: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 (1 ms) 59: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 (1 ms) 59: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest (11 ms total) 59: 59: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles 59: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/0 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/0 (2 ms) 59: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/1 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/1 (1 ms) 59: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/2 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/2 (1 ms) 59: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles (5 ms total) 59: 59: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles 59: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 59: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 (0 ms) 59: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 59: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 (0 ms) 59: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 59: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 (0 ms) 59: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles (0 ms total) 59: 59: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles 59: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/0 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/0 (3 ms) 59: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/1 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/1 (3 ms) 59: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/2 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/2 (4 ms) 59: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/3 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/3 (3 ms) 59: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles (15 ms total) 59: 59: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles 59: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/0 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/0 (1 ms) 59: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/1 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/1 (1 ms) 59: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/2 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/2 (1 ms) 59: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles (5 ms total) 59: 59: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles 59: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 59: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 (0 ms) 59: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 59: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 (0 ms) 59: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 59: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 (0 ms) 59: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles (0 ms total) 59: 59: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles 59: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/0 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/0 (1 ms) 59: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/1 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/1 (1 ms) 59: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles (3 ms total) 59: 59: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles 59: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 59: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 (0 ms) 59: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 59: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 (0 ms) 59: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 59: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 (0 ms) 59: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 59: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 (0 ms) 59: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles (0 ms total) 59: 59: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles 59: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 (1 ms) 59: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 (1 ms) 59: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles (3 ms total) 59: 59: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles 59: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 59: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 (0 ms) 59: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 59: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 (0 ms) 59: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 59: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 (0 ms) 59: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 59: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 (0 ms) 59: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles (0 ms total) 59: 59: [----------] 4 tests from ModuleSupported/NoOptionalOutput 59: [ RUN ] ModuleSupported/NoOptionalOutput.Works/0 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/NoOptionalOutput.Works/0 (1 ms) 59: [ RUN ] ModuleSupported/NoOptionalOutput.Works/1 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/NoOptionalOutput.Works/1 (1 ms) 59: [ RUN ] ModuleSupported/NoOptionalOutput.Works/2 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/NoOptionalOutput.Works/2 (1 ms) 59: [ RUN ] ModuleSupported/NoOptionalOutput.Works/3 59: 59: WARNING: Masses and atomic (Van der Waals) radii will be guessed 59: based on residue and atom names, since they could not be 59: definitively assigned from the information in your input 59: files. These guessed numbers might deviate from the mass 59: and radius of the atom type. Please check the output 59: files if necessary. Note, that this functionality may 59: be removed in a future GROMACS version. Please, consider 59: using another file format for your input. 59: 59: [ OK ] ModuleSupported/NoOptionalOutput.Works/3 (1 ms) 59: [----------] 4 tests from ModuleSupported/NoOptionalOutput (6 ms total) 59: 59: [----------] Global test environment tear-down 59: [==========] 67 tests from 20 test suites ran. (76 ms total) 59: [ PASSED ] 67 tests. 59/94 Test #59: CoordinateIOTests ............................ Passed 0.42 sec test 60 Start 60: TrajectoryAnalysisUnitTests 60: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/trajectoryanalysis-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/TrajectoryAnalysisUnitTests.xml" 60: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests 60: Test timeout computed to be: 1920 60: [==========] Running 393 tests from 21 test suites. 60: [----------] Global test environment set-up. 60: [----------] 11 tests from AngleModuleTest 60: [ RUN ] AngleModuleTest.ComputesSimpleAngles 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.ComputesSimpleAngles (3 ms) 60: [ RUN ] AngleModuleTest.ComputesDihedrals 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.ComputesDihedrals (2 ms) 60: [ RUN ] AngleModuleTest.ComputesVectorPairAngles 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.ComputesVectorPairAngles (2 ms) 60: [ RUN ] AngleModuleTest.ComputesVectorPlanePairAngles 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.ComputesVectorPlanePairAngles (1 ms) 60: [ RUN ] AngleModuleTest.ComputesPlaneZAxisAngles 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.ComputesPlaneZAxisAngles (2 ms) 60: [ RUN ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles (1 ms) 60: [ RUN ] AngleModuleTest.ComputesVectorTimeZeroAngles 60: Reading frames from gro file 'Test system for different angles', 33 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.ComputesVectorTimeZeroAngles (2 ms) 60: [ RUN ] AngleModuleTest.ComputesMultipleAngles 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.ComputesMultipleAngles (2 ms) 60: [ RUN ] AngleModuleTest.HandlesDynamicSelections 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.HandlesDynamicSelections (1 ms) 60: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorAngles 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorAngles (1 ms) 60: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles (2 ms) 60: [----------] 11 tests from AngleModuleTest (23 ms total) 60: 60: [----------] 5 tests from ClustsizeTest 60: [ RUN ] ClustsizeTest.NoMolDefaultCutoff 60: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 60: There is one group in the index 60: '', 24 atoms 60: Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Total number of atoms in clusters = 24 60: cmid: 2, cmax: 4, max_size: 6 60: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 60: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolDefaultCutoff (5 ms) 60: [ RUN ] ClustsizeTest.NoMolShortCutoff 60: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 60: There is one group in the index 60: '', 24 atoms 60: Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Total number of atoms in clusters = 24 60: cmid: 1, cmax: 6, max_size: 6 60: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 60: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolShortCutoff (1 ms) 60: [ RUN ] ClustsizeTest.MolDefaultCutoff 60: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 60: '', 24 atoms 60: Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Total number of atoms in clusters = 8 60: cmid: 2, cmax: 4, max_size: 2 60: 50%100%cmid: 2, cmax: 6, max_size: 2 60: 50%100%[ OK ] ClustsizeTest.MolDefaultCutoff (2 ms) 60: [ RUN ] ClustsizeTest.MolShortCutoff 60: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 60: '', 24 atoms 60: Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Total number of atoms in clusters = 8 60: cmid: 1, cmax: 6, max_size: 2 60: 50%100%cmid: 2, cmax: 6, max_size: 2 60: 50%100%[ OK ] ClustsizeTest.MolShortCutoff (3 ms) 60: [ RUN ] ClustsizeTest.MolCSize 60: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 60: '', 24 atoms 60: Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Total number of atoms in clusters = 8 60: cmid: 2, cmax: 4, max_size: 2 60: 50%100%cmid: 2, cmax: 6, max_size: 2 60: 50%100%[ OK ] ClustsizeTest.MolCSize (2 ms) 60: [----------] 5 tests from ClustsizeTest (14 ms total) 60: 60: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest 60: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp 60: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp (0 ms) 60: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory 60: Reading frames from gro file 'Test system', 8 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory (1 ms) 60: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset 60: Reading frames from gro file 'Test system', 8 atoms. 60: Reading frame 0 time 0.000 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset (2 ms) 60: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory 60: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory (0 ms) 60: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest (5 ms total) 60: 60: [----------] 4 tests from ConvertTrjModuleTest 60: [ RUN ] ConvertTrjModuleTest.WritesNormalOutput 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 60: Reading frame 0 time 0.000 Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: [ OK ] ConvertTrjModuleTest.WritesNormalOutput (11 ms) 60: [ RUN ] ConvertTrjModuleTest.WritesAtomSubset 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 60: Reading frame 0 time 0.000 Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: [ OK ] ConvertTrjModuleTest.WritesAtomSubset (13 ms) 60: [ RUN ] ConvertTrjModuleTest.WorksWithAtomAdding 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms 60: Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: [ OK ] ConvertTrjModuleTest.WorksWithAtomAdding (2 ms) 60: [ RUN ] ConvertTrjModuleTest.WorksWithAtomsAndSelection 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms 60: Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: [ OK ] ConvertTrjModuleTest.WorksWithAtomsAndSelection (3 ms) 60: [----------] 4 tests from ConvertTrjModuleTest (30 ms total) 60: 60: [----------] 6 tests from DistanceModuleTest 60: [ RUN ] DistanceModuleTest.ComputesDistances 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: atomname S1 S2: 60: Number of samples: 5 60: Average distance: 1.43246 nm 60: Standard deviation: 0.96700 nm 60: [ OK ] DistanceModuleTest.ComputesDistances (2 ms) 60: [ RUN ] DistanceModuleTest.ComputesMultipleDistances 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: atomname S1 S2: 60: Number of samples: 5 60: Average distance: 1.43246 nm 60: Standard deviation: 0.96700 nm 60: resindex 1 to 4 and atomname CB merge resindex 2 to 5 and atomname CB: 60: Number of samples: 4 60: Average distance: 1.81066 nm 60: Standard deviation: 0.79289 nm 60: [ OK ] DistanceModuleTest.ComputesMultipleDistances (2 ms) 60: [ RUN ] DistanceModuleTest.HandlesDynamicSelections 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: atomname S1 S2 and res_cog x < 2.8: 60: Number of samples: 3 60: Average distance: 1.72076 nm 60: Standard deviation: 1.24839 nm 60: [ OK ] DistanceModuleTest.HandlesDynamicSelections (2 ms) 60: [ RUN ] DistanceModuleTest.HandlesSelectionFromGroup 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: Contacts: 60: Number of samples: 2 60: Average distance: 1.00000 nm 60: Standard deviation: 0.00000 nm 60: [ OK ] DistanceModuleTest.HandlesSelectionFromGroup (7 ms) 60: [ RUN ] DistanceModuleTest.HandlesSelectionFromGroupWithSuccessiveIndices 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: SuccessiveContacts: 60: Number of samples: 2 60: Average distance: 1.00000 nm 60: Standard deviation: 0.00000 nm 60: [ OK ] DistanceModuleTest.HandlesSelectionFromGroupWithSuccessiveIndices (6 ms) 60: [ RUN ] DistanceModuleTest.HandlesSelectionFromLargeGroup 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: ManyContacts: 60: Number of samples: 10 60: Average distance: 1.82913 nm 60: Standard deviation: 0.78478 nm 60: [ OK ] DistanceModuleTest.HandlesSelectionFromLargeGroup (7 ms) 60: [----------] 6 tests from DistanceModuleTest (31 ms total) 60: 60: [----------] 2 tests from ExtractClusterModuleTest 60: [ RUN ] ExtractClusterModuleTest.WorksWithAllAtoms 60: trr version: GMX_trn_file (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 60: Analyzed 26 frames, last time 0.050 60: There are 8 clusters containing 26 structures, highest framenr is 25 60: [ OK ] ExtractClusterModuleTest.WorksWithAllAtoms (4 ms) 60: [ RUN ] ExtractClusterModuleTest.WorksWithAtomSubset 60: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 60: Analyzed 26 frames, last time 0.050 60: There are 8 clusters containing 26 structures, highest framenr is 25 60: [ OK ] ExtractClusterModuleTest.WorksWithAtomSubset (4 ms) 60: [----------] 2 tests from ExtractClusterModuleTest (9 ms total) 60: 60: [----------] 2 tests from FreeVolumeModuleTest 60: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolume 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 60: from the source below. This means the results may be different 60: compared to previous GROMACS versions. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. Bondi 60: van der Waals Volumes and Radii 60: J. Phys. Chem. (1964) 60: DOI: 10.1021/j100785a001 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Could not determine VDW radius for CO2-RM. Set to zero. 60: Could not determine VDW radius for CO2-RM. Set to zero. 60: Could not determine VDW radius for CO2-RM. Set to zero. 60: Could not determine VDW radius for CO2-RM. Set to zero. 60: Could not determine VDW radius for CO2-RM. Set to zero. 60: Could not determine VDW radius for CO2-RM. Set to zero. 60: Could not determine VDW radius for CO2-RM. Set to zero. 60: Could not determine VDW radius for CO2-RM. Set to zero. 60: Could not determine VDW radius for CO2-RM. Set to zero. 60: Could not determine VDW radius for 40 particles. These were set to zero. 60: Reading frame 0 time 0.000 Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: cutoff = 0.18 nm 60: probe_radius = 0 nm 60: seed = 13 60: ninsert = 1000 probes per nm^3 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. Bondi 60: van der Waals Volumes and Radii 60: J. Phys. Chem. (1964) 60: DOI: 10.1021/j100785a001 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: Tuanan C. Lourenco, Mariny F. C. Coelho, Teodorico C. Ramalho, David van der 60: Spoel, Luciano T. Costa 60: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 60: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 60: Environ. Sci. Technol. (2013) 60: DOI: 10.1021/es4020986 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Free volume 38.02 +/- 0.00 % 60: Total volume 68.92 +/- 0.00 nm^3 60: Number of molecules 340 total mass 63491.38 Dalton 60: Average molar mass: 186.74 Dalton 60: Density rho: 1529.71 +/- 0.00 nm^3 60: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 60: Molecular van der Waals volume assuming homogeneity: 0.1256 +/- 0.0000 nm^3 60: Fractional free volume 0.194 +/- 0.000 60: [ OK ] FreeVolumeModuleTest.ComputesFreeVolume (91 ms) 60: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolumeSelection 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 60: from the source below. This means the results may be different 60: compared to previous GROMACS versions. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. Bondi 60: van der Waals Volumes and Radii 60: J. Phys. Chem. (1964) 60: DOI: 10.1021/j100785a001 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Reading frame 0 time 0.000 Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: cutoff = 0.18 nm 60: probe_radius = 0 nm 60: seed = 17 60: ninsert = 1000 probes per nm^3 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. Bondi 60: van der Waals Volumes and Radii 60: J. Phys. Chem. (1964) 60: DOI: 10.1021/j100785a001 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: Tuanan C. Lourenco, Mariny F. C. Coelho, Teodorico C. Ramalho, David van der 60: Spoel, Luciano T. Costa 60: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 60: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 60: Environ. Sci. Technol. (2013) 60: DOI: 10.1021/es4020986 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Free volume 38.48 +/- 0.00 % 60: Total volume 68.92 +/- 0.00 nm^3 60: Number of molecules 340 total mass 63491.38 Dalton 60: Average molar mass: 186.74 Dalton 60: Density rho: 1529.71 +/- 0.00 nm^3 60: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 60: Molecular van der Waals volume assuming homogeneity: 0.1247 +/- 0.0000 nm^3 60: Fractional free volume 0.200 +/- 0.000 60: [ OK ] FreeVolumeModuleTest.ComputesFreeVolumeSelection (94 ms) 60: [----------] 2 tests from FreeVolumeModuleTest (185 ms total) 60: 60: [----------] 13 tests from MsdModuleTest 60: [ RUN ] MsdModuleTest.threeDimensionalDiffusion 60: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 60: Analyzed 10 frames, last time 9.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] MsdModuleTest.threeDimensionalDiffusion (3 ms) 60: [ RUN ] MsdModuleTest.twoDimensionalDiffusion 60: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 60: Analyzed 10 frames, last time 9.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] MsdModuleTest.twoDimensionalDiffusion (3 ms) 60: [ RUN ] MsdModuleTest.oneDimensionalDiffusion 60: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 60: Analyzed 10 frames, last time 9.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] MsdModuleTest.oneDimensionalDiffusion (3 ms) 60: [ RUN ] MsdModuleTest.oneDimensionalDiffusionWithMaxTau 60: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 60: Analyzed 10 frames, last time 9.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] MsdModuleTest.oneDimensionalDiffusionWithMaxTau (4 ms) 60: [ RUN ] MsdModuleTest.multipleGroupsWork 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 60: For energy conservation with LINCS, lincs_iter should be 2 or larger. 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 1818.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 60: NVE simulation: will use the initial temperature of 288.764 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 2.000 60: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 60: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 60: Analyzed 21 frames, last time 40.000 60: Setting the LD random seed to 1205075959 60: 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Converted 15 Bonds with virtual sites to connections, 7 left 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] MsdModuleTest.multipleGroupsWork (43 ms) 60: [ RUN ] MsdModuleTest.subPicosecondTrajectoryWorks 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 60: For energy conservation with LINCS, lincs_iter should be 2 or larger. 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 1818.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 60: NVE simulation: will use the initial temperature of 288.764 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 0.100 60: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 60: Reading frame 2 time 0.200 Reading frame 3 time 0.300 Reading frame 4 time 0.400 Reading frame 5 time 0.500 Reading frame 6 time 0.600 Reading frame 7 time 0.700 Reading frame 8 time 0.800 Reading frame 9 time 0.900 Reading frame 10 time 1.000 Reading frame 11 time 1.100 Reading frame 12 time 1.200 Reading frame 13 time 1.300 Reading frame 14 time 1.400 Reading frame 15 time 1.500 Reading frame 16 time 1.600 Reading frame 17 time 1.700 Reading frame 18 time 1.800 Reading frame 19 time 1.900 Reading frame 20 time 2.000 Last frame 20 time 2.000 60: Analyzed 21 frames, last time 2.000 60: Setting the LD random seed to -279219763 60: 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Converted 15 Bonds with virtual sites to connections, 7 left 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] MsdModuleTest.subPicosecondTrajectoryWorks (43 ms) 60: [ RUN ] MsdModuleTest.trestartLessThanDt 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 60: For energy conservation with LINCS, lincs_iter should be 2 or larger. 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 1818.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 60: NVE simulation: will use the initial temperature of 288.764 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Setting the LD random seed to -1414070433 60: 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Converted 15 Bonds with virtual sites to connections, 7 left 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] MsdModuleTest.trestartLessThanDt (33 ms) 60: [ RUN ] MsdModuleTest.trestartGreaterThanDt 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 60: For energy conservation with LINCS, lincs_iter should be 2 or larger. 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 1818.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 60: NVE simulation: will use the initial temperature of 288.764 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 60: Analyzed 21 frames, last time 40.000 60: Setting the LD random seed to -541689926 60: 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Converted 15 Bonds with virtual sites to connections, 7 left 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] MsdModuleTest.trestartGreaterThanDt (35 ms) 60: [ RUN ] MsdModuleTest.trestartGreaterThanDtAndNotAMultipleOfDt 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 60: For energy conservation with LINCS, lincs_iter should be 2 or larger. 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 1818.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 60: NVE simulation: will use the initial temperature of 288.764 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Setting the LD random seed to 2147404467 60: 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Converted 15 Bonds with virtual sites to connections, 7 left 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] MsdModuleTest.trestartGreaterThanDtAndNotAMultipleOfDt (32 ms) 60: [ RUN ] MsdModuleTest.molTest 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 60: For energy conservation with LINCS, lincs_iter should be 2 or larger. 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 1818.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 60: NVE simulation: will use the initial temperature of 288.764 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 60: Analyzed 21 frames, last time 40.000 60: Setting the LD random seed to -2365593 60: 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Converted 15 Bonds with virtual sites to connections, 7 left 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] MsdModuleTest.molTest (33 ms) 60: [ RUN ] MsdModuleTest.beginFit 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 60: For energy conservation with LINCS, lincs_iter should be 2 or larger. 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 1818.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 60: NVE simulation: will use the initial temperature of 288.764 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 2.000 60: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 60: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 60: Analyzed 21 frames, last time 40.000 60: Setting the LD random seed to -324026530 60: 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Converted 15 Bonds with virtual sites to connections, 7 left 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] MsdModuleTest.beginFit (31 ms) 60: [ RUN ] MsdModuleTest.endFit 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 60: For energy conservation with LINCS, lincs_iter should be 2 or larger. 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 1818.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 60: NVE simulation: will use the initial temperature of 288.764 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 2.000 60: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 60: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 60: Analyzed 21 frames, last time 40.000 60: Setting the LD random seed to -526353 60: 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Converted 15 Bonds with virtual sites to connections, 7 left 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] MsdModuleTest.endFit (37 ms) 60: [ RUN ] MsdModuleTest.notEnoughPointsForFitErrorEstimate 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 60: For energy conservation with LINCS, lincs_iter should be 2 or larger. 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 1818.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 60: NVE simulation: will use the initial temperature of 288.764 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 NOTEs 60: NOTE: You provided an index file 60: /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_solvated.ndx 60: (with -n), but it was not used by any selection. 60: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 2.000 60: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 60: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 60: Analyzed 21 frames, last time 40.000 60: Setting the LD random seed to -82392322 60: 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Converted 15 Bonds with virtual sites to connections, 7 left 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] MsdModuleTest.notEnoughPointsForFitErrorEstimate (32 ms) 60: [----------] 13 tests from MsdModuleTest (339 ms total) 60: 60: [----------] 9 tests from PairDistanceModuleTest 60: [ RUN ] PairDistanceModuleTest.ComputesAllDistances 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] PairDistanceModuleTest.ComputesAllDistances (11 ms) 60: [ RUN ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff (2 ms) 60: [ RUN ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff (2 ms) 60: [ RUN ] PairDistanceModuleTest.ComputesMaxDistance 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] PairDistanceModuleTest.ComputesMaxDistance (13 ms) 60: [ RUN ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff (3 ms) 60: [ RUN ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff (3 ms) 60: [ RUN ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff (2 ms) 60: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten (2 ms) 60: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup (4 ms) 60: [----------] 9 tests from PairDistanceModuleTest (47 ms total) 60: 60: [----------] 5 tests from RdfModuleTest 60: [ RUN ] RdfModuleTest.BasicTest 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] RdfModuleTest.BasicTest (19 ms) 60: [ RUN ] RdfModuleTest.SelectionsSolelyFromIndexFileWork 60: Reading frames from gro file '216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984', 648 atoms. 60: Reading frame 0 time 0.000 Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: [ OK ] RdfModuleTest.SelectionsSolelyFromIndexFileWork (16 ms) 60: [ RUN ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork (19 ms) 60: [ RUN ] RdfModuleTest.CalculatesSurf 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] RdfModuleTest.CalculatesSurf (8 ms) 60: [ RUN ] RdfModuleTest.CalculatesXY 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] RdfModuleTest.CalculatesXY (20 ms) 60: [----------] 5 tests from RdfModuleTest (84 ms total) 60: 60: [----------] 5 tests from SasaModuleTest 60: [ RUN ] SasaModuleTest.BasicTest 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 60: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 60: of Surface Area and Volume and to Dot Surface Contouring of Molecular 60: Assemblies 60: J. Comp. Chem. (1995) 60: DOI: 10.1002/jcc.540160303 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 60: from the source below. This means the results may be different 60: compared to previous GROMACS versions. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. Bondi 60: van der Waals Volumes and Radii 60: J. Phys. Chem. (1964) 60: DOI: 10.1021/j100785a001 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Analyzed topology coordinates 60: [ OK ] SasaModuleTest.BasicTest (10 ms) 60: [ RUN ] SasaModuleTest.HandlesSelectedResidues 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 60: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 60: of Surface Area and Volume and to Dot Surface Contouring of Molecular 60: Assemblies 60: J. Comp. Chem. (1995) 60: DOI: 10.1002/jcc.540160303 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 60: from the source below. This means the results may be different 60: compared to previous GROMACS versions. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. Bondi 60: van der Waals Volumes and Radii 60: J. Phys. Chem. (1964) 60: DOI: 10.1021/j100785a001 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Analyzed topology coordinates 60: [ OK ] SasaModuleTest.HandlesSelectedResidues (6 ms) 60: [ RUN ] SasaModuleTest.WritesConnollySurfaceWithSolute 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 60: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 60: of Surface Area and Volume and to Dot Surface Contouring of Molecular 60: Assemblies 60: J. Comp. Chem. (1995) 60: DOI: 10.1002/jcc.540160303 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 60: from the source below. This means the results may be different 60: compared to previous GROMACS versions. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. Bondi 60: van der Waals Volumes and Radii 60: J. Phys. Chem. (1964) 60: DOI: 10.1021/j100785a001 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Analyzed topology coordinates 60: [ OK ] SasaModuleTest.WritesConnollySurfaceWithSolute (4 ms) 60: [ RUN ] SasaModuleTest.HandlesDynamicOutputGroup 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 60: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 60: of Surface Area and Volume and to Dot Surface Contouring of Molecular 60: Assemblies 60: J. Comp. Chem. (1995) 60: DOI: 10.1002/jcc.540160303 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 60: from the source below. This means the results may be different 60: compared to previous GROMACS versions. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. Bondi 60: van der Waals Volumes and Radii 60: J. Phys. Chem. (1964) 60: DOI: 10.1021/j100785a001 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Analyzed topology coordinates 60: [ OK ] SasaModuleTest.HandlesDynamicOutputGroup (8 ms) 60: [ RUN ] SasaModuleTest.HandlesDynamicCalculationGroup 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 60: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 60: of Surface Area and Volume and to Dot Surface Contouring of Molecular 60: Assemblies 60: J. Comp. Chem. (1995) 60: DOI: 10.1002/jcc.540160303 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 60: from the source below. This means the results may be different 60: compared to previous GROMACS versions. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. Bondi 60: van der Waals Volumes and Radii 60: J. Phys. Chem. (1964) 60: DOI: 10.1021/j100785a001 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Analyzed topology coordinates 60: [ OK ] SasaModuleTest.HandlesDynamicCalculationGroup (7 ms) 60: [----------] 5 tests from SasaModuleTest (39 ms total) 60: 60: [----------] 8 tests from SelectModuleTest 60: [ RUN ] SelectModuleTest.BasicTest 60: Reading frames from gro file 'Test system', 15 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] SelectModuleTest.BasicTest (4 ms) 60: [ RUN ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput 60: Reading frames from gro file 'Test system', 15 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput (2 ms) 60: [ RUN ] SelectModuleTest.HandlesPDBOutputWithPDBInput 60: Reading frames from gro file 'Test system', 15 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] SelectModuleTest.HandlesPDBOutputWithPDBInput (3 ms) 60: [ RUN ] SelectModuleTest.HandlesMaxPDBOutput 60: Reading frames from gro file 'Test system', 15 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] SelectModuleTest.HandlesMaxPDBOutput (2 ms) 60: [ RUN ] SelectModuleTest.HandlesSelectedPDBOutput 60: Reading frames from gro file 'Test system', 15 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] SelectModuleTest.HandlesSelectedPDBOutput (2 ms) 60: [ RUN ] SelectModuleTest.NormalizesSizes 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] SelectModuleTest.NormalizesSizes (1 ms) 60: [ RUN ] SelectModuleTest.WritesResidueNumbers 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] SelectModuleTest.WritesResidueNumbers (1 ms) 60: [ RUN ] SelectModuleTest.WritesResidueIndices 60: Analyzed topology coordinates 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] SelectModuleTest.WritesResidueIndices (2 ms) 60: [----------] 8 tests from SelectModuleTest (23 ms total) 60: 60: [----------] 10 tests from SurfaceAreaTest 60: [ RUN ] SurfaceAreaTest.ComputesSinglePoint 60: [ OK ] SurfaceAreaTest.ComputesSinglePoint (0 ms) 60: [ RUN ] SurfaceAreaTest.ComputesTwoPoints 60: [ OK ] SurfaceAreaTest.ComputesTwoPoints (0 ms) 60: [ RUN ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius 60: [ OK ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius (0 ms) 60: [ RUN ] SurfaceAreaTest.SurfacePoints12 60: [ OK ] SurfaceAreaTest.SurfacePoints12 (0 ms) 60: [ RUN ] SurfaceAreaTest.SurfacePoints32 60: [ OK ] SurfaceAreaTest.SurfacePoints32 (0 ms) 60: [ RUN ] SurfaceAreaTest.SurfacePoints42 60: [ OK ] SurfaceAreaTest.SurfacePoints42 (0 ms) 60: [ RUN ] SurfaceAreaTest.SurfacePoints122 60: [ OK ] SurfaceAreaTest.SurfacePoints122 (0 ms) 60: [ RUN ] SurfaceAreaTest.Computes100Points 60: [ OK ] SurfaceAreaTest.Computes100Points (0 ms) 60: [ RUN ] SurfaceAreaTest.Computes100PointsWithRectangularPBC 60: [ OK ] SurfaceAreaTest.Computes100PointsWithRectangularPBC (2 ms) 60: [ RUN ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC 60: [ OK ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC (3 ms) 60: [----------] 10 tests from SurfaceAreaTest (9 ms total) 60: 60: [----------] 4 tests from TopologyInformation 60: [ RUN ] TopologyInformation.CantWorkWithoutReadingAFile 60: [ OK ] TopologyInformation.CantWorkWithoutReadingAFile (0 ms) 60: [ RUN ] TopologyInformation.WorksWithGroFile 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] TopologyInformation.WorksWithGroFile (1 ms) 60: [ RUN ] TopologyInformation.WorksWithPdbFile 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] TopologyInformation.WorksWithPdbFile (2 ms) 60: [ RUN ] TopologyInformation.WorksWithTprFromPdbFile 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file lysozyme.top, line 1465]: 60: System has non-zero total charge: 2.000000 60: Total charge should normally be an integer. See 60: https://manual.gromacs.org/current/user-guide/floating-point.html 60: for discussion on how close it should be to an integer. 60: 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 465.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 60: NVE simulation with an initial temperature of zero: will use a Verlet 60: buffer of 10%. Check your energy drift! 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 NOTEs 60: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 60: Setting the LD random seed to 1338224583 60: 60: Generated 330891 of the 330891 non-bonded parameter combinations 60: 60: Generated 330891 of the 330891 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 60: 60: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 60: Analysing residue names: 60: There are: 10 Protein residues 60: Analysing Protein... 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] TopologyInformation.WorksWithTprFromPdbFile (772 ms) 60: [----------] 4 tests from TopologyInformation (776 ms total) 60: 60: [----------] 4 tests from TrajectoryModuleTest 60: [ RUN ] TrajectoryModuleTest.BasicTest 60: Reading frames from gro file 'Test system', 15 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] TrajectoryModuleTest.BasicTest (2 ms) 60: [ RUN ] TrajectoryModuleTest.PlotsXOnly 60: Reading frames from gro file 'Test system', 15 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] TrajectoryModuleTest.PlotsXOnly (2 ms) 60: [ RUN ] TrajectoryModuleTest.HandlesNoVelocities 60: Reading frames from gro file 'Test system', 15 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] TrajectoryModuleTest.HandlesNoVelocities (2 ms) 60: [ RUN ] TrajectoryModuleTest.HandlesNoForces 60: Reading frames from gro file 'Test system', 15 atoms. 60: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 60: Analyzed 2 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: [ OK ] TrajectoryModuleTest.HandlesNoForces (1 ms) 60: [----------] 4 tests from TrajectoryModuleTest (9 ms total) 60: 60: [----------] 5 tests from UnionFinderTest 60: [ RUN ] UnionFinderTest.WorksEmpty 60: [ OK ] UnionFinderTest.WorksEmpty (0 ms) 60: [ RUN ] UnionFinderTest.BasicMerges 60: [ OK ] UnionFinderTest.BasicMerges (0 ms) 60: [ RUN ] UnionFinderTest.LargerMerges 60: [ OK ] UnionFinderTest.LargerMerges (0 ms) 60: [ RUN ] UnionFinderTest.LongRightMerge 60: [ OK ] UnionFinderTest.LongRightMerge (0 ms) 60: [ RUN ] UnionFinderTest.LongLeftMerge 60: [ OK ] UnionFinderTest.LongLeftMerge (0 ms) 60: [----------] 5 tests from UnionFinderTest (0 ms total) 60: 60: [----------] 1 test from MappedUnionFinderTest 60: [ RUN ] MappedUnionFinderTest.BasicMerges 60: [ OK ] MappedUnionFinderTest.BasicMerges (0 ms) 60: [----------] 1 test from MappedUnionFinderTest (0 ms total) 60: 60: [----------] 192 tests from MoleculeTests/DsspModuleTest 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/0 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/0 (33 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/1 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/1 (23 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/2 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/2 (23 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/3 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/3 (21 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/4 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/4 (21 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/5 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/5 (21 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/6 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/6 (21 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/7 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/7 (21 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/8 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/8 (21 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/9 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/9 (22 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/10 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/10 (22 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/11 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/11 (22 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/12 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/12 (22 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/13 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/13 (21 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/14 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/14 (21 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/15 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/15 (30 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/16 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/16 (22 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/17 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/17 (23 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/18 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/18 (21 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/19 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/19 (21 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/20 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/20 (21 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/21 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/21 (21 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/22 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/22 (21 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/23 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/23 (21 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/24 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/24 (26 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/25 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/25 (46 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/26 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/26 (23 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/27 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/27 (22 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/28 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/28 (21 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/29 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/29 (21 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/30 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/30 (21 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/31 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/31 (21 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/32 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/32 (22 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/33 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/33 (21 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/34 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/34 (21 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/35 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/35 (21 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/36 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/36 (22 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/37 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/37 (22 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/38 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/38 (21 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/39 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/39 (21 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/40 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/40 (22 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/41 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/41 (22 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/42 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/42 (23 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/43 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/43 (23 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/44 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/44 (23 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/45 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/45 (22 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/46 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/46 (23 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/47 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/47 (21 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/48 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/48 (22 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/49 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/49 (25 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/50 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/50 (22 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/51 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/51 (23 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/52 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/52 (22 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/53 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/53 (22 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/54 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/54 (21 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/55 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/55 (22 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/56 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/56 (22 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/57 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/57 (24 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/58 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/58 (22 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/59 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/59 (23 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/60 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/60 (23 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/61 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/61 (23 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/62 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/62 (23 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/63 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/63 (22 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/64 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/64 (29 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/65 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/65 (20 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/66 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/66 (20 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/67 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/67 (19 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/68 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/68 (20 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/69 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/69 (22 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/70 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/70 (20 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/71 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/71 (21 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/72 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/72 (20 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/73 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/73 (20 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/74 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/74 (20 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/75 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/75 (20 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/76 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/76 (20 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/77 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/77 (20 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/78 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/78 (20 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/79 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/79 (20 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/80 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/80 (21 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/81 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/81 (20 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/82 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/82 (20 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/83 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/83 (21 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/84 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/84 (20 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/85 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/85 (19 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/86 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/86 (20 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/87 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/87 (20 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/88 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/88 (75 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/89 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/89 (20 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/90 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/90 (48 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/91 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/91 (22 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/92 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/92 (20 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/93 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/93 (19 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/94 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/94 (19 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/95 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/95 (20 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/96 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/96 (19 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/97 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/97 (19 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/98 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/98 (20 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/99 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/99 (20 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/100 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/100 (21 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/101 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/101 (19 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/102 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/102 (19 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/103 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/103 (19 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/104 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/104 (20 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/105 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/105 (20 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/106 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/106 (19 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/107 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/107 (20 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/108 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/108 (19 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/109 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/109 (19 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/110 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/110 (19 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/111 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/111 (20 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/112 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/112 (20 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/113 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/113 (20 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/114 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/114 (21 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/115 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/115 (20 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/116 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/116 (20 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/117 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/117 (20 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/118 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/118 (23 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/119 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/119 (22 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/120 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/120 (21 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/121 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/121 (19 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/122 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/122 (19 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/123 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/123 (21 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/124 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/124 (20 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/125 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/125 (19 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/126 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/126 (20 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/127 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/127 (21 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/128 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/128 (15 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/129 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/129 (16 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/130 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/130 (15 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/131 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/131 (16 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/132 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/132 (15 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/133 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/133 (17 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/134 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/134 (16 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/135 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/135 (16 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/136 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/136 (16 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/137 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/137 (16 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/138 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/138 (15 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/139 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/139 (17 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/140 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/140 (16 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/141 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/141 (72 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/142 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/142 (15 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/143 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/143 (16 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/144 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/144 (15 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/145 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/145 (16 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/146 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/146 (16 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/147 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/147 (15 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/148 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/148 (15 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/149 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/149 (15 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/150 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/150 (15 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/151 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/151 (15 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/152 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/152 (200 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/153 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/153 (15 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/154 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/154 (15 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/155 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/155 (15 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/156 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/156 (126 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/157 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/157 (89 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/158 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/158 (95 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/159 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/159 (15 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/160 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/160 (14 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/161 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/161 (14 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/162 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/162 (376 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/163 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/163 (253 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/164 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/164 (170 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/165 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/165 (168 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/166 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/166 (139 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/167 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/167 (114 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/168 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/168 (16 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/169 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/169 (15 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/170 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/170 (15 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/171 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/171 (15 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/172 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/172 (15 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/173 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/173 (15 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/174 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/174 (15 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/175 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/175 (15 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/176 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/176 (16 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/177 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/177 (16 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/178 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/178 (15 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/179 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/179 (15 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/180 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/180 (15 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/181 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/181 (15 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/182 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/182 (15 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/183 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/183 (14 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/184 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/184 (15 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/185 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/185 (15 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/186 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/186 (35 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/187 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/187 (16 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/188 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/188 (15 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/189 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/189 (17 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/190 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/190 (16 ms) 60: [ RUN ] MoleculeTests/DsspModuleTest.Works/191 60: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 60: Last frame 0 time 500.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: W. Kabsch, C. Sander 60: Dictionary of protein secondary structure: pattern recognition of 60: hydrogen-bonded and geometrical features 60: Biopolymers (1983) 60: DOI: 10.1002/bip.360221211 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 60: Trajectories 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c01344 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/DsspModuleTest.Works/191 (15 ms) 60: [----------] 192 tests from MoleculeTests/DsspModuleTest (5567 ms total) 60: 60: [----------] 3 tests from GyrateTests/GyrateModuleTest 60: [ RUN ] GyrateTests/GyrateModuleTest.Works/0 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: [ OK ] GyrateTests/GyrateModuleTest.Works/0 (7 ms) 60: [ RUN ] GyrateTests/GyrateModuleTest.Works/1 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: [ OK ] GyrateTests/GyrateModuleTest.Works/1 (6 ms) 60: [ RUN ] GyrateTests/GyrateModuleTest.Works/2 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: [ OK ] GyrateTests/GyrateModuleTest.Works/2 (7 ms) 60: [----------] 3 tests from GyrateTests/GyrateModuleTest (21 ms total) 60: 60: [----------] 96 tests from HBondTests/HbondModuleTest 60: [ RUN ] HBondTests/HbondModuleTest.Works/0 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/0 (13 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/1 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/1 (15 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/2 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/2 (13 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/3 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/3 (14 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/4 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/4 (16 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/5 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/5 (18 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/6 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/6 (14 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/7 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/7 (16 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/8 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/8 (15 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/9 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/9 (17 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/10 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/10 (19 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/11 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/11 (13 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/12 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/12 (18 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/13 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/13 (14 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/14 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/14 (13 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/15 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/15 (13 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/16 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/16 (12 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/17 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/17 (20 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/18 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/18 (13 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/19 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/19 (13 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/20 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/20 (12 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/21 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/21 (19 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/22 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/22 (13 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/23 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/23 (14 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/24 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/24 (15 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/25 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/25 (15 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/26 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/26 (13 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/27 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/27 (13 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/28 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/28 (12 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/29 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/29 (13 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/30 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/30 (15 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/31 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/31 (14 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/32 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/32 (95 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/33 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/33 (79 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/34 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/34 (80 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/35 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/35 (77 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/36 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/36 (79 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/37 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/37 (77 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/38 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/38 (81 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/39 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/39 (82 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/40 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/40 (85 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/41 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/41 (83 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/42 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/42 (92 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/43 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/43 (91 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/44 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/44 (75 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/45 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/45 (76 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/46 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/46 (75 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/47 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/47 (75 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/48 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/48 (82 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/49 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/49 (77 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/50 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/50 (77 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/51 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/51 (82 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/52 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/52 (79 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/53 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/53 (85 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/54 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/54 (85 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/55 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/55 (86 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/56 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/56 (78 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/57 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/57 (76 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/58 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/58 (74 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/59 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/59 (70 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/60 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/60 (76 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/61 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 27 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/61 (79 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/62 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 56 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/62 (76 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/63 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 60: Selection 'Protein' has 29 acceptors and 4 donors. 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: Merging hbonds with Acceptor and Donor swapped 60: [ OK ] HBondTests/HbondModuleTest.Works/63 (77 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/64 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/64 (79 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/65 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/65 (88 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/66 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/66 (88 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/67 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/67 (83 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/68 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/68 (82 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/69 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/69 (83 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/70 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/70 (81 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/71 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/71 (84 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/72 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/72 (105 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/73 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/73 (98 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/74 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/74 (83 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/75 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/75 (79 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/76 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/76 (89 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/77 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/77 (78 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/78 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/78 (110 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/79 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/79 (79 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/80 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/80 (113 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/81 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/81 (111 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/82 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/82 (161 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/83 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/83 (101 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/84 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/84 (120 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/85 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/85 (82 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/86 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/86 (73 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/87 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/87 (74 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/88 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/88 (75 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/89 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/89 (113 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/90 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/90 (74 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/91 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/91 (81 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/92 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/92 (78 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/93 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/93 (77 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/94 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/94 (88 ms) 60: [ RUN ] HBondTests/HbondModuleTest.Works/95 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 60: Analyzed 2 frames, last time 10.000 60: 60: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 60: Selection 'Water' has 1160 acceptors and 1160 donors. 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 60: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 60: Memory Limitation 60: Journal of Chemical Information and Modeling (2024) 60: DOI: 10.1021/acs.jcim.3c02087 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] HBondTests/HbondModuleTest.Works/95 (95 ms) 60: [----------] 96 tests from HBondTests/HbondModuleTest (6896 ms total) 60: 60: [----------] 4 tests from MoleculeTests/ScatteringModule 60: [ RUN ] MoleculeTests/ScatteringModule.DirectMode/0 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 60: Method for calculating small-angle neutron scattering spectra using all-atom 60: molecular dynamics trajectories 60: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 60: DOI: 10.1134/S1027451013060372 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/ScatteringModule.DirectMode/0 (21 ms) 60: [ RUN ] MoleculeTests/ScatteringModule.DirectMode/1 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 60: Method for calculating small-angle neutron scattering spectra using all-atom 60: molecular dynamics trajectories 60: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 60: DOI: 10.1134/S1027451013060372 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: D. T. Cromer, J. B. Mann 60: X-ray scattering factors computed from numerical Hartree-Fock wave functions 60: Acta Cryst. A (1968) 60: DOI: 10.1107/S0567739468000550 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/ScatteringModule.DirectMode/1 (358 ms) 60: [ RUN ] MoleculeTests/ScatteringModule.MCMode/0 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 60: Method for calculating small-angle neutron scattering spectra using all-atom 60: molecular dynamics trajectories 60: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 60: DOI: 10.1134/S1027451013060372 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/ScatteringModule.MCMode/0 (10 ms) 60: [ RUN ] MoleculeTests/ScatteringModule.MCMode/1 60: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 60: Last frame 0 time 0.000 60: Analyzed 1 frames, last time 0.000 60: 60: WARNING: Masses and atomic (Van der Waals) radii will be guessed 60: based on residue and atom names, since they could not be 60: definitively assigned from the information in your input 60: files. These guessed numbers might deviate from the mass 60: and radius of the atom type. Please check the output 60: files if necessary. Note, that this functionality may 60: be removed in a future GROMACS version. Please, consider 60: using another file format for your input. 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 60: Method for calculating small-angle neutron scattering spectra using all-atom 60: molecular dynamics trajectories 60: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 60: DOI: 10.1134/S1027451013060372 60: -------- -------- --- Thank You --- -------- -------- 60: 60: 60: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 60: D. T. Cromer, J. B. Mann 60: X-ray scattering factors computed from numerical Hartree-Fock wave functions 60: Acta Cryst. A (1968) 60: DOI: 10.1107/S0567739468000550 60: -------- -------- --- Thank You --- -------- -------- 60: 60: [ OK ] MoleculeTests/ScatteringModule.MCMode/1 (80 ms) 60: [----------] 4 tests from MoleculeTests/ScatteringModule (474 ms total) 60: 60: [----------] Global test environment tear-down 60: [==========] 393 tests from 21 test suites ran. (14590 ms total) 60: [ PASSED ] 393 tests. 60/94 Test #60: TrajectoryAnalysisUnitTests .................. Passed 14.97 sec test 61 Start 61: EnergyAnalysisUnitTests 61: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/energyanalysis-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/EnergyAnalysisUnitTests.xml" 61: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/energyanalysis/tests 61: Test timeout computed to be: 30 61: [==========] Running 12 tests from 5 test suites. 61: [----------] Global test environment set-up. 61: [----------] 2 tests from EnergyTermTest 61: [ RUN ] EnergyTermTest.ConstructWorks 61: [ OK ] EnergyTermTest.ConstructWorks (0 ms) 61: [ RUN ] EnergyTermTest.AddFrameWorks 61: [ OK ] EnergyTermTest.AddFrameWorks (0 ms) 61: [----------] 2 tests from EnergyTermTest (0 ms total) 61: 61: [----------] 1 test from DhdlTest 61: [ RUN ] DhdlTest.ExtractDhdl 61: Opened /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/dhdl.edr as double precision energy file 61: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/dhdl.tpr, VERSION 2016-dev-20160810-e3ded7f (double precision) 61: Note: file tpx version 110, software tpx version 137 61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Reading energy frame 6 time 0.060 Reading energy frame 7 time 0.070 Reading energy frame 8 time 0.080 Reading energy frame 9 time 0.090 Reading energy frame 10 time 0.100 Reading energy frame 11 time 0.110 Reading energy frame 12 time 0.120 Reading energy frame 13 time 0.130 Reading energy frame 14 time 0.140 Reading energy frame 15 time 0.150 Reading energy frame 16 time 0.160 Reading energy frame 17 time 0.170 Reading energy frame 18 time 0.180 Reading energy frame 19 time 0.190 Reading energy frame 20 time 0.200 Reading energy frame 30 time 0.300 Reading energy frame 40 time 0.400 Reading energy frame 50 time 0.500 Reading energy frame 60 time 0.600 Reading energy frame 70 time 0.700 Reading energy frame 80 time 0.800 Reading energy frame 90 time 0.900 Reading energy frame 100 time 1.000 Last energy frame read 100 time 1.000 61: 61: 61: Wrote 8 lambda values with 101 samples as 808 dH data blocks to /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/energyanalysis/tests/Testing/Temporary/DhdlTest_ExtractDhdl_dhdl.xvg 61: [ OK ] DhdlTest.ExtractDhdl (10 ms) 61: [----------] 1 test from DhdlTest (10 ms total) 61: 61: [----------] 1 test from OriresTest 61: [ RUN ] OriresTest.ExtractOrires 61: Opened /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/orires.edr as single precision energy file 61: Reading file /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/orires.tpr, VERSION 2017-dev-20170725-fea8651 (single precision) 61: Note: file tpx version 111, software tpx version 137 61: Found 7 orientation restraints with 1 experimentsSelect the orientation restraint labels you want (-1 is all) 61: End your selection with 0 61: Selecting all 7 orientation restraints 61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Reading energy frame 3 time 0.006 Reading energy frame 4 time 0.008 Reading energy frame 5 time 0.010 Reading energy frame 6 time 0.012 Reading energy frame 7 time 0.014 Reading energy frame 8 time 0.016 Reading energy frame 9 time 0.018 Reading energy frame 10 time 0.020 Last energy frame read 10 time 0.020 61: [ OK ] OriresTest.ExtractOrires (11 ms) 61: [----------] 1 test from OriresTest (11 ms total) 61: 61: [----------] 5 tests from EnergyTest 61: [ RUN ] EnergyTest.ExtractEnergy 61: Opened /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 61: 61: Select the terms you want from the following list by 61: selecting either (part of) the name or the number or a combination. 61: End your selection with an empty line or a zero. 61: ------------------------------------------------------------------- 61: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 61: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 61: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 61: 13 Box-Z 14 Volume 15 Density 16 pV 61: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 61: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 61: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 61: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 61: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 61: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 61: 61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 61: 61: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 61: All statistics are over 5001 points 61: 61: Energy Average Err.Est. RMSD Tot-Drift 61: ------------------------------------------------------------------------------- 61: Potential -34142.2 39 228.993 -62.8906 (kJ/mol) 61: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 61: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 61: [ OK ] EnergyTest.ExtractEnergy (2 ms) 61: [ RUN ] EnergyTest.ExtractEnergyByNumber 61: Opened /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 61: 61: Select the terms you want from the following list by 61: selecting either (part of) the name or the number or a combination. 61: End your selection with an empty line or a zero. 61: ------------------------------------------------------------------- 61: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 61: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 61: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 61: 13 Box-Z 14 Volume 15 Density 16 pV 61: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 61: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 61: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 61: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 61: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 61: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 61: 61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 61: 61: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 61: All statistics are over 5001 points 61: 61: Energy Average Err.Est. RMSD Tot-Drift 61: ------------------------------------------------------------------------------- 61: Coul. recip. 302.771 2.8 17.5152 12.5403 (kJ/mol) 61: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 61: Pres. DC -268.49 3 8.52175 13.2804 (bar) 61: [ OK ] EnergyTest.ExtractEnergyByNumber (2 ms) 61: [ RUN ] EnergyTest.ExtractEnergyMixed 61: Opened /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 61: 61: Select the terms you want from the following list by 61: selecting either (part of) the name or the number or a combination. 61: End your selection with an empty line or a zero. 61: ------------------------------------------------------------------- 61: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 61: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 61: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 61: 13 Box-Z 14 Volume 15 Density 16 pV 61: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 61: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 61: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 61: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 61: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 61: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 61: 61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 61: 61: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 4 data sets 61: All statistics are over 5001 points 61: 61: Energy Average Err.Est. RMSD Tot-Drift 61: ------------------------------------------------------------------------------- 61: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 61: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 61: Box-Z 2.92457 0.0054 0.0151558 0.0234974 (nm) 61: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 61: [ OK ] EnergyTest.ExtractEnergyMixed (4 ms) 61: [ RUN ] EnergyTest.ExtractEnergyWithNumberInName 61: Opened /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/ener_numberInName.edr as single precision energy file 61: 61: Select the terms you want from the following list by 61: selecting either (part of) the name or the number or a combination. 61: End your selection with an empty line or a zero. 61: ------------------------------------------------------------------- 61: 1 Bond 2 Angle 3 Proper-Dih. 4 Per.-Imp.-Dih. 61: 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 Coulomb-(SR) 61: 9 Coul.-recip. 10 Potential 11 Kinetic-En. 12 Total-Energy 61: 13 Conserved-En. 14 Temperature 15 Pressure 16 Constr.-rmsd 61: 17 Vir-XX 18 Vir-XY 19 Vir-XZ 20 Vir-YX 61: 21 Vir-YY 22 Vir-YZ 23 Vir-ZX 24 Vir-ZY 61: 25 Vir-ZZ 26 Pres-XX 27 Pres-XY 28 Pres-XZ 61: 29 Pres-YX 30 Pres-YY 31 Pres-YZ 32 Pres-ZX 61: 33 Pres-ZY 34 Pres-ZZ 35 #Surf*SurfTen 36 2CosZ*Vel-X 61: 37 1/Viscosity 38 T-System 39 Lamb-System 61: 61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Last energy frame read 2 time 0.004 61: 61: Statistics over 3 steps [ 0.0000 through 0.0040 ps ], 1 data sets 61: All statistics are over 3 points (frames) 61: 61: Energy Average Err.Est. RMSD Tot-Drift 61: ------------------------------------------------------------------------------- 61: 1/Viscosity 57767.2 -- 10666.2 -25998 (m s/kg) 61: [ OK ] EnergyTest.ExtractEnergyWithNumberInName (0 ms) 61: [ RUN ] EnergyTest.ExtractEnergyWithNumberInNameAndAlsoByNumber 61: Opened /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/ener_numberInName.edr as single precision energy file 61: 61: Select the terms you want from the following list by 61: selecting either (part of) the name or the number or a combination. 61: End your selection with an empty line or a zero. 61: ------------------------------------------------------------------- 61: 1 Bond 2 Angle 3 Proper-Dih. 4 Per.-Imp.-Dih. 61: 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 Coulomb-(SR) 61: 9 Coul.-recip. 10 Potential 11 Kinetic-En. 12 Total-Energy 61: 13 Conserved-En. 14 Temperature 15 Pressure 16 Constr.-rmsd 61: 17 Vir-XX 18 Vir-XY 19 Vir-XZ 20 Vir-YX 61: 21 Vir-YY 22 Vir-YZ 23 Vir-ZX 24 Vir-ZY 61: 25 Vir-ZZ 26 Pres-XX 27 Pres-XY 28 Pres-XZ 61: 29 Pres-YX 30 Pres-YY 31 Pres-YZ 32 Pres-ZX 61: 33 Pres-ZY 34 Pres-ZZ 35 #Surf*SurfTen 36 2CosZ*Vel-X 61: 37 1/Viscosity 38 T-System 39 Lamb-System 61: 61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Last energy frame read 2 time 0.004 61: 61: Statistics over 3 steps [ 0.0000 through 0.0040 ps ], 2 data sets 61: All statistics are over 3 points (frames) 61: 61: Energy Average Err.Est. RMSD Tot-Drift 61: ------------------------------------------------------------------------------- 61: LJ (SR) -14.1095 -- 0.384124 0.932214 (kJ/mol) 61: 1/Viscosity 57767.2 -- 10666.2 -25998 (m s/kg) 61: [ OK ] EnergyTest.ExtractEnergyWithNumberInNameAndAlsoByNumber (1 ms) 61: [----------] 5 tests from EnergyTest (12 ms total) 61: 61: [----------] 3 tests from ViscosityTest 61: [ RUN ] ViscosityTest.EinsteinViscosity 61: Opened /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 61: 61: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 61: All statistics are over 5001 points 61: 61: Energy Average Err.Est. RMSD Tot-Drift 61: ------------------------------------------------------------------------------- 61: Pres-XX 20.2092 65 717.193 185.978 (bar) 61: Pres-XY -47.7351 39 372.522 207.456 (bar) 61: Pres-XZ 11.477 31 379.79 6.80818 (bar) 61: Pres-YX -47.7106 39 372.525 207.5 (bar) 61: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 61: Pres-YZ -41.3534 45 401.216 114.663 (bar) 61: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 61: Pres-ZY -41.3119 45 401.196 114.743 (bar) 61: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 61: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 61: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 61: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 61: 61: Computing shear viscosity using the Einstein relation with 6 start points separated by 0.2 ps 61: [ OK ] ViscosityTest.EinsteinViscosity (168 ms) 61: [ RUN ] ViscosityTest.EinsteinViscosityIntegral 61: Opened /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 61: 61: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 61: All statistics are over 5001 points 61: 61: Energy Average Err.Est. RMSD Tot-Drift 61: ------------------------------------------------------------------------------- 61: Pres-XX 20.2092 65 717.193 185.978 (bar) 61: Pres-XY -47.7351 39 372.522 207.456 (bar) 61: Pres-XZ 11.477 31 379.79 6.80818 (bar) 61: Pres-YX -47.7106 39 372.525 207.5 (bar) 61: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 61: Pres-YZ -41.3534 45 401.216 114.663 (bar) 61: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 61: Pres-ZY -41.3119 45 401.196 114.743 (bar) 61: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 61: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 61: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 61: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 61: 61: Computing shear viscosity using the Einstein relation with 6 start points separated by 0.2 ps 61: [ OK ] ViscosityTest.EinsteinViscosityIntegral (134 ms) 61: [ RUN ] ViscosityTest.EinsteinViscosityDefaultArguments 61: Opened /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 61: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 61: 61: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 61: All statistics are over 5001 points 61: 61: Energy Average Err.Est. RMSD Tot-Drift 61: ------------------------------------------------------------------------------- 61: Pres-XX 20.2092 65 717.193 185.978 (bar) 61: Pres-XY -47.7351 39 372.522 207.456 (bar) 61: Pres-XZ 11.477 31 379.79 6.80818 (bar) 61: Pres-YX -47.7106 39 372.525 207.5 (bar) 61: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 61: Pres-YZ -41.3534 45 401.216 114.663 (bar) 61: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 61: Pres-ZY -41.3119 45 401.196 114.743 (bar) 61: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 61: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 61: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 61: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 61: 61: Computing shear viscosity using the Einstein relation with 6 start points separated by 0.2 ps 61: [ OK ] ViscosityTest.EinsteinViscosityDefaultArguments (137 ms) 61: [----------] 3 tests from ViscosityTest (440 ms total) 61: 61: [----------] Global test environment tear-down 61: [==========] 12 tests from 5 test suites ran. (475 ms total) 61: [ PASSED ] 12 tests. 61/94 Test #61: EnergyAnalysisUnitTests ...................... Passed 0.89 sec test 62 Start 62: ToolUnitTests 62: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/tool-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/ToolUnitTests.xml" 62: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests 62: Test timeout computed to be: 1920 62: [==========] Running 63 tests from 8 test suites. 62: [----------] Global test environment set-up. 62: [----------] 2 tests from DumpTest 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file lysozyme.top, line 1465]: 62: System has non-zero total charge: 2.000000 62: Total charge should normally be an integer. See 62: https://manual.gromacs.org/current/user-guide/floating-point.html 62: for discussion on how close it should be to an integer. 62: 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 465.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 NOTEs 62: Setting the LD random seed to 1792881851 62: 62: Generated 330891 of the 330891 non-bonded parameter combinations 62: 62: Generated 330891 of the 330891 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 62: Analysing residue names: 62: There are: 10 Protein residues 62: Analysing Protein... 62: 62: This run will generate roughly 0 Mb of data 62: [ RUN ] DumpTest.WorksWithTpr 62: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 62: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr: 62: inputrec: 62: integrator = md 62: tinit = 0 62: dt = 0.001 62: nsteps = 0 62: init-step = 0 62: simulation-part = 1 62: mts = false 62: mass-repartition-factor = 1 62: comm-mode = Linear 62: nstcomm = 100 62: bd-fric = 0 62: ld-seed = 1792881851 62: emtol = 10 62: emstep = 0.01 62: niter = 20 62: fcstep = 0 62: nstcgsteep = 1000 62: nbfgscorr = 10 62: rtpi = 0.05 62: nstxout = 0 62: nstvout = 0 62: nstfout = 0 62: nstlog = 1000 62: nstcalcenergy = 100 62: nstenergy = 1000 62: nstxout-compressed = 0 62: compressed-x-precision = 1000 62: cutoff-scheme = Verlet 62: nstlist = 10 62: pbc = xyz 62: periodic-molecules = false 62: verlet-buffer-tolerance = -1 62: verlet-buffer-pressure-tolerance = 0.5 62: rlist = 1.1 62: coulombtype = Cut-off 62: coulomb-modifier = Potential-shift 62: rcoulomb-switch = 0 62: rcoulomb = 1 62: epsilon-r = 1 62: epsilon-rf = inf 62: vdw-type = Cut-off 62: vdw-modifier = Potential-shift 62: rvdw-switch = 0 62: rvdw = 1 62: DispCorr = No 62: table-extension = 1 62: fourierspacing = 0.12 62: fourier-nx = 0 62: fourier-ny = 0 62: fourier-nz = 0 62: pme-order = 4 62: ewald-rtol = 1e-05 62: ewald-rtol-lj = 0.001 62: lj-pme-comb-rule = Geometric 62: ewald-geometry = 3d 62: epsilon-surface = 0 62: ensemble-temperature-setting = not available 62: tcoupl = No 62: nsttcouple = -1 62: nh-chain-length = 0 62: print-nose-hoover-chain-variables = false 62: pcoupl = No 62: refcoord-scaling = No 62: posres-com: not available 62: posres-comB: not available 62: QMMM = false 62: qm-opts: 62: ngQM = 0 62: constraint-algorithm = Lincs 62: continuation = false 62: Shake-SOR = false 62: shake-tol = 0.0001 62: lincs-order = 4 62: lincs-iter = 1 62: lincs-warnangle = 30 62: nwall = 0 62: wall-type = 9-3 62: wall-r-linpot = -1 62: wall-atomtype[0] = -1 62: wall-atomtype[1] = -1 62: wall-density[0] = 0 62: wall-density[1] = 0 62: wall-ewald-zfac = 3 62: pull = false 62: awh = false 62: rotation = false 62: interactiveMD = false 62: disre = No 62: disre-weighting = Conservative 62: disre-mixed = false 62: dr-fc = 1000 62: dr-tau = 0 62: nstdisreout = 100 62: orire-fc = 0 62: orire-tau = 0 62: nstorireout = 100 62: free-energy = no 62: cos-acceleration = 0 62: deform (3x3): 62: deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: simulated-tempering = false 62: swapcoords = no 62: userint1 = 0 62: userint2 = 0 62: userint3 = 0 62: userint4 = 0 62: userreal1 = 0 62: userreal2 = 0 62: userreal3 = 0 62: userreal4 = 0 62: applied-forces: 62: electric-field: 62: x: 62: E0 = 0 62: omega = 0 62: t0 = 0 62: sigma = 0 62: y: 62: E0 = 0 62: omega = 0 62: t0 = 0 62: sigma = 0 62: z: 62: E0 = 0 62: omega = 0 62: t0 = 0 62: sigma = 0 62: density-guided-simulation: 62: active = false 62: group = protein 62: similarity-measure = inner-product 62: atom-spreading-weight = unity 62: force-constant = 1e+09 62: gaussian-transform-spreading-width = 0.2 62: gaussian-transform-spreading-range-in-multiples-of-width = 4 62: reference-density-filename = reference.mrc 62: nst = 1 62: normalize-densities = true 62: adaptive-force-scaling = false 62: adaptive-force-scaling-time-constant = 4 62: shift-vector = 62: transformation-matrix = 62: qmmm-cp2k: 62: active = false 62: qmgroup = System 62: qmmethod = PBE 62: qmfilenames = 62: qmcharge = 0 62: qmmultiplicity = 1 62: colvars: 62: active = false 62: configfile = 62: seed = -1 62: nnpot: 62: active = false 62: modelfile = model.pt 62: input-group = System 62: model-input1 = 62: model-input2 = 62: model-input3 = 62: model-input4 = 62: grpopts: 62: nrdf: 465 62: ref-t: 0 62: tau-t: 0 62: annealing: No 62: annealing-npoints: 0 62: acc: 0 0 0 62: nfreeze: N N N 62: energygrp-flags[ 0]: 0 62: header: 62: bIr = present 62: bBox = present 62: bTop = present 62: bX = present 62: bV = present 62: bF = not present 62: natoms = 156 62: lambda = 0.000000e+00 62: buffer size = 46382 62: topology: 62: name="First 10 residues from 1AKI" 62: #atoms = 156 62: #molblock = 1 62: molblock (0): 62: moltype = 0 "Protein_chain_B" 62: #molecules = 1 62: #posres_xA = 0 62: #posres_xB = 0 62: bIntermolecularInteractions = false 62: ffparams: 62: atnr=10 62: ntypes=212 62: functype[0]=LJ_SR, c6= 3.35274590e-03, c12= 3.95094276e-06 62: functype[1]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[2]=LJ_SR, c6= 2.60916958e-03, c12= 3.84022405e-06 62: functype[3]=LJ_SR, c6= 6.41072227e-04, c12= 3.43856414e-07 62: functype[4]=LJ_SR, c6= 4.04775795e-03, c12= 7.32754188e-06 62: functype[5]=LJ_SR, c6= 2.81521026e-03, c12= 2.50631660e-06 62: functype[6]=LJ_SR, c6= 2.80388421e-03, c12= 4.30620821e-06 62: functype[7]=LJ_SR, c6= 5.81477652e-04, c12= 2.82897616e-07 62: functype[8]=LJ_SR, c6= 6.03335386e-04, c12= 2.35915493e-07 62: functype[9]=LJ_SR, c6= 7.20490469e-03, c12= 1.15394714e-05 62: functype[10]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[11]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[12]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[13]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[14]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[15]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[16]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[17]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[18]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[19]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[20]=LJ_SR, c6= 2.60916958e-03, c12= 3.84022405e-06 62: functype[21]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[22]=LJ_SR, c6= 2.03050394e-03, c12= 3.73260514e-06 62: functype[23]=LJ_SR, c6= 4.98894195e-04, c12= 3.34220175e-07 62: functype[24]=LJ_SR, c6= 3.15004122e-03, c12= 7.12220026e-06 62: functype[25]=LJ_SR, c6= 2.19085021e-03, c12= 2.43608270e-06 62: functype[26]=LJ_SR, c6= 2.18203571e-03, c12= 4.18553600e-06 62: functype[27]=LJ_SR, c6= 4.52516542e-04, c12= 2.74969580e-07 62: functype[28]=LJ_SR, c6= 4.69526683e-04, c12= 2.29304163e-07 62: functype[29]=LJ_SR, c6= 5.60698984e-03, c12= 1.12160897e-05 62: functype[30]=LJ_SR, c6= 6.41072227e-04, c12= 3.43856414e-07 62: functype[31]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[32]=LJ_SR, c6= 4.98894195e-04, c12= 3.34220175e-07 62: functype[33]=LJ_SR, c6= 1.22578131e-04, c12= 2.99263014e-08 62: functype[34]=LJ_SR, c6= 7.73964217e-04, c12= 6.37726998e-07 62: functype[35]=LJ_SR, c6= 5.38290828e-04, c12= 2.18128321e-07 62: functype[36]=LJ_SR, c6= 5.36125386e-04, c12= 3.74775709e-07 62: functype[37]=LJ_SR, c6= 1.11183173e-04, c12= 2.46209719e-08 62: functype[38]=LJ_SR, c6= 1.15362534e-04, c12= 2.05320472e-08 62: functype[39]=LJ_SR, c6= 1.37763575e-03, c12= 1.00429668e-06 62: functype[40]=LJ_SR, c6= 4.04775795e-03, c12= 7.32754188e-06 62: functype[41]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[42]=LJ_SR, c6= 3.15004122e-03, c12= 7.12220026e-06 62: functype[43]=LJ_SR, c6= 7.73964217e-04, c12= 6.37726998e-07 62: functype[44]=LJ_SR, c6= 4.88684513e-03, c12= 1.35898972e-05 62: functype[45]=LJ_SR, c6= 3.39879468e-03, c12= 4.64829736e-06 62: functype[46]=LJ_SR, c6= 3.38512054e-03, c12= 7.98643487e-06 62: functype[47]=LJ_SR, c6= 7.02015939e-04, c12= 5.24670895e-07 62: functype[48]=LJ_SR, c6= 7.28404266e-04, c12= 4.37535846e-07 62: functype[49]=LJ_SR, c6= 8.69845692e-03, c12= 2.14014708e-05 62: functype[50]=LJ_SR, c6= 2.81521026e-03, c12= 2.50631660e-06 62: functype[51]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[52]=LJ_SR, c6= 2.19085021e-03, c12= 2.43608270e-06 62: functype[53]=LJ_SR, c6= 5.38290828e-04, c12= 2.18128321e-07 62: functype[54]=LJ_SR, c6= 3.39879468e-03, c12= 4.64829736e-06 62: functype[55]=LJ_SR, c6= 2.36385735e-03, c12= 1.58990645e-06 62: functype[56]=LJ_SR, c6= 2.35434738e-03, c12= 2.73168575e-06 62: functype[57]=LJ_SR, c6= 4.88250953e-04, c12= 1.79458596e-07 62: functype[58]=LJ_SR, c6= 5.06604381e-04, c12= 1.49655136e-07 62: functype[59]=LJ_SR, c6= 6.04976481e-03, c12= 7.32016997e-06 62: functype[60]=LJ_SR, c6= 2.80388421e-03, c12= 4.30620821e-06 62: functype[61]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[62]=LJ_SR, c6= 2.18203571e-03, c12= 4.18553600e-06 62: functype[63]=LJ_SR, c6= 5.36125386e-04, c12= 3.74775709e-07 62: functype[64]=LJ_SR, c6= 3.38512054e-03, c12= 7.98643487e-06 62: functype[65]=LJ_SR, c6= 2.35434738e-03, c12= 2.73168575e-06 62: functype[66]=LJ_SR, c6= 2.34487536e-03, c12= 4.69342376e-06 62: functype[67]=LJ_SR, c6= 4.86286852e-04, c12= 3.08335643e-07 62: functype[68]=LJ_SR, c6= 5.04566357e-04, c12= 2.57128875e-07 62: functype[69]=LJ_SR, c6= 6.02542516e-03, c12= 1.25770912e-05 62: functype[70]=LJ_SR, c6= 5.81477652e-04, c12= 2.82897616e-07 62: functype[71]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[72]=LJ_SR, c6= 4.52516542e-04, c12= 2.74969580e-07 62: functype[73]=LJ_SR, c6= 1.11183173e-04, c12= 2.46209719e-08 62: functype[74]=LJ_SR, c6= 7.02015939e-04, c12= 5.24670895e-07 62: functype[75]=LJ_SR, c6= 4.88250953e-04, c12= 1.79458596e-07 62: functype[76]=LJ_SR, c6= 4.86286852e-04, c12= 3.08335643e-07 62: functype[77]=LJ_SR, c6= 1.00847494e-04, c12= 2.02561683e-08 62: functype[78]=LJ_SR, c6= 1.04638377e-04, c12= 1.68921392e-08 62: functype[79]=LJ_SR, c6= 1.24956947e-03, c12= 8.26254961e-07 62: functype[80]=LJ_SR, c6= 6.03335386e-04, c12= 2.35915493e-07 62: functype[81]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[82]=LJ_SR, c6= 4.69526683e-04, c12= 2.29304163e-07 62: functype[83]=LJ_SR, c6= 1.15362534e-04, c12= 2.05320472e-08 62: functype[84]=LJ_SR, c6= 7.28404266e-04, c12= 4.37535846e-07 62: functype[85]=LJ_SR, c6= 5.06604381e-04, c12= 1.49655136e-07 62: functype[86]=LJ_SR, c6= 5.04566357e-04, c12= 2.57128875e-07 62: functype[87]=LJ_SR, c6= 1.04638377e-04, c12= 1.68921392e-08 62: functype[88]=LJ_SR, c6= 1.08571716e-04, c12= 1.40867806e-08 62: functype[89]=LJ_SR, c6= 1.29654107e-03, c12= 6.89035176e-07 62: functype[90]=LJ_SR, c6= 7.20490469e-03, c12= 1.15394714e-05 62: functype[91]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 62: functype[92]=LJ_SR, c6= 5.60698984e-03, c12= 1.12160897e-05 62: functype[93]=LJ_SR, c6= 1.37763575e-03, c12= 1.00429668e-06 62: functype[94]=LJ_SR, c6= 8.69845692e-03, c12= 2.14014708e-05 62: functype[95]=LJ_SR, c6= 6.04976481e-03, c12= 7.32016997e-06 62: functype[96]=LJ_SR, c6= 6.02542516e-03, c12= 1.25770912e-05 62: functype[97]=LJ_SR, c6= 1.24956947e-03, 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2.65266e+05 62: functype[109]=BONDS, b0A= 1.40000e-01, cbA= 3.92459e+05, b0B= 1.40000e-01, cbB= 3.92459e+05 62: functype[110]=BONDS, b0A= 1.08000e-01, cbA= 3.07106e+05, b0B= 1.08000e-01, cbB= 3.07106e+05 62: functype[111]=BONDS, b0A= 1.46300e-01, cbA= 2.82002e+05, b0B= 1.46300e-01, cbB= 2.82002e+05 62: functype[112]=BONDS, b0A= 1.34000e-01, cbA= 4.02501e+05, b0B= 1.34000e-01, cbB= 4.02501e+05 62: functype[113]=BONDS, b0A= 1.81000e-01, cbA= 1.85770e+05, b0B= 1.81000e-01, cbB= 1.85770e+05 62: functype[114]=BONDS, b0A= 1.33600e-01, cbA= 2.29283e+05, b0B= 1.33600e-01, cbB= 2.29283e+05 62: functype[115]=BONDS, b0A= 1.25000e-01, cbA= 5.48941e+05, b0B= 1.25000e-01, cbB= 5.48941e+05 62: functype[116]=ANGLES, thA= 1.09500e+02, ctA= 2.92880e+02, thB= 1.09500e+02, ctB= 2.92880e+02 62: functype[117]=ANGLES, thA= 1.11200e+02, ctA= 6.69440e+02, thB= 1.11200e+02, ctB= 6.69440e+02 62: functype[118]=ANGLES, thA= 1.10700e+02, ctA= 3.13800e+02, thB= 1.10700e+02, ctB= 3.13800e+02 62: functype[119]=ANGLES, thA= 1.11100e+02, ctA= 5.27184e+02, thB= 1.11100e+02, ctB= 5.27184e+02 62: functype[120]=ANGLES, thA= 1.12700e+02, ctA= 4.88273e+02, thB= 1.12700e+02, ctB= 4.88273e+02 62: functype[121]=ANGLES, thA= 1.07800e+02, ctA= 2.76144e+02, thB= 1.07800e+02, ctB= 2.76144e+02 62: functype[122]=ANGLES, thA= 1.20400e+02, ctA= 6.69440e+02, thB= 1.20400e+02, ctB= 6.69440e+02 62: functype[123]=ANGLES, thA= 1.16600e+02, ctA= 5.85760e+02, thB= 1.16600e+02, ctB= 5.85760e+02 62: functype[124]=ANGLES, thA= 1.22900e+02, ctA= 6.69440e+02, thB= 1.22900e+02, ctB= 6.69440e+02 62: functype[125]=ANGLES, thA= 1.19800e+02, ctA= 2.92880e+02, thB= 1.19800e+02, ctB= 2.92880e+02 62: functype[126]=ANGLES, thA= 1.21900e+02, ctA= 4.18400e+02, thB= 1.21900e+02, ctB= 4.18400e+02 62: functype[127]=ANGLES, thA= 1.18400e+02, ctA= 3.17984e+02, thB= 1.18400e+02, ctB= 3.17984e+02 62: functype[128]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09700e+02, ctB= 6.69440e+02 62: functype[129]=ANGLES, thA= 1.10100e+02, ctA= 5.27184e+02, thB= 1.10100e+02, ctB= 5.27184e+02 62: functype[130]=ANGLES, thA= 1.14000e+02, ctA= 5.27184e+02, thB= 1.14000e+02, ctB= 5.27184e+02 62: functype[131]=ANGLES, thA= 1.20000e+02, ctA= 5.85760e+02, thB= 1.20000e+02, ctB= 5.85760e+02 62: functype[132]=ANGLES, thA= 1.20000e+02, ctA= 5.27184e+02, thB= 1.20000e+02, ctB= 5.27184e+02 62: functype[133]=ANGLES, thA= 1.20000e+02, ctA= 2.92880e+02, thB= 1.20000e+02, ctB= 2.92880e+02 62: functype[134]=ANGLES, thA= 1.18400e+02, ctA= 2.92880e+02, thB= 1.18400e+02, ctB= 2.92880e+02 62: functype[135]=ANGLES, thA= 1.23200e+02, ctA= 4.18400e+02, thB= 1.23200e+02, ctB= 4.18400e+02 62: functype[136]=ANGLES, thA= 1.08600e+02, ctA= 4.18400e+02, thB= 1.08600e+02, ctB= 4.18400e+02 62: functype[137]=ANGLES, thA= 9.60000e+01, ctA= 3.68192e+02, thB= 9.60000e+01, ctB= 3.68192e+02 62: functype[138]=ANGLES, thA= 1.17000e+02, ctA= 5.85760e+02, thB= 1.17000e+02, ctB= 5.85760e+02 62: functype[139]=ANGLES, thA= 1.26000e+02, ctA= 6.69440e+02, thB= 1.26000e+02, ctB= 6.69440e+02 62: functype[140]=PDIHS, phiA= 1.80000000e+02, cpA= 4.39319992e+01, phiB= 1.80000000e+02, cpB= 4.39319992e+01, mult=2 62: functype[141]=PDIHS, phiA= 1.80000000e+02, cpA= 4.18400002e+00, phiB= 1.80000000e+02, cpB= 4.18400002e+00, mult=2 62: functype[142]=PDIHS, phiA= 1.80000000e+02, cpA= 4.60239983e+00, phiB= 1.80000000e+02, cpB= 4.60239983e+00, mult=2 62: functype[143]=RBDIHS, rbcA[0]= 5.46010017e-01, rbcA[1]= 1.63803005e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.18405008e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 5.46010017e-01, rbcB[1]= 1.63803005e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.18405008e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[144]=RBDIHS, rbcA[0]= 7.25920022e-01, rbcA[1]= 2.17776990e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.90370011e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 7.25920022e-01, rbcB[1]= 2.17776990e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.90370011e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[145]=RBDIHS, rbcA[0]= 1.27611995e+00, rbcA[1]= 1.16734004e+00, rbcA[2]= 8.95380020e-01, rbcA[3]=-3.33884001e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 1.27611995e+00, rbcB[1]= 1.16734004e+00, rbcB[2]= 8.95380020e-01, rbcB[3]=-3.33884001e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[146]=RBDIHS, rbcA[0]=-6.91824007e+00, rbcA[1]= 4.67562008e+00, rbcA[2]= 2.24261999e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-6.91824007e+00, rbcB[1]= 4.67562008e+00, rbcB[2]= 2.24261999e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[147]=RBDIHS, rbcA[0]= 9.70690012e-01, rbcA[1]= 2.91206002e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.88275003e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 9.70690012e-01, rbcB[1]= 2.91206002e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.88275003e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[148]=RBDIHS, rbcA[0]= 6.27600014e-01, rbcA[1]= 1.88279998e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.51040006e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 6.27600014e-01, rbcB[1]= 1.88279998e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.51040006e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[149]=RBDIHS, rbcA[0]=-1.58989996e-01, rbcA[1]=-4.76980001e-01, rbcA[2]= 0.00000000e+00, rbcA[3]= 6.35959983e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-1.58989996e-01, rbcB[1]=-4.76980001e-01, rbcB[2]= 0.00000000e+00, rbcB[3]= 6.35959983e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[150]=RBDIHS, rbcA[0]= 1.03637600e+01, rbcA[1]=-6.60654020e+00, rbcA[2]=-1.04934702e+01, rbcA[3]= 6.73623991e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 1.03637600e+01, rbcB[1]=-6.60654020e+00, rbcB[2]=-1.04934702e+01, rbcB[3]= 6.73623991e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[151]=RBDIHS, rbcA[0]= 5.00825024e+00, rbcA[1]=-1.69869995e+00, rbcA[2]=-3.72379988e-01, rbcA[3]=-2.93716002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 5.00825024e+00, rbcB[1]=-1.69869995e+00, rbcB[2]=-3.72379988e-01, rbcB[3]=-2.93716002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[152]=RBDIHS, rbcA[0]= 2.92880011e+00, rbcA[1]=-1.46440005e+00, rbcA[2]= 2.09199995e-01, rbcA[3]=-1.67359996e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 2.92880011e+00, rbcB[1]=-1.46440005e+00, rbcB[2]= 2.09199995e-01, rbcB[3]=-1.67359996e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[153]=RBDIHS, rbcA[0]= 5.77183008e+00, rbcA[1]=-2.67147994e+00, rbcA[2]= 9.58140016e-01, rbcA[3]=-4.05847979e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 5.77183008e+00, rbcB[1]=-2.67147994e+00, rbcB[2]= 9.58140016e-01, rbcB[3]=-4.05847979e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[154]=RBDIHS, rbcA[0]= 8.03330004e-01, rbcA[1]= 2.40999007e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.21331000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 8.03330004e-01, rbcB[1]= 2.40999007e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.21331000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[155]=RBDIHS, rbcA[0]= 2.05016003e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.05016003e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 2.05016003e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.05016003e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[156]=RBDIHS, rbcA[0]= 3.02879791e+01, rbcA[1]=-4.81160021e+00, rbcA[2]=-2.54763794e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 3.02879791e+01, rbcB[1]=-4.81160021e+00, rbcB[2]=-2.54763794e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[157]=RBDIHS, rbcA[0]= 2.54763794e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.54763794e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 2.54763794e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.54763794e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[158]=RBDIHS, rbcA[0]= 1.57025499e+01, rbcA[1]= 3.17565594e+01, rbcA[2]=-3.66935992e+00, rbcA[3]=-4.37897491e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 1.57025499e+01, rbcB[1]= 3.17565594e+01, rbcB[2]=-3.66935992e+00, rbcB[3]=-4.37897491e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[159]=RBDIHS, rbcA[0]=-1.03574896e+01, rbcA[1]=-2.95871601e+01, rbcA[2]=-1.16734004e+00, rbcA[3]= 4.11119919e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-1.03574896e+01, rbcB[1]=-2.95871601e+01, rbcB[2]=-1.16734004e+00, rbcB[3]= 4.11119919e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[160]=RBDIHS, rbcA[0]= 4.50198984e+00, rbcA[1]= 7.82410026e-01, rbcA[2]=-1.60247004e+00, rbcA[3]=-3.68192005e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 4.50198984e+00, rbcB[1]= 7.82410026e-01, rbcB[2]=-1.60247004e+00, rbcB[3]=-3.68192005e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[161]=RBDIHS, rbcA[0]= 4.22589988e-01, rbcA[1]= 2.70705009e+00, rbcA[2]=-3.12964010e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 4.22589988e-01, rbcB[1]= 2.70705009e+00, rbcB[2]=-3.12964010e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[162]=RBDIHS, rbcA[0]=-7.65670002e-01, rbcA[1]= 2.70705009e+00, rbcA[2]= 4.02501011e+00, rbcA[3]=-5.96639013e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-7.65670002e-01, rbcB[1]= 2.70705009e+00, rbcB[2]= 4.02501011e+00, rbcB[3]=-5.96639013e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[163]=RBDIHS, rbcA[0]= 9.66499984e-01, rbcA[1]= 2.89950991e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.86600995e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 9.66499984e-01, rbcB[1]= 2.89950991e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.86600995e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[164]=RBDIHS, rbcA[0]=-4.23421001e+00, rbcA[1]= 7.22159004e+00, rbcA[2]= 1.90789998e+00, rbcA[3]=-4.89527988e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-4.23421001e+00, rbcB[1]= 7.22159004e+00, rbcB[2]= 1.90789998e+00, rbcB[3]=-4.89527988e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[165]=RBDIHS, rbcA[0]= 3.03339996e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.03339996e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 3.03339996e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.03339996e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[166]=RBDIHS, rbcA[0]= 1.02319698e+01, rbcA[1]= 3.52082992e+00, rbcA[2]=-3.97899008e+00, rbcA[3]=-9.77381992e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 1.02319698e+01, rbcB[1]= 3.52082992e+00, rbcB[2]=-3.97899008e+00, rbcB[3]=-9.77381992e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[167]=RBDIHS, rbcA[0]= 5.49777985e+00, rbcA[1]= 1.41838002e+00, rbcA[2]=-6.91615009e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 5.49777985e+00, rbcB[1]= 1.41838002e+00, rbcB[2]=-6.91615009e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[168]=RBDIHS, rbcA[0]=-1.21755004e+00, rbcA[1]=-3.65264010e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 4.87018013e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-1.21755004e+00, rbcB[1]=-3.65264010e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 4.87018013e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[169]=RBDIHS, rbcA[0]=-1.26775002e+00, rbcA[1]= 3.02084994e+00, rbcA[2]= 1.74473000e+00, rbcA[3]=-3.49781990e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-1.26775002e+00, rbcB[1]= 3.02084994e+00, rbcB[2]= 1.74473000e+00, rbcB[3]=-3.49781990e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[170]=RBDIHS, rbcA[0]= 3.80117011e+00, rbcA[1]=-6.95172024e+00, rbcA[2]=-1.01671004e+00, rbcA[3]= 4.16726017e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 3.80117011e+00, rbcB[1]=-6.95172024e+00, rbcB[2]=-1.01671004e+00, rbcB[3]= 4.16726017e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[171]=RBDIHS, rbcA[0]= 3.70279998e-01, rbcA[1]= 1.11085999e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-1.48114002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 3.70279998e-01, rbcB[1]= 1.11085999e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-1.48114002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[172]=RBDIHS, rbcA[0]= 3.32042198e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.32042198e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 3.32042198e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.32042198e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[173]=RBDIHS, rbcA[0]= 1.63176003e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-1.63176003e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 1.63176003e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-1.63176003e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[174]=RBDIHS, rbcA[0]= 3.40787005e+00, rbcA[1]=-2.80537009e+00, rbcA[2]=-3.59820008e-01, rbcA[3]=-2.42670000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 3.40787005e+00, rbcB[1]=-2.80537009e+00, rbcB[2]=-3.59820008e-01, rbcB[3]=-2.42670000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[175]=RBDIHS, rbcA[0]=-1.62590199e+01, rbcA[1]= 9.08765030e+00, rbcA[2]= 7.17138004e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-1.62590199e+01, rbcB[1]= 9.08765030e+00, rbcB[2]= 7.17138004e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[176]=RBDIHS, rbcA[0]= 9.45590019e-01, rbcA[1]= 2.83675003e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.78234005e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 9.45590019e-01, rbcB[1]= 2.83675003e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.78234005e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[177]=RBDIHS, rbcA[0]=-1.50624001e+00, rbcA[1]= 5.37225008e+00, rbcA[2]= 1.17989004e+00, rbcA[3]=-5.04589987e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-1.50624001e+00, rbcB[1]= 5.37225008e+00, rbcB[2]= 1.17989004e+00, rbcB[3]=-5.04589987e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[178]=RBDIHS, rbcA[0]= 1.00416005e+00, rbcA[1]= 3.01248002e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-4.01664019e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 1.00416005e+00, rbcB[1]= 3.01248002e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-4.01664019e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[179]=RBDIHS, rbcA[0]= 8.79267979e+00, rbcA[1]=-1.18344402e+01, rbcA[2]= 1.07528996e+00, rbcA[3]= 1.96648002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 8.79267979e+00, rbcB[1]=-1.18344402e+01, rbcB[2]= 1.07528996e+00, rbcB[3]= 1.96648002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[180]=RBDIHS, rbcA[0]=-5.77392006e+00, rbcA[1]= 3.38485003e+00, rbcA[2]= 2.38906002e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-5.77392006e+00, rbcB[1]= 3.38485003e+00, rbcB[2]= 2.38906002e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[181]=RBDIHS, rbcA[0]=-9.08345985e+00, rbcA[1]= 9.75708961e+00, rbcA[2]= 3.45180011e+00, rbcA[3]=-4.12542009e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-9.08345985e+00, rbcB[1]= 9.75708961e+00, rbcB[2]= 3.45180011e+00, rbcB[3]=-4.12542009e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[182]=RBDIHS, rbcA[0]=-4.70699996e-01, rbcA[1]=-1.41209996e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 1.88279998e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-4.70699996e-01, rbcB[1]=-1.41209996e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 1.88279998e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[183]=RBDIHS, rbcA[0]= 3.43088007e+00, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.43088007e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 3.43088007e+00, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.43088007e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[184]=RBDIHS, rbcA[0]= 2.57315993e+00, rbcA[1]= 3.49781990e+00, rbcA[2]=-1.10038996e+00, rbcA[3]=-4.97059011e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]= 2.57315993e+00, rbcB[1]= 3.49781990e+00, rbcB[2]=-1.10038996e+00, rbcB[3]=-4.97059011e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[185]=RBDIHS, rbcA[0]=-8.22160006e-01, rbcA[1]= 1.12758994e+00, rbcA[2]=-3.05440009e-01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 62: rbcB[0]=-8.22160006e-01, rbcB[1]= 1.12758994e+00, rbcB[2]=-3.05440009e-01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 62: functype[186]=LJ14, c6A= 3.20536114e-04, c12A= 1.71928207e-07, c6B= 3.20536114e-04, c12B= 1.71928207e-07 62: functype[187]=LJ14, c6A= 1.30458479e-03, c12A= 1.92011203e-06, c6B= 1.30458479e-03, c12B= 1.92011203e-06 62: functype[188]=LJ14, c6A= 1.40760513e-03, c12A= 1.25315830e-06, c6B= 1.40760513e-03, c12B= 1.25315830e-06 62: functype[189]=LJ14, c6A= 1.67637295e-03, c12A= 1.97547138e-06, c6B= 1.67637295e-03, c12B= 1.97547138e-06 62: functype[190]=LJ14, c6A= 0.00000000e+00, c12A= 0.00000000e+00, c6B= 0.00000000e+00, c12B= 0.00000000e+00 62: functype[191]=LJ14, c6A= 2.49447097e-04, c12A= 1.67110088e-07, c6B= 2.49447097e-04, c12B= 1.67110088e-07 62: functype[192]=LJ14, c6A= 1.01525197e-03, c12A= 1.86630257e-06, c6B= 1.01525197e-03, c12B= 1.86630257e-06 62: functype[193]=LJ14, c6A= 6.12890653e-05, c12A= 1.49631507e-08, c6B= 6.12890653e-05, c12B= 1.49631507e-08 62: functype[194]=LJ14, c6A= 2.69145414e-04, c12A= 1.09064160e-07, c6B= 2.69145414e-04, c12B= 1.09064160e-07 62: functype[195]=LJ14, c6A= 1.09542510e-03, c12A= 1.21804135e-06, c6B= 1.09542510e-03, c12B= 1.21804135e-06 62: functype[196]=LJ14, c6A= 3.86982108e-04, c12A= 3.18863499e-07, c6B= 3.86982108e-04, c12B= 3.18863499e-07 62: functype[197]=LJ14, c6A= 1.57502061e-03, c12A= 3.56110013e-06, c6B= 1.57502061e-03, c12B= 3.56110013e-06 62: functype[198]=LJ14, c6A= 2.44342256e-03, c12A= 6.79494860e-06, c6B= 2.44342256e-03, c12B= 6.79494860e-06 62: functype[199]=LJ14, c6A= 1.40194211e-03, c12A= 2.15310411e-06, c6B= 1.40194211e-03, c12B= 2.15310411e-06 62: functype[200]=LJ14, c6A= 1.09101785e-03, c12A= 2.09276800e-06, c6B= 1.09101785e-03, c12B= 2.09276800e-06 62: functype[201]=LJ14, c6A= 2.68062693e-04, c12A= 1.87387855e-07, c6B= 2.68062693e-04, c12B= 1.87387855e-07 62: functype[202]=LJ14, c6A= 2.26258271e-04, c12A= 1.37484790e-07, c6B= 2.26258271e-04, c12B= 1.37484790e-07 62: functype[203]=LJ14, c6A= 2.43143426e-04, c12A= 1.54167822e-07, c6B= 2.43143426e-04, c12B= 1.54167822e-07 62: functype[204]=LJ14, c6A= 1.17243768e-03, c12A= 2.34671188e-06, c6B= 1.17243768e-03, c12B= 2.34671188e-06 62: functype[205]=LJ14, c6A= 1.69256027e-03, c12A= 3.99321743e-06, c6B= 1.69256027e-03, c12B= 3.99321743e-06 62: functype[206]=LJ14, c6A= 5.04237469e-05, c12A= 1.01280841e-08, c6B= 5.04237469e-05, c12B= 1.01280841e-08 62: functype[207]=LJ14, c6A= 2.34763342e-04, c12A= 1.14652082e-07, c6B= 2.34763342e-04, c12B= 1.14652082e-07 62: functype[208]=LJ14, c6A= 5.76812672e-05, c12A= 1.02660236e-08, c6B= 5.76812672e-05, c12B= 1.02660236e-08 62: functype[209]=LJ14, c6A= 3.60245234e-03, c12A= 5.76973571e-06, c6B= 3.60245234e-03, c12B= 5.76973571e-06 62: functype[210]=LJ14, c6A= 6.88817876e-04, c12A= 5.02148339e-07, c6B= 6.88817876e-04, c12B= 5.02148339e-07 62: functype[211]=LJ14, c6A= 4.34922846e-03, c12A= 1.07007354e-05, c6B= 4.34922846e-03, c12B= 1.07007354e-05 62: reppow = 12 62: fudgeQQ = 0.5 62: cmap 62: moltype (0): 62: name="Protein_chain_B" 62: atoms: 62: atom (156): 62: atom[ 0]={type= 0, typeB= 0, ptype= Atom, m= 1.40027e+01, q=-3.00000e-01, mB= 1.40027e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} 62: atom[ 1]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 62: atom[ 2]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 62: atom[ 3]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 62: atom[ 4]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 2.50000e-01, mB= 1.20110e+01, qB= 2.50000e-01, resind= 0, atomnumber= 6} 62: atom[ 5]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 62: atom[ 6]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 62: atom[ 7]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 62: atom[ 8]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 62: atom[ 9]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 62: atom[ 10]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 62: atom[ 11]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 62: atom[ 12]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 62: atom[ 13]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 62: atom[ 14]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 62: atom[ 15]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 0, atomnumber= 6} 62: atom[ 16]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 62: atom[ 17]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 62: atom[ 18]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-3.00000e-01, mB= 1.40067e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} 62: atom[ 19]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 62: atom[ 20]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 62: atom[ 21]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 62: atom[ 22]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 0, atomnumber= 6} 62: atom[ 23]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 0, atomnumber= 8} 62: atom[ 24]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 1, atomnumber= 7} 62: atom[ 25]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 1, atomnumber= 1} 62: atom[ 26]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 1, atomnumber= 6} 62: atom[ 27]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 62: atom[ 28]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 1, atomnumber= 6} 62: atom[ 29]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 62: atom[ 30]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} 62: atom[ 31]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 62: atom[ 32]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 62: atom[ 33]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 62: atom[ 34]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} 62: atom[ 35]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 62: atom[ 36]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 62: atom[ 37]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 62: atom[ 38]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 1, atomnumber= 6} 62: atom[ 39]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 1, atomnumber= 8} 62: atom[ 40]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 2, atomnumber= 7} 62: atom[ 41]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 2, atomnumber= 1} 62: atom[ 42]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 2, atomnumber= 6} 62: atom[ 43]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 62: atom[ 44]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-03, mB= 1.20110e+01, qB=-5.00000e-03, resind= 2, atomnumber= 6} 62: atom[ 45]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 62: atom[ 46]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 62: atom[ 47]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 62: atom[ 48]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 62: atom[ 49]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 62: atom[ 50]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 62: atom[ 51]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 62: atom[ 52]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 62: atom[ 53]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 62: atom[ 54]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 62: atom[ 55]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 62: atom[ 56]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 62: atom[ 57]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 62: atom[ 58]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 2, atomnumber= 6} 62: atom[ 59]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 2, atomnumber= 8} 62: atom[ 60]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 3, atomnumber= 7} 62: atom[ 61]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 3, atomnumber= 1} 62: atom[ 62]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 8.00000e-02, mB= 1.20110e+01, qB= 8.00000e-02, resind= 3, atomnumber= 6} 62: atom[ 63]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} 62: atom[ 64]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} 62: atom[ 65]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 3, atomnumber= 6} 62: atom[ 66]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 3, atomnumber= 8} 62: atom[ 67]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 4, atomnumber= 7} 62: atom[ 68]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 4, atomnumber= 1} 62: atom[ 69]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 4, atomnumber= 6} 62: atom[ 70]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 62: atom[ 71]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 4, atomnumber= 6} 62: atom[ 72]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 62: atom[ 73]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 62: atom[ 74]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-02, mB= 1.20110e+01, qB=-5.00000e-02, resind= 4, atomnumber= 6} 62: atom[ 75]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 62: atom[ 76]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 62: atom[ 77]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 4, atomnumber= 6} 62: atom[ 78]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 62: atom[ 79]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 62: atom[ 80]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-7.00000e-01, mB= 1.40067e+01, qB=-7.00000e-01, resind= 4, atomnumber= 7} 62: atom[ 81]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.40000e-01, mB= 1.00800e+00, qB= 4.40000e-01, resind= 4, atomnumber= 1} 62: atom[ 82]={type= 8, typeB= 8, ptype= Atom, m= 1.20110e+01, q= 6.40000e-01, mB= 1.20110e+01, qB= 6.40000e-01, resind= 4, atomnumber= 6} 62: atom[ 83]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} 62: atom[ 84]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 62: atom[ 85]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 62: atom[ 86]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} 62: atom[ 87]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 62: atom[ 88]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 62: atom[ 89]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 4, atomnumber= 6} 62: atom[ 90]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 4, atomnumber= 8} 62: atom[ 91]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 5, atomnumber= 7} 62: atom[ 92]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 5, atomnumber= 1} 62: atom[ 93]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 5, atomnumber= 6} 62: atom[ 94]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 62: atom[ 95]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 6.00000e-02, mB= 1.20110e+01, qB= 6.00000e-02, resind= 5, atomnumber= 6} 62: atom[ 96]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 62: atom[ 97]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 62: atom[ 98]={type= 9, typeB= 9, ptype= Atom, m= 3.20600e+01, q=-3.35000e-01, mB= 3.20600e+01, qB=-3.35000e-01, resind= 5, atomnumber= 16} 62: atom[ 99]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 1.55000e-01, mB= 1.00800e+00, qB= 1.55000e-01, resind= 5, atomnumber= 1} 62: atom[ 100]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 5, atomnumber= 6} 62: atom[ 101]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 5, atomnumber= 8} 62: atom[ 102]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 6, atomnumber= 7} 62: atom[ 103]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 6, atomnumber= 1} 62: atom[ 104]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 6, atomnumber= 6} 62: atom[ 105]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 62: atom[ 106]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 6, atomnumber= 6} 62: atom[ 107]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 62: atom[ 108]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 62: atom[ 109]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-2.20000e-01, mB= 1.20110e+01, qB=-2.20000e-01, resind= 6, atomnumber= 6} 62: atom[ 110]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 62: atom[ 111]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 62: atom[ 112]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 7.00000e-01, mB= 1.20110e+01, qB= 7.00000e-01, resind= 6, atomnumber= 6} 62: atom[ 113]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} 62: atom[ 114]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} 62: atom[ 115]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 6, atomnumber= 6} 62: atom[ 116]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 6, atomnumber= 8} 62: atom[ 117]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 7, atomnumber= 7} 62: atom[ 118]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 7, atomnumber= 1} 62: atom[ 119]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 7, atomnumber= 6} 62: atom[ 120]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 62: atom[ 121]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 7, atomnumber= 6} 62: atom[ 122]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 62: atom[ 123]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 62: atom[ 124]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 7, atomnumber= 6} 62: atom[ 125]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 62: atom[ 126]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} 62: atom[ 127]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 62: atom[ 128]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 62: atom[ 129]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 62: atom[ 130]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} 62: atom[ 131]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 62: atom[ 132]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 62: atom[ 133]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 62: atom[ 134]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 7, atomnumber= 6} 62: atom[ 135]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 7, atomnumber= 8} 62: atom[ 136]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 8, atomnumber= 7} 62: atom[ 137]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 8, atomnumber= 1} 62: atom[ 138]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 8, atomnumber= 6} 62: atom[ 139]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 62: atom[ 140]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 8, atomnumber= 6} 62: atom[ 141]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 62: atom[ 142]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 62: atom[ 143]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 62: atom[ 144]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 8, atomnumber= 6} 62: atom[ 145]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 8, atomnumber= 8} 62: atom[ 146]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 9, atomnumber= 7} 62: atom[ 147]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 9, atomnumber= 1} 62: atom[ 148]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 9, atomnumber= 6} 62: atom[ 149]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 62: atom[ 150]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 9, atomnumber= 6} 62: atom[ 151]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 62: atom[ 152]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 62: atom[ 153]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 62: atom[ 154]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 9, atomnumber= 6} 62: atom[ 155]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 9, atomnumber= 8} 62: atom (156): 62: atom[0]={name="N"} 62: atom[1]={name="H1"} 62: atom[2]={name="H2"} 62: atom[3]={name="H3"} 62: atom[4]={name="CA"} 62: atom[5]={name="HA"} 62: atom[6]={name="CB"} 62: atom[7]={name="HB1"} 62: atom[8]={name="HB2"} 62: atom[9]={name="CG"} 62: atom[10]={name="HG1"} 62: atom[11]={name="HG2"} 62: atom[12]={name="CD"} 62: atom[13]={name="HD1"} 62: atom[14]={name="HD2"} 62: atom[15]={name="CE"} 62: atom[16]={name="HE1"} 62: atom[17]={name="HE2"} 62: atom[18]={name="NZ"} 62: atom[19]={name="HZ1"} 62: atom[20]={name="HZ2"} 62: atom[21]={name="HZ3"} 62: atom[22]={name="C"} 62: atom[23]={name="O"} 62: atom[24]={name="N"} 62: atom[25]={name="H"} 62: atom[26]={name="CA"} 62: atom[27]={name="HA"} 62: atom[28]={name="CB"} 62: atom[29]={name="HB"} 62: atom[30]={name="CG1"} 62: atom[31]={name="HG11"} 62: atom[32]={name="HG12"} 62: atom[33]={name="HG13"} 62: atom[34]={name="CG2"} 62: atom[35]={name="HG21"} 62: atom[36]={name="HG22"} 62: atom[37]={name="HG23"} 62: atom[38]={name="C"} 62: atom[39]={name="O"} 62: atom[40]={name="N"} 62: atom[41]={name="H"} 62: atom[42]={name="CA"} 62: atom[43]={name="HA"} 62: atom[44]={name="CB"} 62: atom[45]={name="HB1"} 62: atom[46]={name="HB2"} 62: atom[47]={name="CG"} 62: atom[48]={name="CD1"} 62: atom[49]={name="HD1"} 62: atom[50]={name="CD2"} 62: atom[51]={name="HD2"} 62: atom[52]={name="CE1"} 62: atom[53]={name="HE1"} 62: atom[54]={name="CE2"} 62: atom[55]={name="HE2"} 62: atom[56]={name="CZ"} 62: atom[57]={name="HZ"} 62: atom[58]={name="C"} 62: atom[59]={name="O"} 62: atom[60]={name="N"} 62: atom[61]={name="H"} 62: atom[62]={name="CA"} 62: atom[63]={name="HA1"} 62: atom[64]={name="HA2"} 62: atom[65]={name="C"} 62: atom[66]={name="O"} 62: atom[67]={name="N"} 62: atom[68]={name="H"} 62: atom[69]={name="CA"} 62: atom[70]={name="HA"} 62: atom[71]={name="CB"} 62: atom[72]={name="HB1"} 62: atom[73]={name="HB2"} 62: atom[74]={name="CG"} 62: atom[75]={name="HG1"} 62: atom[76]={name="HG2"} 62: atom[77]={name="CD"} 62: atom[78]={name="HD1"} 62: atom[79]={name="HD2"} 62: atom[80]={name="NE"} 62: atom[81]={name="HE"} 62: atom[82]={name="CZ"} 62: atom[83]={name="NH1"} 62: atom[84]={name="HH11"} 62: atom[85]={name="HH12"} 62: atom[86]={name="NH2"} 62: atom[87]={name="HH21"} 62: atom[88]={name="HH22"} 62: atom[89]={name="C"} 62: atom[90]={name="O"} 62: atom[91]={name="N"} 62: atom[92]={name="H"} 62: atom[93]={name="CA"} 62: atom[94]={name="HA"} 62: atom[95]={name="CB"} 62: atom[96]={name="HB1"} 62: atom[97]={name="HB2"} 62: atom[98]={name="SG"} 62: atom[99]={name="HG"} 62: atom[100]={name="C"} 62: atom[101]={name="O"} 62: atom[102]={name="N"} 62: atom[103]={name="H"} 62: atom[104]={name="CA"} 62: atom[105]={name="HA"} 62: atom[106]={name="CB"} 62: atom[107]={name="HB1"} 62: atom[108]={name="HB2"} 62: atom[109]={name="CG"} 62: atom[110]={name="HG1"} 62: atom[111]={name="HG2"} 62: atom[112]={name="CD"} 62: atom[113]={name="OE1"} 62: atom[114]={name="OE2"} 62: atom[115]={name="C"} 62: atom[116]={name="O"} 62: atom[117]={name="N"} 62: atom[118]={name="H"} 62: atom[119]={name="CA"} 62: atom[120]={name="HA"} 62: atom[121]={name="CB"} 62: atom[122]={name="HB1"} 62: atom[123]={name="HB2"} 62: atom[124]={name="CG"} 62: atom[125]={name="HG"} 62: atom[126]={name="CD1"} 62: atom[127]={name="HD11"} 62: atom[128]={name="HD12"} 62: atom[129]={name="HD13"} 62: atom[130]={name="CD2"} 62: atom[131]={name="HD21"} 62: atom[132]={name="HD22"} 62: atom[133]={name="HD23"} 62: atom[134]={name="C"} 62: atom[135]={name="O"} 62: atom[136]={name="N"} 62: atom[137]={name="H"} 62: atom[138]={name="CA"} 62: atom[139]={name="HA"} 62: atom[140]={name="CB"} 62: atom[141]={name="HB1"} 62: atom[142]={name="HB2"} 62: atom[143]={name="HB3"} 62: atom[144]={name="C"} 62: atom[145]={name="O"} 62: atom[146]={name="N"} 62: atom[147]={name="H"} 62: atom[148]={name="CA"} 62: atom[149]={name="HA"} 62: atom[150]={name="CB"} 62: atom[151]={name="HB1"} 62: atom[152]={name="HB2"} 62: atom[153]={name="HB3"} 62: atom[154]={name="C"} 62: atom[155]={name="O"} 62: type (156): 62: type[0]={name="opls_287",nameB="opls_287"} 62: type[1]={name="opls_290",nameB="opls_290"} 62: type[2]={name="opls_290",nameB="opls_290"} 62: type[3]={name="opls_290",nameB="opls_290"} 62: type[4]={name="opls_293B",nameB="opls_293B"} 62: type[5]={name="opls_140",nameB="opls_140"} 62: type[6]={name="opls_136",nameB="opls_136"} 62: type[7]={name="opls_140",nameB="opls_140"} 62: type[8]={name="opls_140",nameB="opls_140"} 62: type[9]={name="opls_136",nameB="opls_136"} 62: type[10]={name="opls_140",nameB="opls_140"} 62: type[11]={name="opls_140",nameB="opls_140"} 62: type[12]={name="opls_136",nameB="opls_136"} 62: type[13]={name="opls_140",nameB="opls_140"} 62: type[14]={name="opls_140",nameB="opls_140"} 62: type[15]={name="opls_292",nameB="opls_292"} 62: type[16]={name="opls_140",nameB="opls_140"} 62: type[17]={name="opls_140",nameB="opls_140"} 62: type[18]={name="opls_287",nameB="opls_287"} 62: type[19]={name="opls_290",nameB="opls_290"} 62: type[20]={name="opls_290",nameB="opls_290"} 62: type[21]={name="opls_290",nameB="opls_290"} 62: type[22]={name="opls_235",nameB="opls_235"} 62: type[23]={name="opls_236",nameB="opls_236"} 62: type[24]={name="opls_238",nameB="opls_238"} 62: type[25]={name="opls_241",nameB="opls_241"} 62: type[26]={name="opls_224B",nameB="opls_224B"} 62: type[27]={name="opls_140",nameB="opls_140"} 62: type[28]={name="opls_137",nameB="opls_137"} 62: type[29]={name="opls_140",nameB="opls_140"} 62: type[30]={name="opls_135",nameB="opls_135"} 62: type[31]={name="opls_140",nameB="opls_140"} 62: type[32]={name="opls_140",nameB="opls_140"} 62: type[33]={name="opls_140",nameB="opls_140"} 62: type[34]={name="opls_135",nameB="opls_135"} 62: type[35]={name="opls_140",nameB="opls_140"} 62: type[36]={name="opls_140",nameB="opls_140"} 62: type[37]={name="opls_140",nameB="opls_140"} 62: type[38]={name="opls_235",nameB="opls_235"} 62: type[39]={name="opls_236",nameB="opls_236"} 62: type[40]={name="opls_238",nameB="opls_238"} 62: type[41]={name="opls_241",nameB="opls_241"} 62: type[42]={name="opls_224B",nameB="opls_224B"} 62: type[43]={name="opls_140",nameB="opls_140"} 62: type[44]={name="opls_149",nameB="opls_149"} 62: type[45]={name="opls_140",nameB="opls_140"} 62: type[46]={name="opls_140",nameB="opls_140"} 62: type[47]={name="opls_145",nameB="opls_145"} 62: type[48]={name="opls_145",nameB="opls_145"} 62: type[49]={name="opls_146",nameB="opls_146"} 62: type[50]={name="opls_145",nameB="opls_145"} 62: type[51]={name="opls_146",nameB="opls_146"} 62: type[52]={name="opls_145",nameB="opls_145"} 62: type[53]={name="opls_146",nameB="opls_146"} 62: type[54]={name="opls_145",nameB="opls_145"} 62: type[55]={name="opls_146",nameB="opls_146"} 62: type[56]={name="opls_145",nameB="opls_145"} 62: type[57]={name="opls_146",nameB="opls_146"} 62: type[58]={name="opls_235",nameB="opls_235"} 62: type[59]={name="opls_236",nameB="opls_236"} 62: type[60]={name="opls_238",nameB="opls_238"} 62: type[61]={name="opls_241",nameB="opls_241"} 62: type[62]={name="opls_223B",nameB="opls_223B"} 62: type[63]={name="opls_140",nameB="opls_140"} 62: type[64]={name="opls_140",nameB="opls_140"} 62: type[65]={name="opls_235",nameB="opls_235"} 62: type[66]={name="opls_236",nameB="opls_236"} 62: type[67]={name="opls_238",nameB="opls_238"} 62: type[68]={name="opls_241",nameB="opls_241"} 62: type[69]={name="opls_224B",nameB="opls_224B"} 62: type[70]={name="opls_140",nameB="opls_140"} 62: type[71]={name="opls_136",nameB="opls_136"} 62: type[72]={name="opls_140",nameB="opls_140"} 62: type[73]={name="opls_140",nameB="opls_140"} 62: type[74]={name="opls_308",nameB="opls_308"} 62: type[75]={name="opls_140",nameB="opls_140"} 62: type[76]={name="opls_140",nameB="opls_140"} 62: type[77]={name="opls_307",nameB="opls_307"} 62: type[78]={name="opls_140",nameB="opls_140"} 62: type[79]={name="opls_140",nameB="opls_140"} 62: type[80]={name="opls_303",nameB="opls_303"} 62: type[81]={name="opls_304",nameB="opls_304"} 62: type[82]={name="opls_302",nameB="opls_302"} 62: type[83]={name="opls_300",nameB="opls_300"} 62: type[84]={name="opls_301",nameB="opls_301"} 62: type[85]={name="opls_301",nameB="opls_301"} 62: type[86]={name="opls_300",nameB="opls_300"} 62: type[87]={name="opls_301",nameB="opls_301"} 62: type[88]={name="opls_301",nameB="opls_301"} 62: type[89]={name="opls_235",nameB="opls_235"} 62: type[90]={name="opls_236",nameB="opls_236"} 62: type[91]={name="opls_238",nameB="opls_238"} 62: type[92]={name="opls_241",nameB="opls_241"} 62: type[93]={name="opls_224B",nameB="opls_224B"} 62: type[94]={name="opls_140",nameB="opls_140"} 62: type[95]={name="opls_206",nameB="opls_206"} 62: type[96]={name="opls_140",nameB="opls_140"} 62: type[97]={name="opls_140",nameB="opls_140"} 62: type[98]={name="opls_200",nameB="opls_200"} 62: type[99]={name="opls_204",nameB="opls_204"} 62: type[100]={name="opls_235",nameB="opls_235"} 62: type[101]={name="opls_236",nameB="opls_236"} 62: type[102]={name="opls_238",nameB="opls_238"} 62: type[103]={name="opls_241",nameB="opls_241"} 62: type[104]={name="opls_224B",nameB="opls_224B"} 62: type[105]={name="opls_140",nameB="opls_140"} 62: type[106]={name="opls_136",nameB="opls_136"} 62: type[107]={name="opls_140",nameB="opls_140"} 62: type[108]={name="opls_140",nameB="opls_140"} 62: type[109]={name="opls_274",nameB="opls_274"} 62: type[110]={name="opls_140",nameB="opls_140"} 62: type[111]={name="opls_140",nameB="opls_140"} 62: type[112]={name="opls_271",nameB="opls_271"} 62: type[113]={name="opls_272",nameB="opls_272"} 62: type[114]={name="opls_272",nameB="opls_272"} 62: type[115]={name="opls_235",nameB="opls_235"} 62: type[116]={name="opls_236",nameB="opls_236"} 62: type[117]={name="opls_238",nameB="opls_238"} 62: type[118]={name="opls_241",nameB="opls_241"} 62: type[119]={name="opls_224B",nameB="opls_224B"} 62: type[120]={name="opls_140",nameB="opls_140"} 62: type[121]={name="opls_136",nameB="opls_136"} 62: type[122]={name="opls_140",nameB="opls_140"} 62: type[123]={name="opls_140",nameB="opls_140"} 62: type[124]={name="opls_137",nameB="opls_137"} 62: type[125]={name="opls_140",nameB="opls_140"} 62: type[126]={name="opls_135",nameB="opls_135"} 62: type[127]={name="opls_140",nameB="opls_140"} 62: type[128]={name="opls_140",nameB="opls_140"} 62: type[129]={name="opls_140",nameB="opls_140"} 62: type[130]={name="opls_135",nameB="opls_135"} 62: type[131]={name="opls_140",nameB="opls_140"} 62: type[132]={name="opls_140",nameB="opls_140"} 62: type[133]={name="opls_140",nameB="opls_140"} 62: type[134]={name="opls_235",nameB="opls_235"} 62: type[135]={name="opls_236",nameB="opls_236"} 62: type[136]={name="opls_238",nameB="opls_238"} 62: type[137]={name="opls_241",nameB="opls_241"} 62: type[138]={name="opls_224B",nameB="opls_224B"} 62: type[139]={name="opls_140",nameB="opls_140"} 62: type[140]={name="opls_135",nameB="opls_135"} 62: type[141]={name="opls_140",nameB="opls_140"} 62: type[142]={name="opls_140",nameB="opls_140"} 62: type[143]={name="opls_140",nameB="opls_140"} 62: type[144]={name="opls_235",nameB="opls_235"} 62: type[145]={name="opls_236",nameB="opls_236"} 62: type[146]={name="opls_238",nameB="opls_238"} 62: type[147]={name="opls_241",nameB="opls_241"} 62: type[148]={name="opls_224B",nameB="opls_224B"} 62: type[149]={name="opls_140",nameB="opls_140"} 62: type[150]={name="opls_135",nameB="opls_135"} 62: type[151]={name="opls_140",nameB="opls_140"} 62: type[152]={name="opls_140",nameB="opls_140"} 62: type[153]={name="opls_140",nameB="opls_140"} 62: type[154]={name="opls_235",nameB="opls_235"} 62: type[155]={name="opls_236",nameB="opls_236"} 62: residue (10): 62: residue[0]={name="LYS", nr=1, ic=' '} 62: residue[1]={name="VAL", nr=2, ic=' '} 62: residue[2]={name="PHE", nr=3, ic=' '} 62: residue[3]={name="GLY", nr=4, ic=' '} 62: residue[4]={name="ARG", nr=5, ic=' '} 62: residue[5]={name="CYS", nr=6, ic=' '} 62: residue[6]={name="GLU", nr=7, ic=' '} 62: residue[7]={name="LEU", nr=8, ic=' '} 62: residue[8]={name="ALA", nr=9, ic=' '} 62: residue[9]={name="ALA", nr=10, ic=' '} 62: excls: 62: numLists=156 62: numElements=1828 62: excls[0][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} 62: excls[1][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 62: excls[2][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 62: excls[3][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 62: excls[4][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 62: 23, 24, 25, 26} 62: excls[5][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} 62: excls[6][num=19]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 62: 14, 15, 22, 23, 24} 62: excls[7][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} 62: excls[8][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} 62: excls[9][num=17]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 62: 16, 17, 18, 22} 62: excls[10][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} 62: excls[11][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} 62: excls[12][num=17]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 62: 17, 18, 19, 20, 21} 62: excls[13][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} 62: excls[14][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} 62: excls[15][num=14]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 62: 20, 21} 62: excls[16][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 62: excls[17][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 62: excls[18][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 62: excls[19][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 62: excls[20][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 62: excls[21][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 62: excls[22][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 62: 26, 27, 28, 38} 62: excls[23][num=9]={0, 4, 5, 6, 22, 23, 24, 25, 26} 62: excls[24][num=17]={0, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 62: 30, 34, 38, 39, 40} 62: excls[25][num=9]={4, 22, 23, 24, 25, 26, 27, 28, 38} 62: excls[26][num=22]={4, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 62: 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42} 62: excls[27][num=12]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, 62: 40} 62: excls[28][num=18]={22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 62: 34, 35, 36, 37, 38, 39, 40} 62: excls[29][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 62: 36, 37, 38} 62: excls[30][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 62: 36, 37, 38} 62: excls[31][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 62: excls[32][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 62: excls[33][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 62: excls[34][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 62: 36, 37, 38} 62: excls[35][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 62: excls[36][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 62: excls[37][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 62: excls[38][num=17]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, 62: 40, 41, 42, 43, 44, 58} 62: excls[39][num=9]={24, 26, 27, 28, 38, 39, 40, 41, 42} 62: excls[40][num=17]={24, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 62: 45, 46, 47, 58, 59, 60} 62: excls[41][num=9]={26, 38, 39, 40, 41, 42, 43, 44, 58} 62: excls[42][num=18]={26, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 62: 48, 50, 58, 59, 60, 61, 62} 62: excls[43][num=12]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 62: 60} 62: excls[44][num=18]={38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 62: 50, 51, 52, 54, 58, 59, 60} 62: excls[45][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} 62: excls[46][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} 62: excls[47][num=17]={40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 62: 52, 53, 54, 55, 56, 58} 62: excls[48][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 62: 54, 56, 57} 62: excls[49][num=8]={44, 47, 48, 49, 50, 52, 53, 56} 62: excls[50][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 62: 55, 56, 57} 62: excls[51][num=8]={44, 47, 48, 50, 51, 54, 55, 56} 62: excls[52][num=11]={44, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57} 62: excls[53][num=8]={47, 48, 49, 52, 53, 54, 56, 57} 62: excls[54][num=11]={44, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57} 62: excls[55][num=8]={47, 50, 51, 52, 54, 55, 56, 57} 62: excls[56][num=11]={47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57} 62: excls[57][num=8]={48, 50, 52, 53, 54, 55, 56, 57} 62: excls[58][num=17]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 62: 60, 61, 62, 63, 64, 65} 62: excls[59][num=9]={40, 42, 43, 44, 58, 59, 60, 61, 62} 62: excls[60][num=14]={40, 42, 43, 44, 58, 59, 60, 61, 62, 63, 64, 62: 65, 66, 67} 62: excls[61][num=9]={42, 58, 59, 60, 61, 62, 63, 64, 65} 62: excls[62][num=13]={42, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 62: 68, 69} 62: excls[63][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67} 62: excls[64][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67} 62: excls[65][num=14]={58, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 62: 70, 71, 89} 62: excls[66][num=9]={60, 62, 63, 64, 65, 66, 67, 68, 69} 62: excls[67][num=17]={60, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 62: 72, 73, 74, 89, 90, 91} 62: excls[68][num=9]={62, 65, 66, 67, 68, 69, 70, 71, 89} 62: excls[69][num=19]={62, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 62: 75, 76, 77, 89, 90, 91, 92, 93} 62: excls[70][num=12]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, 62: 91} 62: excls[71][num=18]={65, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 62: 77, 78, 79, 80, 89, 90, 91} 62: excls[72][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} 62: excls[73][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} 62: excls[74][num=16]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 62: 79, 80, 81, 82, 89} 62: excls[75][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} 62: excls[76][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} 62: excls[77][num=15]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 62: 81, 82, 83, 86} 62: excls[78][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} 62: excls[79][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} 62: excls[80][num=16]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 62: 84, 85, 86, 87, 88} 62: excls[81][num=9]={74, 77, 78, 79, 80, 81, 82, 83, 86} 62: excls[82][num=13]={74, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 62: 87, 88} 62: excls[83][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} 62: excls[84][num=6]={80, 82, 83, 84, 85, 86} 62: excls[85][num=6]={80, 82, 83, 84, 85, 86} 62: excls[86][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} 62: excls[87][num=6]={80, 82, 83, 86, 87, 88} 62: excls[88][num=6]={80, 82, 83, 86, 87, 88} 62: excls[89][num=17]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, 62: 91, 92, 93, 94, 95, 100} 62: excls[90][num=9]={67, 69, 70, 71, 89, 90, 91, 92, 93} 62: excls[91][num=17]={67, 69, 70, 71, 89, 90, 91, 92, 93, 94, 95, 62: 96, 97, 98, 100, 101, 102} 62: excls[92][num=9]={69, 89, 90, 91, 92, 93, 94, 95, 100} 62: excls[93][num=17]={69, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 62: 99, 100, 101, 102, 103, 104} 62: excls[94][num=12]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101, 62: 102} 62: excls[95][num=13]={89, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 62: 101, 102} 62: excls[96][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 62: excls[97][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 62: excls[98][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 62: excls[99][num=6]={93, 95, 96, 97, 98, 99} 62: excls[100][num=17]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101, 62: 102, 103, 104, 105, 106, 115} 62: excls[101][num=9]={91, 93, 94, 95, 100, 101, 102, 103, 104} 62: excls[102][num=17]={91, 93, 94, 95, 100, 101, 102, 103, 104, 105, 62: 106, 107, 108, 109, 115, 116, 117} 62: excls[103][num=9]={93, 100, 101, 102, 103, 104, 105, 106, 115} 62: excls[104][num=19]={93, 100, 101, 102, 103, 104, 105, 106, 107, 62: 108, 109, 110, 111, 112, 115, 116, 117, 118, 119} 62: excls[105][num=12]={100, 102, 103, 104, 105, 106, 107, 108, 109, 62: 115, 116, 117} 62: excls[106][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109, 62: 110, 111, 112, 113, 114, 115, 116, 117} 62: excls[107][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111, 62: 112, 115} 62: excls[108][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111, 62: 112, 115} 62: excls[109][num=13]={102, 104, 105, 106, 107, 108, 109, 110, 111, 62: 112, 113, 114, 115} 62: excls[110][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 62: 114} 62: excls[111][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 62: 114} 62: excls[112][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 62: 114} 62: excls[113][num=7]={106, 109, 110, 111, 112, 113, 114} 62: excls[114][num=7]={106, 109, 110, 111, 112, 113, 114} 62: excls[115][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109, 62: 115, 116, 117, 118, 119, 120, 121, 134} 62: excls[116][num=9]={102, 104, 105, 106, 115, 116, 117, 118, 119} 62: excls[117][num=17]={102, 104, 105, 106, 115, 116, 117, 118, 119, 62: 120, 121, 122, 123, 124, 134, 135, 136} 62: excls[118][num=9]={104, 115, 116, 117, 118, 119, 120, 121, 134} 62: excls[119][num=19]={104, 115, 116, 117, 118, 119, 120, 121, 122, 62: 123, 124, 125, 126, 130, 134, 135, 136, 137, 138} 62: excls[120][num=12]={115, 117, 118, 119, 120, 121, 122, 123, 124, 62: 134, 135, 136} 62: excls[121][num=21]={115, 117, 118, 119, 120, 121, 122, 123, 124, 62: 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136} 62: excls[122][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126, 62: 130, 134} 62: excls[123][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126, 62: 130, 134} 62: excls[124][num=17]={117, 119, 120, 121, 122, 123, 124, 125, 126, 62: 127, 128, 129, 130, 131, 132, 133, 134} 62: excls[125][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 62: 129, 130, 131, 132, 133} 62: excls[126][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 62: 129, 130, 131, 132, 133} 62: excls[127][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 62: excls[128][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 62: excls[129][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 62: excls[130][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 62: 129, 130, 131, 132, 133} 62: excls[131][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 62: excls[132][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 62: excls[133][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 62: excls[134][num=17]={115, 117, 118, 119, 120, 121, 122, 123, 124, 62: 134, 135, 136, 137, 138, 139, 140, 144} 62: excls[135][num=9]={117, 119, 120, 121, 134, 135, 136, 137, 138} 62: excls[136][num=17]={117, 119, 120, 121, 134, 135, 136, 137, 138, 62: 139, 140, 141, 142, 143, 144, 145, 146} 62: excls[137][num=9]={119, 134, 135, 136, 137, 138, 139, 140, 144} 62: excls[138][num=16]={119, 134, 135, 136, 137, 138, 139, 140, 141, 62: 142, 143, 144, 145, 146, 147, 148} 62: excls[139][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143, 62: 144, 145, 146} 62: excls[140][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143, 62: 144, 145, 146} 62: excls[141][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 62: excls[142][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 62: excls[143][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 62: excls[144][num=17]={134, 136, 137, 138, 139, 140, 141, 142, 143, 62: 144, 145, 146, 147, 148, 149, 150, 154} 62: excls[145][num=9]={136, 138, 139, 140, 144, 145, 146, 147, 148} 62: excls[146][num=16]={136, 138, 139, 140, 144, 145, 146, 147, 148, 62: 149, 150, 151, 152, 153, 154, 155} 62: excls[147][num=9]={138, 144, 145, 146, 147, 148, 149, 150, 154} 62: excls[148][num=13]={138, 144, 145, 146, 147, 148, 149, 150, 151, 62: 152, 153, 154, 155} 62: excls[149][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 62: 154, 155} 62: excls[150][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 62: 154, 155} 62: excls[151][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 62: excls[152][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 62: excls[153][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 62: excls[154][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 62: 154, 155} 62: excls[155][num=6]={146, 148, 149, 150, 154, 155} 62: Bond: 62: nr: 468 62: iatoms: 62: 0 type=100 (BONDS) 0 1 62: 1 type=100 (BONDS) 0 2 62: 2 type=100 (BONDS) 0 3 62: 3 type=101 (BONDS) 0 4 62: 4 type=102 (BONDS) 4 5 62: 5 type=103 (BONDS) 4 6 62: 6 type=104 (BONDS) 4 22 62: 7 type=102 (BONDS) 6 7 62: 8 type=102 (BONDS) 6 8 62: 9 type=103 (BONDS) 6 9 62: 10 type=102 (BONDS) 9 10 62: 11 type=102 (BONDS) 9 11 62: 12 type=103 (BONDS) 9 12 62: 13 type=102 (BONDS) 12 13 62: 14 type=102 (BONDS) 12 14 62: 15 type=103 (BONDS) 12 15 62: 16 type=102 (BONDS) 15 16 62: 17 type=102 (BONDS) 15 17 62: 18 type=101 (BONDS) 15 18 62: 19 type=100 (BONDS) 18 19 62: 20 type=100 (BONDS) 18 20 62: 21 type=100 (BONDS) 18 21 62: 22 type=105 (BONDS) 22 23 62: 23 type=106 (BONDS) 22 24 62: 24 type=100 (BONDS) 24 25 62: 25 type=107 (BONDS) 24 26 62: 26 type=102 (BONDS) 26 27 62: 27 type=103 (BONDS) 26 28 62: 28 type=104 (BONDS) 26 38 62: 29 type=102 (BONDS) 28 29 62: 30 type=103 (BONDS) 28 30 62: 31 type=103 (BONDS) 28 34 62: 32 type=102 (BONDS) 30 31 62: 33 type=102 (BONDS) 30 32 62: 34 type=102 (BONDS) 30 33 62: 35 type=102 (BONDS) 34 35 62: 36 type=102 (BONDS) 34 36 62: 37 type=102 (BONDS) 34 37 62: 38 type=105 (BONDS) 38 39 62: 39 type=106 (BONDS) 38 40 62: 40 type=100 (BONDS) 40 41 62: 41 type=107 (BONDS) 40 42 62: 42 type=102 (BONDS) 42 43 62: 43 type=103 (BONDS) 42 44 62: 44 type=104 (BONDS) 42 58 62: 45 type=102 (BONDS) 44 45 62: 46 type=102 (BONDS) 44 46 62: 47 type=108 (BONDS) 44 47 62: 48 type=109 (BONDS) 47 48 62: 49 type=109 (BONDS) 47 50 62: 50 type=110 (BONDS) 48 49 62: 51 type=109 (BONDS) 48 52 62: 52 type=110 (BONDS) 50 51 62: 53 type=109 (BONDS) 50 54 62: 54 type=110 (BONDS) 52 53 62: 55 type=109 (BONDS) 52 56 62: 56 type=110 (BONDS) 54 55 62: 57 type=109 (BONDS) 54 56 62: 58 type=110 (BONDS) 56 57 62: 59 type=105 (BONDS) 58 59 62: 60 type=106 (BONDS) 58 60 62: 61 type=100 (BONDS) 60 61 62: 62 type=107 (BONDS) 60 62 62: 63 type=102 (BONDS) 62 63 62: 64 type=102 (BONDS) 62 64 62: 65 type=104 (BONDS) 62 65 62: 66 type=105 (BONDS) 65 66 62: 67 type=106 (BONDS) 65 67 62: 68 type=100 (BONDS) 67 68 62: 69 type=107 (BONDS) 67 69 62: 70 type=102 (BONDS) 69 70 62: 71 type=103 (BONDS) 69 71 62: 72 type=104 (BONDS) 69 89 62: 73 type=102 (BONDS) 71 72 62: 74 type=102 (BONDS) 71 73 62: 75 type=103 (BONDS) 71 74 62: 76 type=102 (BONDS) 74 75 62: 77 type=102 (BONDS) 74 76 62: 78 type=103 (BONDS) 74 77 62: 79 type=102 (BONDS) 77 78 62: 80 type=102 (BONDS) 77 79 62: 81 type=111 (BONDS) 77 80 62: 82 type=100 (BONDS) 80 81 62: 83 type=112 (BONDS) 80 82 62: 84 type=112 (BONDS) 82 83 62: 85 type=112 (BONDS) 82 86 62: 86 type=100 (BONDS) 83 84 62: 87 type=100 (BONDS) 83 85 62: 88 type=100 (BONDS) 86 87 62: 89 type=100 (BONDS) 86 88 62: 90 type=105 (BONDS) 89 90 62: 91 type=106 (BONDS) 89 91 62: 92 type=100 (BONDS) 91 92 62: 93 type=107 (BONDS) 91 93 62: 94 type=102 (BONDS) 93 94 62: 95 type=103 (BONDS) 93 95 62: 96 type=104 (BONDS) 93 100 62: 97 type=102 (BONDS) 95 96 62: 98 type=102 (BONDS) 95 97 62: 99 type=113 (BONDS) 95 98 62: 100 type=114 (BONDS) 98 99 62: 101 type=105 (BONDS) 100 101 62: 102 type=106 (BONDS) 100 102 62: 103 type=100 (BONDS) 102 103 62: 104 type=107 (BONDS) 102 104 62: 105 type=102 (BONDS) 104 105 62: 106 type=103 (BONDS) 104 106 62: 107 type=104 (BONDS) 104 115 62: 108 type=102 (BONDS) 106 107 62: 109 type=102 (BONDS) 106 108 62: 110 type=103 (BONDS) 106 109 62: 111 type=102 (BONDS) 109 110 62: 112 type=102 (BONDS) 109 111 62: 113 type=104 (BONDS) 109 112 62: 114 type=115 (BONDS) 112 113 62: 115 type=115 (BONDS) 112 114 62: 116 type=105 (BONDS) 115 116 62: 117 type=106 (BONDS) 115 117 62: 118 type=100 (BONDS) 117 118 62: 119 type=107 (BONDS) 117 119 62: 120 type=102 (BONDS) 119 120 62: 121 type=103 (BONDS) 119 121 62: 122 type=104 (BONDS) 119 134 62: 123 type=102 (BONDS) 121 122 62: 124 type=102 (BONDS) 121 123 62: 125 type=103 (BONDS) 121 124 62: 126 type=102 (BONDS) 124 125 62: 127 type=103 (BONDS) 124 126 62: 128 type=103 (BONDS) 124 130 62: 129 type=102 (BONDS) 126 127 62: 130 type=102 (BONDS) 126 128 62: 131 type=102 (BONDS) 126 129 62: 132 type=102 (BONDS) 130 131 62: 133 type=102 (BONDS) 130 132 62: 134 type=102 (BONDS) 130 133 62: 135 type=105 (BONDS) 134 135 62: 136 type=106 (BONDS) 134 136 62: 137 type=100 (BONDS) 136 137 62: 138 type=107 (BONDS) 136 138 62: 139 type=102 (BONDS) 138 139 62: 140 type=103 (BONDS) 138 140 62: 141 type=104 (BONDS) 138 144 62: 142 type=102 (BONDS) 140 141 62: 143 type=102 (BONDS) 140 142 62: 144 type=102 (BONDS) 140 143 62: 145 type=105 (BONDS) 144 145 62: 146 type=106 (BONDS) 144 146 62: 147 type=100 (BONDS) 146 147 62: 148 type=107 (BONDS) 146 148 62: 149 type=102 (BONDS) 148 149 62: 150 type=103 (BONDS) 148 150 62: 151 type=104 (BONDS) 148 154 62: 152 type=102 (BONDS) 150 151 62: 153 type=102 (BONDS) 150 152 62: 154 type=102 (BONDS) 150 153 62: 155 type=105 (BONDS) 154 155 62: G96Bond: 62: nr: 0 62: Morse: 62: nr: 0 62: Cubic Bonds: 62: nr: 0 62: Connect Bonds: 62: nr: 0 62: Harmonic Pot.: 62: nr: 0 62: FENE Bonds: 62: nr: 0 62: Tab. Bonds: 62: nr: 0 62: Tab. Bonds NC: 62: nr: 0 62: Restraint Pot.: 62: nr: 0 62: Angle: 62: nr: 1124 62: iatoms: 62: 0 type=116 (ANGLES) 1 0 2 62: 1 type=116 (ANGLES) 1 0 3 62: 2 type=116 (ANGLES) 1 0 4 62: 3 type=116 (ANGLES) 2 0 3 62: 4 type=116 (ANGLES) 2 0 4 62: 5 type=116 (ANGLES) 3 0 4 62: 6 type=116 (ANGLES) 0 4 5 62: 7 type=117 (ANGLES) 0 4 6 62: 8 type=117 (ANGLES) 0 4 22 62: 9 type=118 (ANGLES) 5 4 6 62: 10 type=116 (ANGLES) 5 4 22 62: 11 type=119 (ANGLES) 6 4 22 62: 12 type=118 (ANGLES) 4 6 7 62: 13 type=118 (ANGLES) 4 6 8 62: 14 type=120 (ANGLES) 4 6 9 62: 15 type=121 (ANGLES) 7 6 8 62: 16 type=118 (ANGLES) 7 6 9 62: 17 type=118 (ANGLES) 8 6 9 62: 18 type=118 (ANGLES) 6 9 10 62: 19 type=118 (ANGLES) 6 9 11 62: 20 type=120 (ANGLES) 6 9 12 62: 21 type=121 (ANGLES) 10 9 11 62: 22 type=118 (ANGLES) 10 9 12 62: 23 type=118 (ANGLES) 11 9 12 62: 24 type=118 (ANGLES) 9 12 13 62: 25 type=118 (ANGLES) 9 12 14 62: 26 type=120 (ANGLES) 9 12 15 62: 27 type=121 (ANGLES) 13 12 14 62: 28 type=118 (ANGLES) 13 12 15 62: 29 type=118 (ANGLES) 14 12 15 62: 30 type=118 (ANGLES) 12 15 16 62: 31 type=118 (ANGLES) 12 15 17 62: 32 type=117 (ANGLES) 12 15 18 62: 33 type=121 (ANGLES) 16 15 17 62: 34 type=116 (ANGLES) 16 15 18 62: 35 type=116 (ANGLES) 17 15 18 62: 36 type=116 (ANGLES) 15 18 19 62: 37 type=116 (ANGLES) 15 18 20 62: 38 type=116 (ANGLES) 15 18 21 62: 39 type=116 (ANGLES) 19 18 20 62: 40 type=116 (ANGLES) 19 18 21 62: 41 type=116 (ANGLES) 20 18 21 62: 42 type=122 (ANGLES) 4 22 23 62: 43 type=123 (ANGLES) 4 22 24 62: 44 type=124 (ANGLES) 23 22 24 62: 45 type=125 (ANGLES) 22 24 25 62: 46 type=126 (ANGLES) 22 24 26 62: 47 type=127 (ANGLES) 25 24 26 62: 48 type=116 (ANGLES) 24 26 27 62: 49 type=128 (ANGLES) 24 26 28 62: 50 type=129 (ANGLES) 24 26 38 62: 51 type=118 (ANGLES) 27 26 28 62: 52 type=116 (ANGLES) 27 26 38 62: 53 type=119 (ANGLES) 28 26 38 62: 54 type=118 (ANGLES) 26 28 29 62: 55 type=120 (ANGLES) 26 28 30 62: 56 type=120 (ANGLES) 26 28 34 62: 57 type=118 (ANGLES) 29 28 30 62: 58 type=118 (ANGLES) 29 28 34 62: 59 type=120 (ANGLES) 30 28 34 62: 60 type=118 (ANGLES) 28 30 31 62: 61 type=118 (ANGLES) 28 30 32 62: 62 type=118 (ANGLES) 28 30 33 62: 63 type=121 (ANGLES) 31 30 32 62: 64 type=121 (ANGLES) 31 30 33 62: 65 type=121 (ANGLES) 32 30 33 62: 66 type=118 (ANGLES) 28 34 35 62: 67 type=118 (ANGLES) 28 34 36 62: 68 type=118 (ANGLES) 28 34 37 62: 69 type=121 (ANGLES) 35 34 36 62: 70 type=121 (ANGLES) 35 34 37 62: 71 type=121 (ANGLES) 36 34 37 62: 72 type=122 (ANGLES) 26 38 39 62: 73 type=123 (ANGLES) 26 38 40 62: 74 type=124 (ANGLES) 39 38 40 62: 75 type=125 (ANGLES) 38 40 41 62: 76 type=126 (ANGLES) 38 40 42 62: 77 type=127 (ANGLES) 41 40 42 62: 78 type=116 (ANGLES) 40 42 43 62: 79 type=128 (ANGLES) 40 42 44 62: 80 type=129 (ANGLES) 40 42 58 62: 81 type=118 (ANGLES) 43 42 44 62: 82 type=116 (ANGLES) 43 42 58 62: 83 type=119 (ANGLES) 44 42 58 62: 84 type=118 (ANGLES) 42 44 45 62: 85 type=118 (ANGLES) 42 44 46 62: 86 type=130 (ANGLES) 42 44 47 62: 87 type=121 (ANGLES) 45 44 46 62: 88 type=116 (ANGLES) 45 44 47 62: 89 type=116 (ANGLES) 46 44 47 62: 90 type=131 (ANGLES) 44 47 48 62: 91 type=131 (ANGLES) 44 47 50 62: 92 type=132 (ANGLES) 48 47 50 62: 93 type=133 (ANGLES) 47 48 49 62: 94 type=132 (ANGLES) 47 48 52 62: 95 type=133 (ANGLES) 49 48 52 62: 96 type=133 (ANGLES) 47 50 51 62: 97 type=132 (ANGLES) 47 50 54 62: 98 type=133 (ANGLES) 51 50 54 62: 99 type=133 (ANGLES) 48 52 53 62: 100 type=132 (ANGLES) 48 52 56 62: 101 type=133 (ANGLES) 53 52 56 62: 102 type=133 (ANGLES) 50 54 55 62: 103 type=132 (ANGLES) 50 54 56 62: 104 type=133 (ANGLES) 55 54 56 62: 105 type=132 (ANGLES) 52 56 54 62: 106 type=133 (ANGLES) 52 56 57 62: 107 type=133 (ANGLES) 54 56 57 62: 108 type=122 (ANGLES) 42 58 59 62: 109 type=123 (ANGLES) 42 58 60 62: 110 type=124 (ANGLES) 59 58 60 62: 111 type=125 (ANGLES) 58 60 61 62: 112 type=126 (ANGLES) 58 60 62 62: 113 type=127 (ANGLES) 61 60 62 62: 114 type=116 (ANGLES) 60 62 63 62: 115 type=116 (ANGLES) 60 62 64 62: 116 type=129 (ANGLES) 60 62 65 62: 117 type=121 (ANGLES) 63 62 64 62: 118 type=116 (ANGLES) 63 62 65 62: 119 type=116 (ANGLES) 64 62 65 62: 120 type=122 (ANGLES) 62 65 66 62: 121 type=123 (ANGLES) 62 65 67 62: 122 type=124 (ANGLES) 66 65 67 62: 123 type=125 (ANGLES) 65 67 68 62: 124 type=126 (ANGLES) 65 67 69 62: 125 type=127 (ANGLES) 68 67 69 62: 126 type=116 (ANGLES) 67 69 70 62: 127 type=128 (ANGLES) 67 69 71 62: 128 type=129 (ANGLES) 67 69 89 62: 129 type=118 (ANGLES) 70 69 71 62: 130 type=116 (ANGLES) 70 69 89 62: 131 type=119 (ANGLES) 71 69 89 62: 132 type=118 (ANGLES) 69 71 72 62: 133 type=118 (ANGLES) 69 71 73 62: 134 type=120 (ANGLES) 69 71 74 62: 135 type=121 (ANGLES) 72 71 73 62: 136 type=118 (ANGLES) 72 71 74 62: 137 type=118 (ANGLES) 73 71 74 62: 138 type=118 (ANGLES) 71 74 75 62: 139 type=118 (ANGLES) 71 74 76 62: 140 type=120 (ANGLES) 71 74 77 62: 141 type=121 (ANGLES) 75 74 76 62: 142 type=118 (ANGLES) 75 74 77 62: 143 type=118 (ANGLES) 76 74 77 62: 144 type=118 (ANGLES) 74 77 78 62: 145 type=118 (ANGLES) 74 77 79 62: 146 type=117 (ANGLES) 74 77 80 62: 147 type=121 (ANGLES) 78 77 79 62: 148 type=116 (ANGLES) 78 77 80 62: 149 type=116 (ANGLES) 79 77 80 62: 150 type=134 (ANGLES) 77 80 81 62: 151 type=135 (ANGLES) 77 80 82 62: 152 type=133 (ANGLES) 81 80 82 62: 153 type=131 (ANGLES) 80 82 83 62: 154 type=131 (ANGLES) 80 82 86 62: 155 type=131 (ANGLES) 83 82 86 62: 156 type=133 (ANGLES) 82 83 84 62: 157 type=133 (ANGLES) 82 83 85 62: 158 type=133 (ANGLES) 84 83 85 62: 159 type=133 (ANGLES) 82 86 87 62: 160 type=133 (ANGLES) 82 86 88 62: 161 type=133 (ANGLES) 87 86 88 62: 162 type=122 (ANGLES) 69 89 90 62: 163 type=123 (ANGLES) 69 89 91 62: 164 type=124 (ANGLES) 90 89 91 62: 165 type=125 (ANGLES) 89 91 92 62: 166 type=126 (ANGLES) 89 91 93 62: 167 type=127 (ANGLES) 92 91 93 62: 168 type=116 (ANGLES) 91 93 94 62: 169 type=128 (ANGLES) 91 93 95 62: 170 type=129 (ANGLES) 91 93 100 62: 171 type=118 (ANGLES) 94 93 95 62: 172 type=116 (ANGLES) 94 93 100 62: 173 type=119 (ANGLES) 95 93 100 62: 174 type=118 (ANGLES) 93 95 96 62: 175 type=118 (ANGLES) 93 95 97 62: 176 type=136 (ANGLES) 93 95 98 62: 177 type=121 (ANGLES) 96 95 97 62: 178 type=116 (ANGLES) 96 95 98 62: 179 type=116 (ANGLES) 97 95 98 62: 180 type=137 (ANGLES) 95 98 99 62: 181 type=122 (ANGLES) 93 100 101 62: 182 type=123 (ANGLES) 93 100 102 62: 183 type=124 (ANGLES) 101 100 102 62: 184 type=125 (ANGLES) 100 102 103 62: 185 type=126 (ANGLES) 100 102 104 62: 186 type=127 (ANGLES) 103 102 104 62: 187 type=116 (ANGLES) 102 104 105 62: 188 type=128 (ANGLES) 102 104 106 62: 189 type=129 (ANGLES) 102 104 115 62: 190 type=118 (ANGLES) 105 104 106 62: 191 type=116 (ANGLES) 105 104 115 62: 192 type=119 (ANGLES) 106 104 115 62: 193 type=118 (ANGLES) 104 106 107 62: 194 type=118 (ANGLES) 104 106 108 62: 195 type=120 (ANGLES) 104 106 109 62: 196 type=121 (ANGLES) 107 106 108 62: 197 type=118 (ANGLES) 107 106 109 62: 198 type=118 (ANGLES) 108 106 109 62: 199 type=118 (ANGLES) 106 109 110 62: 200 type=118 (ANGLES) 106 109 111 62: 201 type=119 (ANGLES) 106 109 112 62: 202 type=121 (ANGLES) 110 109 111 62: 203 type=116 (ANGLES) 110 109 112 62: 204 type=116 (ANGLES) 111 109 112 62: 205 type=138 (ANGLES) 109 112 113 62: 206 type=138 (ANGLES) 109 112 114 62: 207 type=139 (ANGLES) 113 112 114 62: 208 type=122 (ANGLES) 104 115 116 62: 209 type=123 (ANGLES) 104 115 117 62: 210 type=124 (ANGLES) 116 115 117 62: 211 type=125 (ANGLES) 115 117 118 62: 212 type=126 (ANGLES) 115 117 119 62: 213 type=127 (ANGLES) 118 117 119 62: 214 type=116 (ANGLES) 117 119 120 62: 215 type=128 (ANGLES) 117 119 121 62: 216 type=129 (ANGLES) 117 119 134 62: 217 type=118 (ANGLES) 120 119 121 62: 218 type=116 (ANGLES) 120 119 134 62: 219 type=119 (ANGLES) 121 119 134 62: 220 type=118 (ANGLES) 119 121 122 62: 221 type=118 (ANGLES) 119 121 123 62: 222 type=120 (ANGLES) 119 121 124 62: 223 type=121 (ANGLES) 122 121 123 62: 224 type=118 (ANGLES) 122 121 124 62: 225 type=118 (ANGLES) 123 121 124 62: 226 type=118 (ANGLES) 121 124 125 62: 227 type=120 (ANGLES) 121 124 126 62: 228 type=120 (ANGLES) 121 124 130 62: 229 type=118 (ANGLES) 125 124 126 62: 230 type=118 (ANGLES) 125 124 130 62: 231 type=120 (ANGLES) 126 124 130 62: 232 type=118 (ANGLES) 124 126 127 62: 233 type=118 (ANGLES) 124 126 128 62: 234 type=118 (ANGLES) 124 126 129 62: 235 type=121 (ANGLES) 127 126 128 62: 236 type=121 (ANGLES) 127 126 129 62: 237 type=121 (ANGLES) 128 126 129 62: 238 type=118 (ANGLES) 124 130 131 62: 239 type=118 (ANGLES) 124 130 132 62: 240 type=118 (ANGLES) 124 130 133 62: 241 type=121 (ANGLES) 131 130 132 62: 242 type=121 (ANGLES) 131 130 133 62: 243 type=121 (ANGLES) 132 130 133 62: 244 type=122 (ANGLES) 119 134 135 62: 245 type=123 (ANGLES) 119 134 136 62: 246 type=124 (ANGLES) 135 134 136 62: 247 type=125 (ANGLES) 134 136 137 62: 248 type=126 (ANGLES) 134 136 138 62: 249 type=127 (ANGLES) 137 136 138 62: 250 type=116 (ANGLES) 136 138 139 62: 251 type=128 (ANGLES) 136 138 140 62: 252 type=129 (ANGLES) 136 138 144 62: 253 type=118 (ANGLES) 139 138 140 62: 254 type=116 (ANGLES) 139 138 144 62: 255 type=119 (ANGLES) 140 138 144 62: 256 type=118 (ANGLES) 138 140 141 62: 257 type=118 (ANGLES) 138 140 142 62: 258 type=118 (ANGLES) 138 140 143 62: 259 type=121 (ANGLES) 141 140 142 62: 260 type=121 (ANGLES) 141 140 143 62: 261 type=121 (ANGLES) 142 140 143 62: 262 type=122 (ANGLES) 138 144 145 62: 263 type=123 (ANGLES) 138 144 146 62: 264 type=124 (ANGLES) 145 144 146 62: 265 type=125 (ANGLES) 144 146 147 62: 266 type=126 (ANGLES) 144 146 148 62: 267 type=127 (ANGLES) 147 146 148 62: 268 type=116 (ANGLES) 146 148 149 62: 269 type=128 (ANGLES) 146 148 150 62: 270 type=129 (ANGLES) 146 148 154 62: 271 type=118 (ANGLES) 149 148 150 62: 272 type=116 (ANGLES) 149 148 154 62: 273 type=119 (ANGLES) 150 148 154 62: 274 type=118 (ANGLES) 148 150 151 62: 275 type=118 (ANGLES) 148 150 152 62: 276 type=118 (ANGLES) 148 150 153 62: 277 type=121 (ANGLES) 151 150 152 62: 278 type=121 (ANGLES) 151 150 153 62: 279 type=121 (ANGLES) 152 150 153 62: 280 type=122 (ANGLES) 148 154 155 62: G96Angle: 62: nr: 0 62: Restr. Angles: 62: nr: 0 62: Lin. Angle: 62: nr: 0 62: Bond-Cross: 62: nr: 0 62: BA-Cross: 62: nr: 0 62: U-B: 62: nr: 0 62: Quartic Angles: 62: nr: 0 62: Tab. Angles: 62: nr: 0 62: Proper Dih.: 62: nr: 145 62: iatoms: 62: 0 type=140 (PDIHS) 4 24 22 23 62: 1 type=141 (PDIHS) 22 26 24 25 62: 2 type=140 (PDIHS) 26 40 38 39 62: 3 type=141 (PDIHS) 38 42 40 41 62: 4 type=140 (PDIHS) 42 60 58 59 62: 5 type=142 (PDIHS) 44 47 50 48 62: 6 type=142 (PDIHS) 47 52 48 49 62: 7 type=142 (PDIHS) 47 54 50 51 62: 8 type=142 (PDIHS) 48 56 52 53 62: 9 type=142 (PDIHS) 50 56 54 55 62: 10 type=142 (PDIHS) 52 54 56 57 62: 11 type=141 (PDIHS) 58 62 60 61 62: 12 type=140 (PDIHS) 62 67 65 66 62: 13 type=141 (PDIHS) 65 69 67 68 62: 14 type=140 (PDIHS) 69 91 89 90 62: 15 type=141 (PDIHS) 77 82 80 81 62: 16 type=140 (PDIHS) 80 83 82 86 62: 17 type=141 (PDIHS) 82 84 83 85 62: 18 type=141 (PDIHS) 82 87 86 88 62: 19 type=141 (PDIHS) 89 93 91 92 62: 20 type=140 (PDIHS) 93 102 100 101 62: 21 type=141 (PDIHS) 100 104 102 103 62: 22 type=140 (PDIHS) 104 117 115 116 62: 23 type=140 (PDIHS) 109 113 112 114 62: 24 type=141 (PDIHS) 115 119 117 118 62: 25 type=140 (PDIHS) 119 136 134 135 62: 26 type=141 (PDIHS) 134 138 136 137 62: 27 type=140 (PDIHS) 138 146 144 145 62: 28 type=141 (PDIHS) 144 148 146 147 62: Ryckaert-Bell.: 62: nr: 1565 62: iatoms: 62: 0 type=143 (RBDIHS) 1 0 4 5 62: 1 type=144 (RBDIHS) 1 0 4 6 62: 2 type=144 (RBDIHS) 1 0 4 22 62: 3 type=143 (RBDIHS) 2 0 4 5 62: 4 type=144 (RBDIHS) 2 0 4 6 62: 5 type=144 (RBDIHS) 2 0 4 22 62: 6 type=143 (RBDIHS) 3 0 4 5 62: 7 type=144 (RBDIHS) 3 0 4 6 62: 8 type=144 (RBDIHS) 3 0 4 22 62: 9 type=145 (RBDIHS) 0 4 6 9 62: 10 type=146 (RBDIHS) 22 4 6 9 62: 11 type=147 (RBDIHS) 0 4 6 7 62: 12 type=147 (RBDIHS) 0 4 6 8 62: 13 type=148 (RBDIHS) 5 4 6 7 62: 14 type=148 (RBDIHS) 5 4 6 8 62: 15 type=148 (RBDIHS) 5 4 6 9 62: 16 type=149 (RBDIHS) 22 4 6 7 62: 17 type=149 (RBDIHS) 22 4 6 8 62: 18 type=150 (RBDIHS) 0 4 22 24 62: 19 type=151 (RBDIHS) 6 4 22 24 62: 20 type=148 (RBDIHS) 4 6 9 10 62: 21 type=148 (RBDIHS) 4 6 9 11 62: 22 type=152 (RBDIHS) 4 6 9 12 62: 23 type=148 (RBDIHS) 7 6 9 10 62: 24 type=148 (RBDIHS) 7 6 9 11 62: 25 type=148 (RBDIHS) 7 6 9 12 62: 26 type=148 (RBDIHS) 8 6 9 10 62: 27 type=148 (RBDIHS) 8 6 9 11 62: 28 type=148 (RBDIHS) 8 6 9 12 62: 29 type=148 (RBDIHS) 6 9 12 13 62: 30 type=148 (RBDIHS) 6 9 12 14 62: 31 type=152 (RBDIHS) 6 9 12 15 62: 32 type=148 (RBDIHS) 10 9 12 13 62: 33 type=148 (RBDIHS) 10 9 12 14 62: 34 type=148 (RBDIHS) 10 9 12 15 62: 35 type=148 (RBDIHS) 11 9 12 13 62: 36 type=148 (RBDIHS) 11 9 12 14 62: 37 type=148 (RBDIHS) 11 9 12 15 62: 38 type=148 (RBDIHS) 9 12 15 16 62: 39 type=148 (RBDIHS) 9 12 15 17 62: 40 type=153 (RBDIHS) 9 12 15 18 62: 41 type=148 (RBDIHS) 13 12 15 16 62: 42 type=148 (RBDIHS) 13 12 15 17 62: 43 type=154 (RBDIHS) 13 12 15 18 62: 44 type=148 (RBDIHS) 14 12 15 16 62: 45 type=148 (RBDIHS) 14 12 15 17 62: 46 type=154 (RBDIHS) 14 12 15 18 62: 47 type=144 (RBDIHS) 12 15 18 19 62: 48 type=144 (RBDIHS) 12 15 18 20 62: 49 type=144 (RBDIHS) 12 15 18 21 62: 50 type=143 (RBDIHS) 16 15 18 19 62: 51 type=143 (RBDIHS) 16 15 18 20 62: 52 type=143 (RBDIHS) 16 15 18 21 62: 53 type=143 (RBDIHS) 17 15 18 19 62: 54 type=143 (RBDIHS) 17 15 18 20 62: 55 type=143 (RBDIHS) 17 15 18 21 62: 56 type=155 (RBDIHS) 4 22 24 25 62: 57 type=156 (RBDIHS) 4 22 24 26 62: 58 type=155 (RBDIHS) 23 22 24 25 62: 59 type=157 (RBDIHS) 23 22 24 26 62: 60 type=158 (RBDIHS) 22 24 26 28 62: 61 type=159 (RBDIHS) 22 24 26 38 62: 62 type=160 (RBDIHS) 24 26 28 30 62: 63 type=160 (RBDIHS) 24 26 28 34 62: 64 type=161 (RBDIHS) 38 26 28 30 62: 65 type=161 (RBDIHS) 38 26 28 34 62: 66 type=147 (RBDIHS) 24 26 28 29 62: 67 type=148 (RBDIHS) 27 26 28 29 62: 68 type=148 (RBDIHS) 27 26 28 30 62: 69 type=148 (RBDIHS) 27 26 28 34 62: 70 type=149 (RBDIHS) 38 26 28 29 62: 71 type=150 (RBDIHS) 24 26 38 40 62: 72 type=151 (RBDIHS) 28 26 38 40 62: 73 type=148 (RBDIHS) 26 28 30 31 62: 74 type=148 (RBDIHS) 26 28 30 32 62: 75 type=148 (RBDIHS) 26 28 30 33 62: 76 type=148 (RBDIHS) 29 28 30 31 62: 77 type=148 (RBDIHS) 29 28 30 32 62: 78 type=148 (RBDIHS) 29 28 30 33 62: 79 type=148 (RBDIHS) 34 28 30 31 62: 80 type=148 (RBDIHS) 34 28 30 32 62: 81 type=148 (RBDIHS) 34 28 30 33 62: 82 type=148 (RBDIHS) 26 28 34 35 62: 83 type=148 (RBDIHS) 26 28 34 36 62: 84 type=148 (RBDIHS) 26 28 34 37 62: 85 type=148 (RBDIHS) 29 28 34 35 62: 86 type=148 (RBDIHS) 29 28 34 36 62: 87 type=148 (RBDIHS) 29 28 34 37 62: 88 type=148 (RBDIHS) 30 28 34 35 62: 89 type=148 (RBDIHS) 30 28 34 36 62: 90 type=148 (RBDIHS) 30 28 34 37 62: 91 type=155 (RBDIHS) 26 38 40 41 62: 92 type=156 (RBDIHS) 26 38 40 42 62: 93 type=155 (RBDIHS) 39 38 40 41 62: 94 type=157 (RBDIHS) 39 38 40 42 62: 95 type=158 (RBDIHS) 38 40 42 44 62: 96 type=159 (RBDIHS) 38 40 42 58 62: 97 type=147 (RBDIHS) 40 42 44 45 62: 98 type=147 (RBDIHS) 40 42 44 46 62: 99 type=162 (RBDIHS) 40 42 44 47 62: 100 type=148 (RBDIHS) 43 42 44 45 62: 101 type=148 (RBDIHS) 43 42 44 46 62: 102 type=163 (RBDIHS) 43 42 44 47 62: 103 type=149 (RBDIHS) 58 42 44 45 62: 104 type=149 (RBDIHS) 58 42 44 46 62: 105 type=164 (RBDIHS) 58 42 44 47 62: 106 type=150 (RBDIHS) 40 42 58 60 62: 107 type=151 (RBDIHS) 44 42 58 60 62: 108 type=165 (RBDIHS) 44 47 48 49 62: 109 type=165 (RBDIHS) 44 47 48 52 62: 110 type=165 (RBDIHS) 50 47 48 49 62: 111 type=165 (RBDIHS) 50 47 48 52 62: 112 type=165 (RBDIHS) 44 47 50 51 62: 113 type=165 (RBDIHS) 44 47 50 54 62: 114 type=165 (RBDIHS) 48 47 50 51 62: 115 type=165 (RBDIHS) 48 47 50 54 62: 116 type=165 (RBDIHS) 47 48 52 53 62: 117 type=165 (RBDIHS) 47 48 52 56 62: 118 type=165 (RBDIHS) 49 48 52 53 62: 119 type=165 (RBDIHS) 49 48 52 56 62: 120 type=165 (RBDIHS) 47 50 54 55 62: 121 type=165 (RBDIHS) 47 50 54 56 62: 122 type=165 (RBDIHS) 51 50 54 55 62: 123 type=165 (RBDIHS) 51 50 54 56 62: 124 type=165 (RBDIHS) 48 52 56 54 62: 125 type=165 (RBDIHS) 48 52 56 57 62: 126 type=165 (RBDIHS) 53 52 56 54 62: 127 type=165 (RBDIHS) 53 52 56 57 62: 128 type=165 (RBDIHS) 50 54 56 52 62: 129 type=165 (RBDIHS) 50 54 56 57 62: 130 type=165 (RBDIHS) 55 54 56 52 62: 131 type=165 (RBDIHS) 55 54 56 57 62: 132 type=155 (RBDIHS) 42 58 60 61 62: 133 type=156 (RBDIHS) 42 58 60 62 62: 134 type=155 (RBDIHS) 59 58 60 61 62: 135 type=157 (RBDIHS) 59 58 60 62 62: 136 type=159 (RBDIHS) 58 60 62 65 62: 137 type=150 (RBDIHS) 60 62 65 67 62: 138 type=155 (RBDIHS) 62 65 67 68 62: 139 type=156 (RBDIHS) 62 65 67 69 62: 140 type=155 (RBDIHS) 66 65 67 68 62: 141 type=157 (RBDIHS) 66 65 67 69 62: 142 type=158 (RBDIHS) 65 67 69 71 62: 143 type=159 (RBDIHS) 65 67 69 89 62: 144 type=166 (RBDIHS) 67 69 71 74 62: 145 type=167 (RBDIHS) 89 69 71 74 62: 146 type=147 (RBDIHS) 67 69 71 72 62: 147 type=147 (RBDIHS) 67 69 71 73 62: 148 type=148 (RBDIHS) 70 69 71 72 62: 149 type=148 (RBDIHS) 70 69 71 73 62: 150 type=148 (RBDIHS) 70 69 71 74 62: 151 type=149 (RBDIHS) 89 69 71 72 62: 152 type=149 (RBDIHS) 89 69 71 73 62: 153 type=150 (RBDIHS) 67 69 89 91 62: 154 type=151 (RBDIHS) 71 69 89 91 62: 155 type=148 (RBDIHS) 69 71 74 75 62: 156 type=148 (RBDIHS) 69 71 74 76 62: 157 type=152 (RBDIHS) 69 71 74 77 62: 158 type=148 (RBDIHS) 72 71 74 75 62: 159 type=148 (RBDIHS) 72 71 74 76 62: 160 type=148 (RBDIHS) 72 71 74 77 62: 161 type=148 (RBDIHS) 73 71 74 75 62: 162 type=148 (RBDIHS) 73 71 74 76 62: 163 type=148 (RBDIHS) 73 71 74 77 62: 164 type=148 (RBDIHS) 71 74 77 78 62: 165 type=148 (RBDIHS) 71 74 77 79 62: 166 type=153 (RBDIHS) 71 74 77 80 62: 167 type=148 (RBDIHS) 75 74 77 78 62: 168 type=148 (RBDIHS) 75 74 77 79 62: 169 type=168 (RBDIHS) 75 74 77 80 62: 170 type=148 (RBDIHS) 76 74 77 78 62: 171 type=148 (RBDIHS) 76 74 77 79 62: 172 type=168 (RBDIHS) 76 74 77 80 62: 173 type=169 (RBDIHS) 74 77 80 81 62: 174 type=170 (RBDIHS) 74 77 80 82 62: 175 type=171 (RBDIHS) 78 77 80 82 62: 176 type=171 (RBDIHS) 79 77 80 82 62: 177 type=172 (RBDIHS) 77 80 82 83 62: 178 type=172 (RBDIHS) 77 80 82 86 62: 179 type=173 (RBDIHS) 81 80 82 83 62: 180 type=173 (RBDIHS) 81 80 82 86 62: 181 type=173 (RBDIHS) 80 82 83 84 62: 182 type=173 (RBDIHS) 80 82 83 85 62: 183 type=173 (RBDIHS) 86 82 83 84 62: 184 type=173 (RBDIHS) 86 82 83 85 62: 185 type=173 (RBDIHS) 80 82 86 87 62: 186 type=173 (RBDIHS) 80 82 86 88 62: 187 type=173 (RBDIHS) 83 82 86 87 62: 188 type=173 (RBDIHS) 83 82 86 88 62: 189 type=155 (RBDIHS) 69 89 91 92 62: 190 type=156 (RBDIHS) 69 89 91 93 62: 191 type=155 (RBDIHS) 90 89 91 92 62: 192 type=157 (RBDIHS) 90 89 91 93 62: 193 type=158 (RBDIHS) 89 91 93 95 62: 194 type=159 (RBDIHS) 89 91 93 100 62: 195 type=174 (RBDIHS) 91 93 95 98 62: 196 type=175 (RBDIHS) 100 93 95 98 62: 197 type=147 (RBDIHS) 91 93 95 96 62: 198 type=147 (RBDIHS) 91 93 95 97 62: 199 type=148 (RBDIHS) 94 93 95 96 62: 200 type=148 (RBDIHS) 94 93 95 97 62: 201 type=176 (RBDIHS) 94 93 95 98 62: 202 type=149 (RBDIHS) 100 93 95 96 62: 203 type=149 (RBDIHS) 100 93 95 97 62: 204 type=150 (RBDIHS) 91 93 100 102 62: 205 type=151 (RBDIHS) 95 93 100 102 62: 206 type=177 (RBDIHS) 93 95 98 99 62: 207 type=178 (RBDIHS) 96 95 98 99 62: 208 type=178 (RBDIHS) 97 95 98 99 62: 209 type=155 (RBDIHS) 93 100 102 103 62: 210 type=156 (RBDIHS) 93 100 102 104 62: 211 type=155 (RBDIHS) 101 100 102 103 62: 212 type=157 (RBDIHS) 101 100 102 104 62: 213 type=158 (RBDIHS) 100 102 104 106 62: 214 type=159 (RBDIHS) 100 102 104 115 62: 215 type=179 (RBDIHS) 102 104 106 109 62: 216 type=180 (RBDIHS) 115 104 106 109 62: 217 type=147 (RBDIHS) 102 104 106 107 62: 218 type=147 (RBDIHS) 102 104 106 108 62: 219 type=148 (RBDIHS) 105 104 106 107 62: 220 type=148 (RBDIHS) 105 104 106 108 62: 221 type=148 (RBDIHS) 105 104 106 109 62: 222 type=149 (RBDIHS) 115 104 106 107 62: 223 type=149 (RBDIHS) 115 104 106 108 62: 224 type=150 (RBDIHS) 102 104 115 117 62: 225 type=151 (RBDIHS) 106 104 115 117 62: 226 type=148 (RBDIHS) 104 106 109 110 62: 227 type=148 (RBDIHS) 104 106 109 111 62: 228 type=181 (RBDIHS) 104 106 109 112 62: 229 type=148 (RBDIHS) 107 106 109 110 62: 230 type=148 (RBDIHS) 107 106 109 111 62: 231 type=182 (RBDIHS) 107 106 109 112 62: 232 type=148 (RBDIHS) 108 106 109 110 62: 233 type=148 (RBDIHS) 108 106 109 111 62: 234 type=182 (RBDIHS) 108 106 109 112 62: 235 type=183 (RBDIHS) 106 109 112 113 62: 236 type=183 (RBDIHS) 106 109 112 114 62: 237 type=155 (RBDIHS) 104 115 117 118 62: 238 type=156 (RBDIHS) 104 115 117 119 62: 239 type=155 (RBDIHS) 116 115 117 118 62: 240 type=157 (RBDIHS) 116 115 117 119 62: 241 type=158 (RBDIHS) 115 117 119 121 62: 242 type=159 (RBDIHS) 115 117 119 134 62: 243 type=184 (RBDIHS) 117 119 121 124 62: 244 type=185 (RBDIHS) 134 119 121 124 62: 245 type=147 (RBDIHS) 117 119 121 122 62: 246 type=147 (RBDIHS) 117 119 121 123 62: 247 type=148 (RBDIHS) 120 119 121 122 62: 248 type=148 (RBDIHS) 120 119 121 123 62: 249 type=148 (RBDIHS) 120 119 121 124 62: 250 type=149 (RBDIHS) 134 119 121 122 62: 251 type=149 (RBDIHS) 134 119 121 123 62: 252 type=150 (RBDIHS) 117 119 134 136 62: 253 type=151 (RBDIHS) 121 119 134 136 62: 254 type=148 (RBDIHS) 119 121 124 125 62: 255 type=152 (RBDIHS) 119 121 124 126 62: 256 type=152 (RBDIHS) 119 121 124 130 62: 257 type=148 (RBDIHS) 122 121 124 125 62: 258 type=148 (RBDIHS) 122 121 124 126 62: 259 type=148 (RBDIHS) 122 121 124 130 62: 260 type=148 (RBDIHS) 123 121 124 125 62: 261 type=148 (RBDIHS) 123 121 124 126 62: 262 type=148 (RBDIHS) 123 121 124 130 62: 263 type=148 (RBDIHS) 121 124 126 127 62: 264 type=148 (RBDIHS) 121 124 126 128 62: 265 type=148 (RBDIHS) 121 124 126 129 62: 266 type=148 (RBDIHS) 125 124 126 127 62: 267 type=148 (RBDIHS) 125 124 126 128 62: 268 type=148 (RBDIHS) 125 124 126 129 62: 269 type=148 (RBDIHS) 130 124 126 127 62: 270 type=148 (RBDIHS) 130 124 126 128 62: 271 type=148 (RBDIHS) 130 124 126 129 62: 272 type=148 (RBDIHS) 121 124 130 131 62: 273 type=148 (RBDIHS) 121 124 130 132 62: 274 type=148 (RBDIHS) 121 124 130 133 62: 275 type=148 (RBDIHS) 125 124 130 131 62: 276 type=148 (RBDIHS) 125 124 130 132 62: 277 type=148 (RBDIHS) 125 124 130 133 62: 278 type=148 (RBDIHS) 126 124 130 131 62: 279 type=148 (RBDIHS) 126 124 130 132 62: 280 type=148 (RBDIHS) 126 124 130 133 62: 281 type=155 (RBDIHS) 119 134 136 137 62: 282 type=156 (RBDIHS) 119 134 136 138 62: 283 type=155 (RBDIHS) 135 134 136 137 62: 284 type=157 (RBDIHS) 135 134 136 138 62: 285 type=158 (RBDIHS) 134 136 138 140 62: 286 type=159 (RBDIHS) 134 136 138 144 62: 287 type=147 (RBDIHS) 136 138 140 141 62: 288 type=147 (RBDIHS) 136 138 140 142 62: 289 type=147 (RBDIHS) 136 138 140 143 62: 290 type=148 (RBDIHS) 139 138 140 141 62: 291 type=148 (RBDIHS) 139 138 140 142 62: 292 type=148 (RBDIHS) 139 138 140 143 62: 293 type=149 (RBDIHS) 144 138 140 141 62: 294 type=149 (RBDIHS) 144 138 140 142 62: 295 type=149 (RBDIHS) 144 138 140 143 62: 296 type=150 (RBDIHS) 136 138 144 146 62: 297 type=151 (RBDIHS) 140 138 144 146 62: 298 type=155 (RBDIHS) 138 144 146 147 62: 299 type=156 (RBDIHS) 138 144 146 148 62: 300 type=155 (RBDIHS) 145 144 146 147 62: 301 type=157 (RBDIHS) 145 144 146 148 62: 302 type=158 (RBDIHS) 144 146 148 150 62: 303 type=159 (RBDIHS) 144 146 148 154 62: 304 type=147 (RBDIHS) 146 148 150 151 62: 305 type=147 (RBDIHS) 146 148 150 152 62: 306 type=147 (RBDIHS) 146 148 150 153 62: 307 type=148 (RBDIHS) 149 148 150 151 62: 308 type=148 (RBDIHS) 149 148 150 152 62: 309 type=148 (RBDIHS) 149 148 150 153 62: 310 type=149 (RBDIHS) 154 148 150 151 62: 311 type=149 (RBDIHS) 154 148 150 152 62: 312 type=149 (RBDIHS) 154 148 150 153 62: Restr. Dih.: 62: nr: 0 62: CBT Dih.: 62: nr: 0 62: Fourier Dih.: 62: nr: 0 62: Improper Dih.: 62: nr: 0 62: Per. Imp. Dih.: 62: nr: 0 62: Tab. Dih.: 62: nr: 0 62: CMAP Dih.: 62: nr: 0 62: GB 1-2 Pol.: 62: nr: 0 62: GB 1-3 Pol.: 62: nr: 0 62: GB 1-4 Pol.: 62: nr: 0 62: GB Polariz.: 62: nr: 0 62: Nonpolar Sol.: 62: nr: 0 62: LJ-14: 62: nr: 1197 62: iatoms: 62: 0 type=186 (LJ14) 0 7 62: 1 type=186 (LJ14) 0 8 62: 2 type=187 (LJ14) 0 9 62: 3 type=188 (LJ14) 0 23 62: 4 type=189 (LJ14) 0 24 62: 5 type=190 (LJ14) 1 5 62: 6 type=190 (LJ14) 1 6 62: 7 type=190 (LJ14) 1 22 62: 8 type=190 (LJ14) 2 5 62: 9 type=190 (LJ14) 2 6 62: 10 type=190 (LJ14) 2 22 62: 11 type=190 (LJ14) 3 5 62: 12 type=190 (LJ14) 3 6 62: 13 type=190 (LJ14) 3 22 62: 14 type=191 (LJ14) 4 10 62: 15 type=191 (LJ14) 4 11 62: 16 type=192 (LJ14) 4 12 62: 17 type=190 (LJ14) 4 25 62: 18 type=192 (LJ14) 4 26 62: 19 type=193 (LJ14) 5 7 62: 20 type=193 (LJ14) 5 8 62: 21 type=191 (LJ14) 5 9 62: 22 type=194 (LJ14) 5 23 62: 23 type=186 (LJ14) 5 24 62: 24 type=191 (LJ14) 6 13 62: 25 type=191 (LJ14) 6 14 62: 26 type=192 (LJ14) 6 15 62: 27 type=195 (LJ14) 6 23 62: 28 type=187 (LJ14) 6 24 62: 29 type=193 (LJ14) 7 10 62: 30 type=193 (LJ14) 7 11 62: 31 type=191 (LJ14) 7 12 62: 32 type=196 (LJ14) 7 22 62: 33 type=193 (LJ14) 8 10 62: 34 type=193 (LJ14) 8 11 62: 35 type=191 (LJ14) 8 12 62: 36 type=196 (LJ14) 8 22 62: 37 type=191 (LJ14) 9 16 62: 38 type=191 (LJ14) 9 17 62: 39 type=187 (LJ14) 9 18 62: 40 type=197 (LJ14) 9 22 62: 41 type=193 (LJ14) 10 13 62: 42 type=193 (LJ14) 10 14 62: 43 type=191 (LJ14) 10 15 62: 44 type=193 (LJ14) 11 13 62: 45 type=193 (LJ14) 11 14 62: 46 type=191 (LJ14) 11 15 62: 47 type=190 (LJ14) 12 19 62: 48 type=190 (LJ14) 12 20 62: 49 type=190 (LJ14) 12 21 62: 50 type=193 (LJ14) 13 16 62: 51 type=193 (LJ14) 13 17 62: 52 type=186 (LJ14) 13 18 62: 53 type=193 (LJ14) 14 16 62: 54 type=193 (LJ14) 14 17 62: 55 type=186 (LJ14) 14 18 62: 56 type=190 (LJ14) 16 19 62: 57 type=190 (LJ14) 16 20 62: 58 type=190 (LJ14) 16 21 62: 59 type=190 (LJ14) 17 19 62: 60 type=190 (LJ14) 17 20 62: 61 type=190 (LJ14) 17 21 62: 62 type=196 (LJ14) 22 27 62: 63 type=197 (LJ14) 22 28 62: 64 type=198 (LJ14) 22 38 62: 65 type=190 (LJ14) 23 25 62: 66 type=195 (LJ14) 23 26 62: 67 type=186 (LJ14) 24 29 62: 68 type=187 (LJ14) 24 30 62: 69 type=187 (LJ14) 24 34 62: 70 type=188 (LJ14) 24 39 62: 71 type=189 (LJ14) 24 40 62: 72 type=190 (LJ14) 25 27 62: 73 type=190 (LJ14) 25 28 62: 74 type=190 (LJ14) 25 38 62: 75 type=191 (LJ14) 26 31 62: 76 type=191 (LJ14) 26 32 62: 77 type=191 (LJ14) 26 33 62: 78 type=191 (LJ14) 26 35 62: 79 type=191 (LJ14) 26 36 62: 80 type=191 (LJ14) 26 37 62: 81 type=190 (LJ14) 26 41 62: 82 type=192 (LJ14) 26 42 62: 83 type=193 (LJ14) 27 29 62: 84 type=191 (LJ14) 27 30 62: 85 type=191 (LJ14) 27 34 62: 86 type=194 (LJ14) 27 39 62: 87 type=186 (LJ14) 27 40 62: 88 type=195 (LJ14) 28 39 62: 89 type=187 (LJ14) 28 40 62: 90 type=193 (LJ14) 29 31 62: 91 type=193 (LJ14) 29 32 62: 92 type=193 (LJ14) 29 33 62: 93 type=193 (LJ14) 29 35 62: 94 type=193 (LJ14) 29 36 62: 95 type=193 (LJ14) 29 37 62: 96 type=196 (LJ14) 29 38 62: 97 type=191 (LJ14) 30 35 62: 98 type=191 (LJ14) 30 36 62: 99 type=191 (LJ14) 30 37 62: 100 type=197 (LJ14) 30 38 62: 101 type=191 (LJ14) 31 34 62: 102 type=191 (LJ14) 32 34 62: 103 type=191 (LJ14) 33 34 62: 104 type=197 (LJ14) 34 38 62: 105 type=196 (LJ14) 38 43 62: 106 type=197 (LJ14) 38 44 62: 107 type=198 (LJ14) 38 58 62: 108 type=190 (LJ14) 39 41 62: 109 type=195 (LJ14) 39 42 62: 110 type=186 (LJ14) 40 45 62: 111 type=186 (LJ14) 40 46 62: 112 type=199 (LJ14) 40 47 62: 113 type=188 (LJ14) 40 59 62: 114 type=189 (LJ14) 40 60 62: 115 type=190 (LJ14) 41 43 62: 116 type=190 (LJ14) 41 44 62: 117 type=190 (LJ14) 41 58 62: 118 type=200 (LJ14) 42 48 62: 119 type=200 (LJ14) 42 50 62: 120 type=190 (LJ14) 42 61 62: 121 type=192 (LJ14) 42 62 62: 122 type=193 (LJ14) 43 45 62: 123 type=193 (LJ14) 43 46 62: 124 type=201 (LJ14) 43 47 62: 125 type=194 (LJ14) 43 59 62: 126 type=186 (LJ14) 43 60 62: 127 type=202 (LJ14) 44 49 62: 128 type=202 (LJ14) 44 51 62: 129 type=200 (LJ14) 44 52 62: 130 type=200 (LJ14) 44 54 62: 131 type=195 (LJ14) 44 59 62: 132 type=187 (LJ14) 44 60 62: 133 type=201 (LJ14) 45 48 62: 134 type=201 (LJ14) 45 50 62: 135 type=196 (LJ14) 45 58 62: 136 type=201 (LJ14) 46 48 62: 137 type=201 (LJ14) 46 50 62: 138 type=196 (LJ14) 46 58 62: 139 type=203 (LJ14) 47 53 62: 140 type=203 (LJ14) 47 55 62: 141 type=204 (LJ14) 47 56 62: 142 type=205 (LJ14) 47 58 62: 143 type=203 (LJ14) 48 51 62: 144 type=204 (LJ14) 48 54 62: 145 type=203 (LJ14) 48 57 62: 146 type=203 (LJ14) 49 50 62: 147 type=206 (LJ14) 49 53 62: 148 type=203 (LJ14) 49 56 62: 149 type=204 (LJ14) 50 52 62: 150 type=203 (LJ14) 50 57 62: 151 type=206 (LJ14) 51 55 62: 152 type=203 (LJ14) 51 56 62: 153 type=203 (LJ14) 52 55 62: 154 type=203 (LJ14) 53 54 62: 155 type=206 (LJ14) 53 57 62: 156 type=206 (LJ14) 55 57 62: 157 type=196 (LJ14) 58 63 62: 158 type=196 (LJ14) 58 64 62: 159 type=198 (LJ14) 58 65 62: 160 type=190 (LJ14) 59 61 62: 161 type=195 (LJ14) 59 62 62: 162 type=188 (LJ14) 60 66 62: 163 type=189 (LJ14) 60 67 62: 164 type=190 (LJ14) 61 63 62: 165 type=190 (LJ14) 61 64 62: 166 type=190 (LJ14) 61 65 62: 167 type=190 (LJ14) 62 68 62: 168 type=192 (LJ14) 62 69 62: 169 type=194 (LJ14) 63 66 62: 170 type=186 (LJ14) 63 67 62: 171 type=194 (LJ14) 64 66 62: 172 type=186 (LJ14) 64 67 62: 173 type=196 (LJ14) 65 70 62: 174 type=197 (LJ14) 65 71 62: 175 type=198 (LJ14) 65 89 62: 176 type=190 (LJ14) 66 68 62: 177 type=195 (LJ14) 66 69 62: 178 type=186 (LJ14) 67 72 62: 179 type=186 (LJ14) 67 73 62: 180 type=187 (LJ14) 67 74 62: 181 type=188 (LJ14) 67 90 62: 182 type=189 (LJ14) 67 91 62: 183 type=190 (LJ14) 68 70 62: 184 type=190 (LJ14) 68 71 62: 185 type=190 (LJ14) 68 89 62: 186 type=191 (LJ14) 69 75 62: 187 type=191 (LJ14) 69 76 62: 188 type=192 (LJ14) 69 77 62: 189 type=190 (LJ14) 69 92 62: 190 type=192 (LJ14) 69 93 62: 191 type=193 (LJ14) 70 72 62: 192 type=193 (LJ14) 70 73 62: 193 type=191 (LJ14) 70 74 62: 194 type=194 (LJ14) 70 90 62: 195 type=186 (LJ14) 70 91 62: 196 type=191 (LJ14) 71 78 62: 197 type=191 (LJ14) 71 79 62: 198 type=187 (LJ14) 71 80 62: 199 type=195 (LJ14) 71 90 62: 200 type=187 (LJ14) 71 91 62: 201 type=193 (LJ14) 72 75 62: 202 type=193 (LJ14) 72 76 62: 203 type=191 (LJ14) 72 77 62: 204 type=196 (LJ14) 72 89 62: 205 type=193 (LJ14) 73 75 62: 206 type=193 (LJ14) 73 76 62: 207 type=191 (LJ14) 73 77 62: 208 type=196 (LJ14) 73 89 62: 209 type=190 (LJ14) 74 81 62: 210 type=207 (LJ14) 74 82 62: 211 type=197 (LJ14) 74 89 62: 212 type=193 (LJ14) 75 78 62: 213 type=193 (LJ14) 75 79 62: 214 type=186 (LJ14) 75 80 62: 215 type=193 (LJ14) 76 78 62: 216 type=193 (LJ14) 76 79 62: 217 type=186 (LJ14) 76 80 62: 218 type=187 (LJ14) 77 83 62: 219 type=187 (LJ14) 77 86 62: 220 type=190 (LJ14) 78 81 62: 221 type=208 (LJ14) 78 82 62: 222 type=190 (LJ14) 79 81 62: 223 type=208 (LJ14) 79 82 62: 224 type=190 (LJ14) 80 84 62: 225 type=190 (LJ14) 80 85 62: 226 type=190 (LJ14) 80 87 62: 227 type=190 (LJ14) 80 88 62: 228 type=190 (LJ14) 81 83 62: 229 type=190 (LJ14) 81 86 62: 230 type=190 (LJ14) 83 87 62: 231 type=190 (LJ14) 83 88 62: 232 type=190 (LJ14) 84 86 62: 233 type=190 (LJ14) 85 86 62: 234 type=196 (LJ14) 89 94 62: 235 type=197 (LJ14) 89 95 62: 236 type=198 (LJ14) 89 100 62: 237 type=190 (LJ14) 90 92 62: 238 type=195 (LJ14) 90 93 62: 239 type=186 (LJ14) 91 96 62: 240 type=186 (LJ14) 91 97 62: 241 type=209 (LJ14) 91 98 62: 242 type=188 (LJ14) 91 101 62: 243 type=189 (LJ14) 91 102 62: 244 type=190 (LJ14) 92 94 62: 245 type=190 (LJ14) 92 95 62: 246 type=190 (LJ14) 92 100 62: 247 type=190 (LJ14) 93 99 62: 248 type=190 (LJ14) 93 103 62: 249 type=192 (LJ14) 93 104 62: 250 type=193 (LJ14) 94 96 62: 251 type=193 (LJ14) 94 97 62: 252 type=210 (LJ14) 94 98 62: 253 type=194 (LJ14) 94 101 62: 254 type=186 (LJ14) 94 102 62: 255 type=195 (LJ14) 95 101 62: 256 type=187 (LJ14) 95 102 62: 257 type=190 (LJ14) 96 99 62: 258 type=196 (LJ14) 96 100 62: 259 type=190 (LJ14) 97 99 62: 260 type=196 (LJ14) 97 100 62: 261 type=211 (LJ14) 98 100 62: 262 type=196 (LJ14) 100 105 62: 263 type=197 (LJ14) 100 106 62: 264 type=198 (LJ14) 100 115 62: 265 type=190 (LJ14) 101 103 62: 266 type=195 (LJ14) 101 104 62: 267 type=186 (LJ14) 102 107 62: 268 type=186 (LJ14) 102 108 62: 269 type=187 (LJ14) 102 109 62: 270 type=188 (LJ14) 102 116 62: 271 type=189 (LJ14) 102 117 62: 272 type=190 (LJ14) 103 105 62: 273 type=190 (LJ14) 103 106 62: 274 type=190 (LJ14) 103 115 62: 275 type=191 (LJ14) 104 110 62: 276 type=191 (LJ14) 104 111 62: 277 type=197 (LJ14) 104 112 62: 278 type=190 (LJ14) 104 118 62: 279 type=192 (LJ14) 104 119 62: 280 type=193 (LJ14) 105 107 62: 281 type=193 (LJ14) 105 108 62: 282 type=191 (LJ14) 105 109 62: 283 type=194 (LJ14) 105 116 62: 284 type=186 (LJ14) 105 117 62: 285 type=195 (LJ14) 106 113 62: 286 type=195 (LJ14) 106 114 62: 287 type=195 (LJ14) 106 116 62: 288 type=187 (LJ14) 106 117 62: 289 type=193 (LJ14) 107 110 62: 290 type=193 (LJ14) 107 111 62: 291 type=196 (LJ14) 107 112 62: 292 type=196 (LJ14) 107 115 62: 293 type=193 (LJ14) 108 110 62: 294 type=193 (LJ14) 108 111 62: 295 type=196 (LJ14) 108 112 62: 296 type=196 (LJ14) 108 115 62: 297 type=197 (LJ14) 109 115 62: 298 type=194 (LJ14) 110 113 62: 299 type=194 (LJ14) 110 114 62: 300 type=194 (LJ14) 111 113 62: 301 type=194 (LJ14) 111 114 62: 302 type=196 (LJ14) 115 120 62: 303 type=197 (LJ14) 115 121 62: 304 type=198 (LJ14) 115 134 62: 305 type=190 (LJ14) 116 118 62: 306 type=195 (LJ14) 116 119 62: 307 type=186 (LJ14) 117 122 62: 308 type=186 (LJ14) 117 123 62: 309 type=187 (LJ14) 117 124 62: 310 type=188 (LJ14) 117 135 62: 311 type=189 (LJ14) 117 136 62: 312 type=190 (LJ14) 118 120 62: 313 type=190 (LJ14) 118 121 62: 314 type=190 (LJ14) 118 134 62: 315 type=191 (LJ14) 119 125 62: 316 type=192 (LJ14) 119 126 62: 317 type=192 (LJ14) 119 130 62: 318 type=190 (LJ14) 119 137 62: 319 type=192 (LJ14) 119 138 62: 320 type=193 (LJ14) 120 122 62: 321 type=193 (LJ14) 120 123 62: 322 type=191 (LJ14) 120 124 62: 323 type=194 (LJ14) 120 135 62: 324 type=186 (LJ14) 120 136 62: 325 type=191 (LJ14) 121 127 62: 326 type=191 (LJ14) 121 128 62: 327 type=191 (LJ14) 121 129 62: 328 type=191 (LJ14) 121 131 62: 329 type=191 (LJ14) 121 132 62: 330 type=191 (LJ14) 121 133 62: 331 type=195 (LJ14) 121 135 62: 332 type=187 (LJ14) 121 136 62: 333 type=193 (LJ14) 122 125 62: 334 type=191 (LJ14) 122 126 62: 335 type=191 (LJ14) 122 130 62: 336 type=196 (LJ14) 122 134 62: 337 type=193 (LJ14) 123 125 62: 338 type=191 (LJ14) 123 126 62: 339 type=191 (LJ14) 123 130 62: 340 type=196 (LJ14) 123 134 62: 341 type=197 (LJ14) 124 134 62: 342 type=193 (LJ14) 125 127 62: 343 type=193 (LJ14) 125 128 62: 344 type=193 (LJ14) 125 129 62: 345 type=193 (LJ14) 125 131 62: 346 type=193 (LJ14) 125 132 62: 347 type=193 (LJ14) 125 133 62: 348 type=191 (LJ14) 126 131 62: 349 type=191 (LJ14) 126 132 62: 350 type=191 (LJ14) 126 133 62: 351 type=191 (LJ14) 127 130 62: 352 type=191 (LJ14) 128 130 62: 353 type=191 (LJ14) 129 130 62: 354 type=196 (LJ14) 134 139 62: 355 type=197 (LJ14) 134 140 62: 356 type=198 (LJ14) 134 144 62: 357 type=190 (LJ14) 135 137 62: 358 type=195 (LJ14) 135 138 62: 359 type=186 (LJ14) 136 141 62: 360 type=186 (LJ14) 136 142 62: 361 type=186 (LJ14) 136 143 62: 362 type=188 (LJ14) 136 145 62: 363 type=189 (LJ14) 136 146 62: 364 type=190 (LJ14) 137 139 62: 365 type=190 (LJ14) 137 140 62: 366 type=190 (LJ14) 137 144 62: 367 type=190 (LJ14) 138 147 62: 368 type=192 (LJ14) 138 148 62: 369 type=193 (LJ14) 139 141 62: 370 type=193 (LJ14) 139 142 62: 371 type=193 (LJ14) 139 143 62: 372 type=194 (LJ14) 139 145 62: 373 type=186 (LJ14) 139 146 62: 374 type=195 (LJ14) 140 145 62: 375 type=187 (LJ14) 140 146 62: 376 type=196 (LJ14) 141 144 62: 377 type=196 (LJ14) 142 144 62: 378 type=196 (LJ14) 143 144 62: 379 type=196 (LJ14) 144 149 62: 380 type=197 (LJ14) 144 150 62: 381 type=198 (LJ14) 144 154 62: 382 type=190 (LJ14) 145 147 62: 383 type=195 (LJ14) 145 148 62: 384 type=186 (LJ14) 146 151 62: 385 type=186 (LJ14) 146 152 62: 386 type=186 (LJ14) 146 153 62: 387 type=188 (LJ14) 146 155 62: 388 type=190 (LJ14) 147 149 62: 389 type=190 (LJ14) 147 150 62: 390 type=190 (LJ14) 147 154 62: 391 type=193 (LJ14) 149 151 62: 392 type=193 (LJ14) 149 152 62: 393 type=193 (LJ14) 149 153 62: 394 type=194 (LJ14) 149 155 62: 395 type=195 (LJ14) 150 155 62: 396 type=196 (LJ14) 151 154 62: 397 type=196 (LJ14) 152 154 62: 398 type=196 (LJ14) 153 154 62: Coulomb-14: 62: nr: 0 62: LJC-14 q: 62: nr: 0 62: LJC Pairs NB: 62: nr: 0 62: LJ (SR): 62: nr: 0 62: Buck.ham (SR): 62: nr: 0 62: LJ: 62: nr: 0 62: B.ham: 62: nr: 0 62: Disper. corr.: 62: nr: 0 62: Coulomb (SR): 62: nr: 0 62: Coul: 62: nr: 0 62: RF excl.: 62: nr: 0 62: Coul. recip.: 62: nr: 0 62: LJ recip.: 62: nr: 0 62: DPD: 62: nr: 0 62: Polarization: 62: nr: 0 62: Water Pol.: 62: nr: 0 62: Thole Pol.: 62: nr: 0 62: Anharm. Pol.: 62: nr: 0 62: Position Rest.: 62: nr: 0 62: Flat-b. P-R.: 62: nr: 0 62: Dis. Rest.: 62: nr: 0 62: D.R.Viol. (nm): 62: nr: 0 62: Orient. Rest.: 62: nr: 0 62: Ori. R. RMSD: 62: nr: 0 62: Angle Rest.: 62: nr: 0 62: Angle Rest. Z: 62: nr: 0 62: Dih. Rest.: 62: nr: 0 62: Dih. Rest. Vi.: 62: nr: 0 62: Constraint: 62: nr: 0 62: Constr. No Co.: 62: nr: 0 62: Settle: 62: nr: 0 62: Virtual site 1: 62: nr: 0 62: Virtual site 2: 62: nr: 0 62: Virt. site 2fd: 62: nr: 0 62: Virtual site 3: 62: nr: 0 62: Virt. site 3fd: 62: nr: 0 62: Vir. site 3fad: 62: nr: 0 62: Vir. site 3out: 62: nr: 0 62: Virt. site 4fd: 62: nr: 0 62: Vir. site 4fdn: 62: nr: 0 62: Virtual site N: 62: nr: 0 62: COM Pull En.: 62: nr: 0 62: Dens. fitting: 62: nr: 0 62: Quantum En.: 62: nr: 0 62: NN Potential: 62: nr: 0 62: Potential: 62: nr: 0 62: Kinetic En.: 62: nr: 0 62: Total Energy: 62: nr: 0 62: Conserved En.: 62: nr: 0 62: Temperature: 62: nr: 0 62: Vir. Temp.: 62: nr: 0 62: Pres. DC: 62: nr: 0 62: Pressure: 62: nr: 0 62: dH/dl constr.: 62: nr: 0 62: dVremain/dl: 62: nr: 0 62: dEkin/dl: 62: nr: 0 62: dVcoul/dl: 62: nr: 0 62: dVvdw/dl: 62: nr: 0 62: dVbonded/dl: 62: nr: 0 62: dVrestraint/dl: 62: nr: 0 62: dVtemp/dl: 62: nr: 0 62: grp[T-Coupling ] nr=1, name=[ rest] 62: grp[Energy Mon. ] nr=1, name=[ rest] 62: grp[Acc. not used] nr=1, name=[ rest] 62: grp[Freeze ] nr=1, name=[ rest] 62: grp[User1 ] nr=1, name=[ rest] 62: grp[User2 ] nr=1, name=[ rest] 62: grp[VCM ] nr=1, name=[ rest] 62: grp[Compressed X] nr=1, name=[ rest] 62: grp[Or. Res. Fit] nr=1, name=[ rest] 62: grp[QMMM ] nr=1, name=[ rest] 62: grpname (11): 62: grpname[0]={name="System"} 62: grpname[1]={name="Protein"} 62: grpname[2]={name="Protein-H"} 62: grpname[3]={name="C-alpha"} 62: grpname[4]={name="Backbone"} 62: grpname[5]={name="MainChain"} 62: grpname[6]={name="MainChain+Cb"} 62: grpname[7]={name="MainChain+H"} 62: grpname[8]={name="SideChain"} 62: grpname[9]={name="SideChain-H"} 62: grpname[10]={name="rest"} 62: groups T-Cou Energ Acc. Freez User1 User2 VCM Compr Or. R QMMM 62: allocated 0 0 0 0 0 0 0 0 0 0 62: groupnr[ *] = 0 0 0 0 0 0 0 0 0 0 62: box (3x3): 62: box[ 0]={ 5.90620e+00, 0.00000e+00, 0.00000e+00} 62: box[ 1]={ 0.00000e+00, 6.84510e+00, 0.00000e+00} 62: box[ 2]={ 0.00000e+00, 0.00000e+00, 3.05170e+00} 62: box_rel (3x3): 62: box_rel[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: box_rel[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: box_rel[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: boxv (3x3): 62: boxv[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: boxv[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: boxv[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: pres_prev (3x3): 62: pres_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: pres_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: pres_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: svir_prev (3x3): 62: svir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: svir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: svir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: fvir_prev (3x3): 62: fvir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: fvir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: fvir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: nosehoover_xi: not available 62: x (156x3): 62: x[ 0]={ 3.53600e+00, 2.23400e+00, -1.19800e+00} 62: x[ 1]={ 3.61200e+00, 2.28800e+00, -1.23600e+00} 62: x[ 2]={ 3.47000e+00, 2.21400e+00, -1.27000e+00} 62: x[ 3]={ 3.49200e+00, 2.28600e+00, -1.12500e+00} 62: x[ 4]={ 3.58900e+00, 2.10700e+00, -1.14300e+00} 62: x[ 5]={ 3.63300e+00, 2.05500e+00, -1.21600e+00} 62: x[ 6]={ 3.68700e+00, 2.14400e+00, -1.03100e+00} 62: x[ 7]={ 3.76300e+00, 2.19500e+00, -1.07000e+00} 62: x[ 8]={ 3.63900e+00, 2.20100e+00, -9.64000e-01} 62: x[ 9]={ 3.74500e+00, 2.02500e+00, -9.56000e-01} 62: x[ 10]={ 3.67600e+00, 1.98900e+00, -8.94000e-01} 62: x[ 11]={ 3.77000e+00, 1.95400e+00, -1.02300e+00} 62: x[ 12]={ 3.86900e+00, 2.06500e+00, -8.77000e-01} 62: x[ 13]={ 3.94500e+00, 2.08300e+00, -9.40000e-01} 62: x[ 14]={ 3.84900e+00, 2.14700e+00, -8.24000e-01} 62: x[ 15]={ 3.90600e+00, 1.95100e+00, -7.84000e-01} 62: x[ 16]={ 3.84100e+00, 1.94600e+00, -7.08000e-01} 62: x[ 17]={ 3.90600e+00, 1.86400e+00, -8.33000e-01} 62: x[ 18]={ 4.04200e+00, 1.97700e+00, -7.30000e-01} 62: x[ 19]={ 4.06900e+00, 1.90300e+00, -6.68000e-01} 62: x[ 20]={ 4.10800e+00, 1.98200e+00, -8.06000e-01} 62: x[ 21]={ 4.04200e+00, 2.06400e+00, -6.80000e-01} 62: x[ 22]={ 3.47400e+00, 2.02600e+00, -1.08400e+00} 62: x[ 23]={ 3.39500e+00, 2.08100e+00, -1.00800e+00} 62: x[ 24]={ 3.47400e+00, 1.89600e+00, -1.10400e+00} 62: x[ 25]={ 3.53600e+00, 1.86000e+00, -1.17400e+00} 62: x[ 26]={ 3.39000e+00, 1.80000e+00, -1.03300e+00} 62: x[ 27]={ 3.31700e+00, 1.85200e+00, -9.90000e-01} 62: x[ 28]={ 3.31400e+00, 1.70300e+00, -1.12300e+00} 62: x[ 29]={ 3.38600e+00, 1.65200e+00, -1.17000e+00} 62: x[ 30]={ 3.22500e+00, 1.60800e+00, -1.04300e+00} 62: x[ 31]={ 3.17700e+00, 1.54700e+00, -1.10600e+00} 62: x[ 32]={ 3.28200e+00, 1.55500e+00, -9.81000e-01} 62: x[ 33]={ 3.15800e+00, 1.66100e+00, -9.91000e-01} 62: x[ 34]={ 3.22900e+00, 1.77100e+00, -1.22900e+00} 62: x[ 35]={ 3.18300e+00, 1.70200e+00, -1.28400e+00} 62: x[ 36]={ 3.16200e+00, 1.83000e+00, -1.18500e+00} 62: x[ 37]={ 3.28800e+00, 1.82700e+00, -1.28800e+00} 62: x[ 38]={ 3.48000e+00, 1.73100e+00, -9.29000e-01} 62: x[ 39]={ 3.57600e+00, 1.66100e+00, -9.66000e-01} 62: x[ 40]={ 3.44900e+00, 1.75500e+00, -8.04000e-01} 62: x[ 41]={ 3.37500e+00, 1.81900e+00, -7.84000e-01} 62: x[ 42]={ 3.51900e+00, 1.69000e+00, -6.92000e-01} 62: x[ 43]={ 3.61500e+00, 1.69700e+00, -7.17000e-01} 62: x[ 44]={ 3.49700e+00, 1.76300e+00, -5.59000e-01} 62: x[ 45]={ 3.40500e+00, 1.80200e+00, -5.58000e-01} 62: x[ 46]={ 3.50600e+00, 1.69800e+00, -4.84000e-01} 62: x[ 47]={ 3.59400e+00, 1.87400e+00, -5.38000e-01} 62: x[ 48]={ 3.56700e+00, 2.00500e+00, -5.80000e-01} 62: x[ 49]={ 3.48100e+00, 2.02500e+00, -6.27000e-01} 62: x[ 50]={ 3.70000e+00, 1.85600e+00, -4.47000e-01} 62: x[ 51]={ 3.71300e+00, 1.76600e+00, -4.05000e-01} 62: x[ 52]={ 3.65800e+00, 2.10800e+00, -5.57000e-01} 62: x[ 53]={ 3.64800e+00, 2.19500e+00, -6.04000e-01} 62: x[ 54]={ 3.78700e+00, 1.95900e+00, -4.16000e-01} 62: x[ 55]={ 3.86600e+00, 1.94200e+00, -3.57000e-01} 62: x[ 56]={ 3.76400e+00, 2.08700e+00, -4.67000e-01} 62: x[ 57]={ 3.82200e+00, 2.16400e+00, -4.39000e-01} 62: x[ 58]={ 3.47400e+00, 1.54400e+00, -6.77000e-01} 62: x[ 59]={ 3.35200e+00, 1.51600e+00, -6.86000e-01} 62: x[ 60]={ 3.57200e+00, 1.46400e+00, -6.33000e-01} 62: x[ 61]={ 3.66700e+00, 1.49500e+00, -6.32000e-01} 62: x[ 62]={ 3.53700e+00, 1.32800e+00, -5.87000e-01} 62: x[ 63]={ 3.46200e+00, 1.29200e+00, -6.43000e-01} 62: x[ 64]={ 3.61600e+00, 1.26800e+00, -5.94000e-01} 62: x[ 65]={ 3.49200e+00, 1.34200e+00, -4.42000e-01} 62: x[ 66]={ 3.53000e+00, 1.44000e+00, -3.78000e-01} 62: x[ 67]={ 3.40500e+00, 1.25400e+00, -3.97000e-01} 62: x[ 68]={ 3.37100e+00, 1.18400e+00, -4.60000e-01} 62: x[ 69]={ 3.35600e+00, 1.25400e+00, -2.59000e-01} 62: x[ 70]={ 3.29800e+00, 1.33400e+00, -2.52000e-01} 62: x[ 71]={ 3.27600e+00, 1.12600e+00, -2.33000e-01} 62: x[ 72]={ 3.20000e+00, 1.12200e+00, -2.97000e-01} 62: x[ 73]={ 3.33600e+00, 1.04700e+00, -2.47000e-01} 62: x[ 74]={ 3.22100e+00, 1.12000e+00, -9.20000e-02} 62: x[ 75]={ 3.29700e+00, 1.11700e+00, -2.70000e-02} 62: x[ 76]={ 3.16500e+00, 1.20100e+00, -7.50000e-02} 62: x[ 77]={ 3.13800e+00, 1.00000e+00, -7.20000e-02} 62: x[ 78]={ 3.10400e+00, 9.99000e-01, 2.20000e-02} 62: x[ 79]={ 3.06000e+00, 1.00500e+00, -1.35000e-01} 62: x[ 80]={ 3.20600e+00, 8.75000e-01, -9.60000e-02} 62: x[ 81]={ 3.20200e+00, 8.40000e-01, -1.89000e-01} 62: x[ 82]={ 3.27300e+00, 8.01000e-01, -1.00000e-02} 62: x[ 83]={ 3.28400e+00, 8.33000e-01, 1.19000e-01} 62: x[ 84]={ 3.23900e+00, 9.16000e-01, 1.53000e-01} 62: x[ 85]={ 3.33600e+00, 7.75000e-01, 1.81000e-01} 62: x[ 86]={ 3.32500e+00, 6.84000e-01, -5.30000e-02} 62: x[ 87]={ 3.31100e+00, 6.55000e-01, -1.47000e-01} 62: x[ 88]={ 3.37600e+00, 6.26000e-01, 1.00000e-02} 62: x[ 89]={ 3.46700e+00, 1.27300e+00, -1.56000e-01} 62: x[ 90]={ 3.46700e+00, 1.36500e+00, -7.00000e-02} 62: x[ 91]={ 3.56700e+00, 1.18500e+00, -1.61000e-01} 62: x[ 92]={ 3.56700e+00, 1.11600e+00, -2.33000e-01} 62: x[ 93]={ 3.67800e+00, 1.18700e+00, -6.50000e-02} 62: x[ 94]={ 3.63100e+00, 1.20200e+00, 2.20000e-02} 62: x[ 95]={ 3.74900e+00, 1.05300e+00, -6.20000e-02} 62: x[ 96]={ 3.77000e+00, 1.03400e+00, -1.58000e-01} 62: x[ 97]={ 3.83400e+00, 1.07200e+00, -1.30000e-02} 62: x[ 98]={ 3.65400e+00, 9.20000e-01, 1.40000e-02} 62: x[ 99]={ 3.70750e+00, 8.35500e-01, 1.20000e-02} 62: x[ 100]={ 3.77500e+00, 1.30500e+00, -7.80000e-02} 62: x[ 101]={ 3.81500e+00, 1.36100e+00, 2.60000e-02} 62: x[ 102]={ 3.78600e+00, 1.34800e+00, -2.02000e-01} 62: x[ 103]={ 3.74000e+00, 1.30000e+00, -2.76000e-01} 62: x[ 104]={ 3.86800e+00, 1.46900e+00, -2.31000e-01} 62: x[ 105]={ 3.96000e+00, 1.45500e+00, -1.93000e-01} 62: x[ 106]={ 3.87800e+00, 1.48500e+00, -3.82000e-01} 62: x[ 107]={ 3.92300e+00, 1.40200e+00, -4.17000e-01} 62: x[ 108]={ 3.78500e+00, 1.48900e+00, -4.17000e-01} 62: x[ 109]={ 3.95400e+00, 1.60500e+00, -4.38000e-01} 62: x[ 110]={ 3.91300e+00, 1.68700e+00, -3.99000e-01} 62: x[ 111]={ 4.04900e+00, 1.59800e+00, -4.07000e-01} 62: x[ 112]={ 3.95800e+00, 1.62400e+00, -5.87000e-01} 62: x[ 113]={ 3.86700e+00, 1.56400e+00, -6.49000e-01} 62: x[ 114]={ 4.04200e+00, 1.69500e+00, -6.38000e-01} 62: x[ 115]={ 3.80500e+00, 1.59300e+00, -1.66000e-01} 62: x[ 116]={ 3.87400e+00, 1.67300e+00, -1.01000e-01} 62: x[ 117]={ 3.67400e+00, 1.60500e+00, -1.82000e-01} 62: x[ 118]={ 3.62600e+00, 1.53500e+00, -2.35000e-01} 62: x[ 119]={ 3.59600e+00, 1.71600e+00, -1.25000e-01} 62: x[ 120]={ 3.64000e+00, 1.80100e+00, -1.56000e-01} 62: x[ 121]={ 3.45300e+00, 1.71700e+00, -1.81000e-01} 62: x[ 122]={ 3.45700e+00, 1.72200e+00, -2.81000e-01} 62: x[ 123]={ 3.40600e+00, 1.63300e+00, -1.53000e-01} 62: x[ 124]={ 3.37200e+00, 1.83500e+00, -1.31000e-01} 62: x[ 125]={ 3.37800e+00, 1.84200e+00, -3.10000e-02} 62: x[ 126]={ 3.43000e+00, 1.96600e+00, -1.84000e-01} 62: x[ 127]={ 3.37600e+00, 2.04300e+00, -1.50000e-01} 62: x[ 128]={ 3.52400e+00, 1.97500e+00, -1.53000e-01} 62: x[ 129]={ 3.42700e+00, 1.96500e+00, -2.84000e-01} 62: x[ 130]={ 3.22500e+00, 1.81400e+00, -1.60000e-01} 62: x[ 131]={ 3.17200e+00, 1.89300e+00, -1.26000e-01} 62: x[ 132]={ 3.21100e+00, 1.80500e+00, -2.58000e-01} 62: x[ 133]={ 3.19300e+00, 1.73100e+00, -1.14000e-01} 62: x[ 134]={ 3.60500e+00, 1.71300e+00, 2.70000e-02} 62: x[ 135]={ 3.61600e+00, 1.81700e+00, 9.20000e-02} 62: x[ 136]={ 3.57500e+00, 1.59800e+00, 8.30000e-02} 62: x[ 137]={ 3.54600e+00, 1.52200e+00, 2.40000e-02} 62: x[ 138]={ 3.58400e+00, 1.57600e+00, 2.28000e-01} 62: x[ 139]={ 3.50800e+00, 1.62600e+00, 2.69000e-01} 62: x[ 140]={ 3.56600e+00, 1.42900e+00, 2.62000e-01} 62: x[ 141]={ 3.57200e+00, 1.41600e+00, 3.61000e-01} 62: x[ 142]={ 3.47600e+00, 1.39800e+00, 2.30000e-01} 62: x[ 143]={ 3.63700e+00, 1.37500e+00, 2.18000e-01} 62: x[ 144]={ 3.71400e+00, 1.63100e+00, 2.84000e-01} 62: x[ 145]={ 3.71500e+00, 1.69800e+00, 3.90000e-01} 62: x[ 146]={ 3.82700e+00, 1.59800e+00, 2.20000e-01} 62: x[ 147]={ 3.82000e+00, 1.53900e+00, 1.40000e-01} 62: x[ 148]={ 3.96100e+00, 1.64300e+00, 2.62000e-01} 62: x[ 149]={ 3.96900e+00, 1.61900e+00, 3.58000e-01} 62: x[ 150]={ 4.07100e+00, 1.57100e+00, 1.84000e-01} 62: x[ 151]={ 4.16000e+00, 1.60300e+00, 2.15000e-01} 62: x[ 152]={ 4.06400e+00, 1.47200e+00, 2.01000e-01} 62: x[ 153]={ 4.06000e+00, 1.58900e+00, 8.60000e-02} 62: x[ 154]={ 3.97400e+00, 1.79400e+00, 2.46000e-01} 62: x[ 155]={ 4.01900e+00, 1.85000e+00, 3.47000e-01} 62: v (156x3): 62: v[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 3]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 4]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 5]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 6]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 7]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 8]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 9]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 10]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 11]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 12]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 13]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 14]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 15]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 16]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 17]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 18]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 19]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 20]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 21]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 22]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 23]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 24]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 25]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 26]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 27]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 28]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 29]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 30]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 31]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 32]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 33]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 34]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 35]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 36]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 37]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 38]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 39]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 40]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 41]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 42]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 43]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 44]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 45]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 46]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 47]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 48]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 49]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 50]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 51]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 52]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 53]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 54]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 55]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 56]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 57]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 58]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 59]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 60]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 61]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 62]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 63]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 64]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 65]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 66]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 67]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 68]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 69]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 70]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 71]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 72]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 73]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 74]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 75]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 76]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 77]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 78]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 79]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 80]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 81]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 82]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 83]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 84]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 85]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 86]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 87]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 88]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 89]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 90]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 91]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 92]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 93]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 94]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 95]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 96]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 97]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 98]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 99]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 100]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 101]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 102]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 103]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 104]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 105]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 106]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 107]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 108]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 109]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 110]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 111]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 112]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 113]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 114]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 115]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 116]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 117]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 118]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 119]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 120]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 121]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 122]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 123]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 124]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 125]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 126]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 127]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 128]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 129]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 130]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 131]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 132]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 133]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 134]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 135]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 136]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 137]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 138]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 139]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 140]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 141]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 142]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 143]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 144]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 145]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 146]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 147]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 148]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 149]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 150]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 151]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 152]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 153]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 154]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: v[ 155]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 62: Group statistics 62: T-Coupling : 156 (total 156 atoms) 62: Energy Mon. : 156 (total 156 atoms) 62: Acc. not used: 156 (total 156 atoms) 62: Freeze : 156 (total 156 atoms) 62: User1 : 156 (total 156 atoms) 62: User2 : 156 (total 156 atoms) 62: VCM : 156 (total 156 atoms) 62: Compressed X: 156 (total 156 atoms) 62: Or. Res. Fit: 156 (total 156 atoms) 62: QMMM : 156 (total 156 atoms) 62: [ OK ] DumpTest.WorksWithTpr (9 ms) 62: [ RUN ] DumpTest.WorksWithTprAndMdpWriting 62: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 62: [ OK ] DumpTest.WorksWithTprAndMdpWriting (1 ms) 62: [----------] 2 tests from DumpTest (10 ms total) 62: 62: [----------] 3 tests from HelpwritingTest 62: [ RUN ] HelpwritingTest.ConvertTprWritesHelp 62: [ OK ] HelpwritingTest.ConvertTprWritesHelp (0 ms) 62: [ RUN ] HelpwritingTest.DumpWritesHelp 62: [ OK ] HelpwritingTest.DumpWritesHelp (0 ms) 62: [ RUN ] HelpwritingTest.ReportMethodsWritesHelp 62: [ OK ] HelpwritingTest.ReportMethodsWritesHelp (0 ms) 62: [----------] 3 tests from HelpwritingTest (1 ms total) 62: 62: [----------] 7 tests from GmxMakeNdx 62: [ RUN ] GmxMakeNdx.WritesDefaultProteinIndexGroups 62: 62: Reading structure file 62: Going to read 0 old index file(s) 62: Analysing residue names: 62: There are: 16 Protein residues 62: Analysing Protein... 62: 62: 0 System : 256 atoms 62: 1 Protein : 256 atoms 62: 2 Protein-H : 139 atoms 62: 3 C-alpha : 16 atoms 62: 4 Backbone : 48 atoms 62: 5 MainChain : 63 atoms 62: 6 MainChain+Cb : 78 atoms 62: 7 MainChain+H : 81 atoms 62: 8 SideChain : 175 atoms 62: 9 SideChain-H : 76 atoms 62: 62: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 62: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 62: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 62: 'r': residue 'res' nr 'chain' char 62: "name": group 'case': case sensitive 'q': save and quit 62: 'ri': residue index 62: 62: > 62: [ OK ] GmxMakeNdx.WritesDefaultProteinIndexGroups (3 ms) 62: [ RUN ] GmxMakeNdx.HandlesNoStructureInput 62: Going to read 1 old index file(s) 62: Deducing 22 atoms in the system from indices in the index file 62: 62: 0 System : 22 atoms 62: 1 Protein : 22 atoms 62: 2 Protein-H : 10 atoms 62: 3 C-alpha : 1 atoms 62: 4 Backbone : 5 atoms 62: 5 MainChain : 7 atoms 62: 6 MainChain+Cb : 8 atoms 62: 7 MainChain+H : 9 atoms 62: 8 SideChain : 13 atoms 62: 9 SideChain-H : 3 atoms 62: 10 CA : 1 atoms 62: 11 C_&_r_1 : 1 atoms 62: 12 C_&_r_2 : 1 atoms 62: 13 N_&_r_2 : 1 atoms 62: 14 N_&_r_3 : 1 atoms 62: 62: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 62: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 62: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 62: 'r': residue 'res' nr 'chain' char 62: "name": group 'case': case sensitive 'q': save and quit 62: 'ri': residue index 62: 62: > 62: Copied index group 1 'Protein' 62: Copied index group 2 'Protein-H' 62: Merged two groups with OR: 22 10 -> 22 62: 62: > 62: [ OK ] GmxMakeNdx.HandlesNoStructureInput (2 ms) 62: [ RUN ] GmxMakeNdx.HandlesNotProtein 62: Going to read 1 old index file(s) 62: Deducing 6 atoms in the system from indices in the index file 62: 62: 0 System : 6 atoms 62: 62: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 62: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 62: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 62: 'r': residue 'res' nr 'chain' char 62: "name": group 'case': case sensitive 'q': save and quit 62: 'ri': residue index 62: 62: > 62: [ OK ] GmxMakeNdx.HandlesNotProtein (2 ms) 62: [ RUN ] GmxMakeNdx.HandlesEmptyIndexResult 62: Going to read 1 old index file(s) 62: Deducing 22 atoms in the system from indices in the index file 62: 62: 0 System : 22 atoms 62: 1 Protein : 22 atoms 62: 2 Protein-H : 10 atoms 62: 3 C-alpha : 1 atoms 62: 4 Backbone : 5 atoms 62: 5 MainChain : 7 atoms 62: 6 MainChain+Cb : 8 atoms 62: 7 MainChain+H : 9 atoms 62: 8 SideChain : 13 atoms 62: 9 SideChain-H : 3 atoms 62: 10 CA : 1 atoms 62: 11 C_&_r_1 : 1 atoms 62: 12 C_&_r_2 : 1 atoms 62: 13 N_&_r_2 : 1 atoms 62: 14 N_&_r_3 : 1 atoms 62: 62: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 62: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 62: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 62: 'r': residue 'res' nr 'chain' char 62: "name": group 'case': case sensitive 'q': save and quit 62: 'ri': residue index 62: 62: > 62: Copied index group 4 'Backbone' 62: Copied index group 8 'SideChain' 62: Merged two groups with AND: 5 13 -> 0 62: Group is empty 62: 62: > 62: [ OK ] GmxMakeNdx.HandlesEmptyIndexResult (0 ms) 62: [ RUN ] GmxMakeNdx.HandlesEmptyIndexFile 62: Going to read 1 old index file(s) 62: Deducing 6 atoms in the system from indices in the index file 62: 62: 0 System : 6 atoms 62: 62: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 62: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 62: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 62: 'r': residue 'res' nr 'chain' char 62: "name": group 'case': case sensitive 'q': save and quit 62: 'ri': residue index 62: 62: > 62: Removed group 0 'System' 62: 62: > 62: [ OK ] GmxMakeNdx.HandlesEmptyIndexFile (1 ms) 62: [ RUN ] GmxMakeNdx.Splitres 62: 62: Reading structure file 62: Going to read 0 old index file(s) 62: Analysing residue names: 62: There are: 2 Water residues 62: 62: 0 System : 6 atoms 62: 1 Water : 6 atoms 62: 2 SOL : 6 atoms 62: 62: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 62: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 62: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 62: 'r': residue 'res' nr 'chain' char 62: "name": group 'case': case sensitive 'q': save and quit 62: 'ri': residue index 62: 62: > 62: Splitting group 1 'Water' into residues 62: 62: > 62: [ OK ] GmxMakeNdx.Splitres (1 ms) 62: [ RUN ] GmxMakeNdx.Splitat 62: 62: Reading structure file 62: Going to read 0 old index file(s) 62: Analysing residue names: 62: There are: 2 Water residues 62: 62: 0 System : 6 atoms 62: 1 Water : 6 atoms 62: 2 SOL : 6 atoms 62: 62: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 62: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 62: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 62: 'r': residue 'res' nr 'chain' char 62: "name": group 'case': case sensitive 'q': save and quit 62: 'ri': residue index 62: 62: > 62: Splitting group 1 'Water' into atoms 62: 62: > 62: [ OK ] GmxMakeNdx.Splitat (1 ms) 62: [----------] 7 tests from GmxMakeNdx (14 ms total) 62: 62: [----------] 4 tests from ReportMethodsTest 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file lysozyme.top, line 1465]: 62: System has non-zero total charge: 2.000000 62: Total charge should normally be an integer. See 62: https://manual.gromacs.org/current/user-guide/floating-point.html 62: for discussion on how close it should be to an integer. 62: 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 465.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 NOTEs 62: Setting the LD random seed to -76752196 62: 62: Generated 330891 of the 330891 non-bonded parameter combinations 62: 62: Generated 330891 of the 330891 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 62: Analysing residue names: 62: There are: 10 Protein residues 62: Analysing Protein... 62: 62: This run will generate roughly 0 Mb of data 62: [ RUN ] ReportMethodsTest.WritesCorrectHeadersFormated 62: [ OK ] ReportMethodsTest.WritesCorrectHeadersFormated (0 ms) 62: [ RUN ] ReportMethodsTest.WritesCorrectHeadersUnformatted 62: [ OK ] ReportMethodsTest.WritesCorrectHeadersUnformatted (0 ms) 62: [ RUN ] ReportMethodsTest.WritesCorrectInformation 62: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 62: [ OK ] ReportMethodsTest.WritesCorrectInformation (1 ms) 62: [ RUN ] ReportMethodsTest.ToolEndToEndTest 62: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 62: section: Methods 62: subsection: Simulation system 62: A system of 1 molecules (156 atoms) was simulated. 62: 62: subsection: Simulation settings 62: A total of 0 ns were simulated with a time step of 1 fs. 62: Neighbor searching was performed every 10 steps. 62: The Cut-off algorithm was used for electrostatic interactions. 62: with a cut-off of 1 nm. 62: A single cut-off of 1.1 nm was used for Van der Waals interactions. 62: [ OK ] ReportMethodsTest.ToolEndToEndTest (0 ms) 62: [----------] 4 tests from ReportMethodsTest (1 ms total) 62: 62: [----------] 4 tests from ConvertTprTest 62: [ RUN ] ConvertTprTest.ExtendRuntimeExtensionTest 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file lysozyme.top, line 1465]: 62: System has non-zero total charge: 2.000000 62: Total charge should normally be an integer. See 62: https://manual.gromacs.org/current/user-guide/floating-point.html 62: for discussion on how close it should be to an integer. 62: 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 465.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 NOTEs 62: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended_again.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 62: Setting the LD random seed to 737042399 62: 62: Generated 330891 of the 330891 non-bonded parameter combinations 62: 62: Generated 330891 of the 330891 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 62: Analysing residue names: 62: There are: 10 Protein residues 62: Analysing Protein... 62: 62: This run will generate roughly 0 Mb of data 62: Input file: 62: Run start step 0 62: Run start time 0 ps 62: Step to be made during run 0 62: Runtime for the run 0 ps 62: Run end step 0 62: Run end time 0 ps 62: 62: Extending remaining runtime by 100 ps 62: 62: Output file: 62: Run start step 0 62: Run start time 0 ps 62: Step to be made during run 100000 62: Runtime for the run 100 ps 62: Run end step 100000 62: Run end time 100 ps 62: 62: Input file: 62: Run start step 0 62: Run start time 0 ps 62: Step to be made during run 100000 62: Runtime for the run 100 ps 62: Run end step 100000 62: Run end time 100 ps 62: 62: Extending remaining runtime by 100 ps 62: 62: Output file: 62: Run start step 0 62: Run start time 0 ps 62: Step to be made during run 200000 62: Runtime for the run 200 ps 62: Run end step 200000 62: Run end time 200 ps 62: 62: [ OK ] ConvertTprTest.ExtendRuntimeExtensionTest (639 ms) 62: [ RUN ] ConvertTprTest.UntilRuntimeExtensionTest 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file lysozyme.top, line 1465]: 62: System has non-zero total charge: 2.000000 62: Total charge should normally be an integer. See 62: https://manual.gromacs.org/current/user-guide/floating-point.html 62: for discussion on how close it should be to an integer. 62: 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 465.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 NOTEs 62: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_extended.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 62: Setting the LD random seed to -713031911 62: 62: Generated 330891 of the 330891 non-bonded parameter combinations 62: 62: Generated 330891 of the 330891 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 62: Analysing residue names: 62: There are: 10 Protein residues 62: Analysing Protein... 62: 62: This run will generate roughly 0 Mb of data 62: Input file: 62: Run start step 0 62: Run start time 0 ps 62: Step to be made during run 0 62: Runtime for the run 0 ps 62: Run end step 0 62: Run end time 0 ps 62: 62: Extending remaining runtime to 100 ps 62: 62: Output file: 62: Run start step 0 62: Run start time 0 ps 62: Step to be made during run 100000 62: Runtime for the run 100 ps 62: Run end step 100000 62: Run end time 100 ps 62: 62: [ OK ] ConvertTprTest.UntilRuntimeExtensionTest (660 ms) 62: [ RUN ] ConvertTprTest.nstepRuntimeExtensionTest 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file lysozyme.top, line 1465]: 62: System has non-zero total charge: 2.000000 62: Total charge should normally be an integer. See 62: https://manual.gromacs.org/current/user-guide/floating-point.html 62: for discussion on how close it should be to an integer. 62: 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 465.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 NOTEs 62: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 62: Setting nsteps to 102 62: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_extended.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 62: Setting the LD random seed to -72228995 62: 62: Generated 330891 of the 330891 non-bonded parameter combinations 62: 62: Generated 330891 of the 330891 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 62: Analysing residue names: 62: There are: 10 Protein residues 62: Analysing Protein... 62: 62: This run will generate roughly 0 Mb of data 62: Input file: 62: Run start step 0 62: Run start time 0 ps 62: Step to be made during run 0 62: Runtime for the run 0 ps 62: Run end step 0 62: Run end time 0 ps 62: 62: 62: Output file: 62: Run start step 0 62: Run start time 0 ps 62: Step to be made during run 102 62: Runtime for the run 0.102 ps 62: Run end step 102 62: Run end time 0.102 ps 62: 62: [ OK ] ConvertTprTest.nstepRuntimeExtensionTest (690 ms) 62: [ RUN ] ConvertTprTest.generateVelocitiesTest 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file lysozyme.top, line 1465]: 62: System has non-zero total charge: 2.000000 62: Total charge should normally be an integer. See 62: https://manual.gromacs.org/current/user-guide/floating-point.html 62: for discussion on how close it should be to an integer. 62: 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 465.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 NOTEs 62: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 62: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_new_velocities.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 62: Setting the LD random seed to 1862229964 62: 62: Generated 330891 of the 330891 non-bonded parameter combinations 62: 62: Generated 330891 of the 330891 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 62: Analysing residue names: 62: There are: 10 Protein residues 62: Analysing Protein... 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] ConvertTprTest.generateVelocitiesTest (654 ms) 62: [----------] 4 tests from ConvertTprTest (2646 ms total) 62: 62: [----------] 1 test from ConvertTprNoVelocityTest 62: [ RUN ] ConvertTprNoVelocityTest.refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest_lysozyme.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 2 [file lysozyme.top, line 1465]: 62: System has non-zero total charge: 2.000000 62: Total charge should normally be an integer. See 62: https://manual.gromacs.org/current/user-guide/floating-point.html 62: for discussion on how close it should be to an integer. 62: 62: 62: 62: 62: NOTE 3 [file lysozyme.top, line 1465]: 62: Zero-step energy minimization will alter the coordinates before 62: calculating the energy. If you just want the energy of a single point, 62: try zero-step MD (with unconstrained_start = yes). To do multiple 62: single-point energy evaluations of different configurations of the same 62: topology, use mdrun -rerun. 62: 62: Number of degrees of freedom in T-Coupling group rest is 465.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest_lysozyme.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 NOTEs 62: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 62: Setting the LD random seed to -557656 62: 62: Generated 330891 of the 330891 non-bonded parameter combinations 62: 62: Generated 330891 of the 330891 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 62: Analysing residue names: 62: There are: 10 Protein residues 62: Analysing Protein... 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] ConvertTprNoVelocityTest.refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest (658 ms) 62: [----------] 1 test from ConvertTprNoVelocityTest (658 ms total) 62: 62: [----------] 12 tests from Works/TrjconvWithDifferentInputFormats 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_trr 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: trr version: GMX_trn_file (single precision) 62: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_trr (1 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_tng 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 62: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_tng (1 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_xtc 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_xtc (0 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_gro 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 62: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_gro (0 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_pdb 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 62: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 62: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_pdb (0 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_g96 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_g96 (5 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_trr 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_trr (0 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_tng 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 62: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_tng (1 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_xtc 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_xtc (0 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_gro 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 62: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_gro (0 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_pdb 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 62: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 62: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_pdb (0 ms) 62: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_g96 62: Will write trr: Trajectory in portable xdr format 62: Group 0 ( System) has 6 elements 62: Group 1 (FirstWaterMolecule) has 3 elements 62: Group 2 (SecondWaterMolecule) has 3 elements 62: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 62: -> frame 1 time 1.000 62: Last written: frame 1 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: Select group for output 62: Selected 2: 'SecondWaterMolecule' 62: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_g96 (0 ms) 62: [----------] 12 tests from Works/TrjconvWithDifferentInputFormats (14 ms total) 62: 62: [----------] 30 tests from Works/TrjconvDumpTest 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time__1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time__1_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_30 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_30 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_1_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_999999_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_999999_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time__1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 62: Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time__1_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 62: Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_30 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_30 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_1_00 (3 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_999999_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_999999_00 (2 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time__1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time__1_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_30 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_30 (4 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_1_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_999999_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_999999_00 (1 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time__1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 62: Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time__1_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 62: Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_00 (1 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_30 62: Will write trr: Trajectory in portable xdr format 62: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_30 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_1_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_999999_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_999999_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time__1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 62: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 62: Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time__1_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 62: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 62: Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_30 62: Will write trr: Trajectory in portable xdr format 62: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 62: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_30 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 62: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_1_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_999999_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 62: Precision of /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 62: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 62: Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_999999_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time__1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time__1_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_00 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_30 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 0 ps 62: -> frame 0 time 0.000 62: Last written: frame 0 time 0.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_30 (0 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_1_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_1_00 (1 ms) 62: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_999999_00 62: Will write trr: Trajectory in portable xdr format 62: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 62: 62: Dumping frame at t= 1 ps 62: -> frame 0 time 1.000 62: Last written: frame 0 time 1.000 62: 62: 62: Note that major changes are planned in future for trjconv, to improve usability and utility. 62: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_999999_00 (0 ms) 62: [----------] 30 tests from Works/TrjconvDumpTest (27 ms total) 62: 62: [----------] Global test environment tear-down 62: [==========] 63 tests from 8 test suites ran. (4703 ms total) 62: [ PASSED ] 63 tests. 62/94 Test #62: ToolUnitTests ................................ Passed 5.07 sec test 63 Start 63: ToolWithLeaksUnitTests 63: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/tool-test-with-leaks "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/ToolWithLeaksUnitTests.xml" 63: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests 63: Test timeout computed to be: 1920 63: [==========] Running 2 tests from 2 test suites. 63: [----------] Global test environment set-up. 63: [----------] 1 test from ConvertTprTest 63: [ RUN ] ConvertTprTest.selectIndexTest 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 2 [file lysozyme.top, line 1465]: 63: System has non-zero total charge: 2.000000 63: Total charge should normally be an integer. See 63: https://manual.gromacs.org/current/user-guide/floating-point.html 63: for discussion on how close it should be to an integer. 63: 63: 63: 63: Number of degrees of freedom in T-Coupling group rest is 465.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.mdp]: 63: NVE simulation with an initial temperature of zero: will use a Verlet 63: buffer of 10%. Check your energy drift! 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 63: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 63: Group 0 ( System) has 156 elements 63: Group 1 ( Protein) has 156 elements 63: Group 2 ( Protein-H) has 75 elements 63: Group 3 ( C-alpha) has 10 elements 63: Group 4 ( Backbone) has 30 elements 63: Group 5 ( MainChain) has 40 elements 63: Group 6 ( MainChain+Cb) has 49 elements 63: Group 7 ( MainChain+H) has 52 elements 63: Group 8 ( SideChain) has 104 elements 63: Group 9 ( SideChain-H) has 35 elements 63: Select a group: Will write subset Protein-H of original tpx containing 75 atoms 63: Reduced ilist BONDS from 156 to 75 entries 63: Reduced ilist ANGLES from 281 to 98 entries 63: Reduced ilist PDIHS from 29 to 12 entries 63: Reduced ilist RBDIHS from 313 to 89 entries 63: Reduced ilist LJ14 from 399 to 107 entries 63: Reduced block excls from 156 to 75 index-, 1828 to 635 a-entries 63: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_extended.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 63: Setting the LD random seed to -173287441 63: 63: Generated 330891 of the 330891 non-bonded parameter combinations 63: 63: Generated 330891 of the 330891 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 63: 63: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 63: Analysing residue names: 63: There are: 10 Protein residues 63: Analysing Protein... 63: 63: This run will generate roughly 0 Mb of data 63: Selected 2: 'Protein-H' 63: [ OK ] ConvertTprTest.selectIndexTest (635 ms) 63: [----------] 1 test from ConvertTprTest (635 ms total) 63: 63: [----------] 1 test from ConvertTprNoVelocityTest 63: [ RUN ] ConvertTprNoVelocityTest.selectIndexTestWithoutVelocity 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 2 [file lysozyme.top, line 1465]: 63: System has non-zero total charge: 2.000000 63: Total charge should normally be an integer. See 63: https://manual.gromacs.org/current/user-guide/floating-point.html 63: for discussion on how close it should be to an integer. 63: 63: 63: 63: 63: NOTE 3 [file lysozyme.top, line 1465]: 63: Zero-step energy minimization will alter the coordinates before 63: calculating the energy. If you just want the energy of a single point, 63: try zero-step MD (with unconstrained_start = yes). To do multiple 63: single-point energy evaluations of different configurations of the same 63: topology, use mdrun -rerun. 63: 63: Number of degrees of freedom in T-Coupling group rest is 465.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 63: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 63: Group 0 ( System) has 156 elements 63: Group 1 ( Protein) has 156 elements 63: Group 2 ( Protein-H) has 75 elements 63: Group 3 ( C-alpha) has 10 elements 63: Group 4 ( Backbone) has 30 elements 63: Group 5 ( MainChain) has 40 elements 63: Group 6 ( MainChain+Cb) has 49 elements 63: Group 7 ( MainChain+H) has 52 elements 63: Group 8 ( SideChain) has 104 elements 63: Group 9 ( SideChain-H) has 35 elements 63: Select a group: Will write subset Protein-H of original tpx containing 75 atoms 63: Reduced ilist BONDS from 156 to 75 entries 63: Reduced ilist ANGLES from 281 to 98 entries 63: Reduced ilist PDIHS from 29 to 12 entries 63: Reduced ilist RBDIHS from 313 to 89 entries 63: Reduced ilist LJ14 from 399 to 107 entries 63: Reduced block excls from 156 to 75 index-, 1828 to 635 a-entries 63: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_extended.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 63: Setting the LD random seed to -105186306 63: 63: Generated 330891 of the 330891 non-bonded parameter combinations 63: 63: Generated 330891 of the 330891 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 63: Analysing residue names: 63: There are: 10 Protein residues 63: Analysing Protein... 63: 63: This run will generate roughly 0 Mb of data 63: Selected 2: 'Protein-H' 63: [ OK ] ConvertTprNoVelocityTest.selectIndexTestWithoutVelocity (643 ms) 63: [----------] 1 test from ConvertTprNoVelocityTest (643 ms total) 63: 63: [----------] Global test environment tear-down 63: [==========] 2 tests from 2 test suites ran. (1279 ms total) 63: [ PASSED ] 2 tests. 63/94 Test #63: ToolWithLeaksUnitTests ....................... Passed 1.63 sec test 64 Start 64: FileIOTests 64: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/fileio-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/FileIOTests.xml" 64: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/fileio/tests 64: Test timeout computed to be: 30 64: [==========] Running 421 tests from 17 test suites. 64: [----------] Global test environment set-up. 64: [----------] 4 tests from Checkpoint 64: [ RUN ] Checkpoint.ReadingThrowsWhenValueNotPresent 64: [ OK ] Checkpoint.ReadingThrowsWhenValueNotPresent (0 ms) 64: [ RUN ] Checkpoint.ReadingDoesNotThrowWhenValuePresent 64: [ OK ] Checkpoint.ReadingDoesNotThrowWhenValuePresent (0 ms) 64: [ RUN ] Checkpoint.KvtRoundTripInt64 64: [ OK ] Checkpoint.KvtRoundTripInt64 (0 ms) 64: [ RUN ] Checkpoint.KvtRoundTripReal 64: [ OK ] Checkpoint.KvtRoundTripReal (0 ms) 64: [----------] 4 tests from Checkpoint (0 ms total) 64: 64: [----------] 1 test from StructureIOTest 64: [ RUN ] StructureIOTest.ReadTpsConfRetainsChainids 64: [ OK ] StructureIOTest.ReadTpsConfRetainsChainids (0 ms) 64: [----------] 1 test from StructureIOTest (0 ms total) 64: 64: [----------] 2 tests from FileMD5Test 64: [ RUN ] FileMD5Test.CanComputeMD5 64: [ OK ] FileMD5Test.CanComputeMD5 (1 ms) 64: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong 64: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (0 ms) 64: [----------] 2 tests from FileMD5Test (1 ms total) 64: 64: [----------] 4 tests from FileTypeTest 64: [ RUN ] FileTypeTest.CorrectValueForEmptyString 64: [ OK ] FileTypeTest.CorrectValueForEmptyString (0 ms) 64: [ RUN ] FileTypeTest.CorrectValueForNoExtension 64: [ OK ] FileTypeTest.CorrectValueForNoExtension (0 ms) 64: [ RUN ] FileTypeTest.CorrectValueForEmptyExtension 64: [ OK ] FileTypeTest.CorrectValueForEmptyExtension (0 ms) 64: [ RUN ] FileTypeTest.CorrectValueForLongExtensionWithStrangeCharacters 64: [ OK ] FileTypeTest.CorrectValueForLongExtensionWithStrangeCharacters (0 ms) 64: [----------] 4 tests from FileTypeTest (0 ms total) 64: 64: [----------] 4 tests from ColorMapTest 64: [ RUN ] ColorMapTest.CanReadFromFile 64: [ OK ] ColorMapTest.CanReadFromFile (0 ms) 64: [ RUN ] ColorMapTest.CanWriteToFile 64: [ OK ] ColorMapTest.CanWriteToFile (0 ms) 64: [ RUN ] ColorMapTest.RoundTrip 64: [ OK ] ColorMapTest.RoundTrip (0 ms) 64: [ RUN ] ColorMapTest.SearchWorks 64: [ OK ] ColorMapTest.SearchWorks (0 ms) 64: [----------] 4 tests from ColorMapTest (0 ms total) 64: 64: [----------] 4 tests from MatioTest 64: [ RUN ] MatioTest.CanWriteToFile 64: 33% 66%100%[ OK ] MatioTest.CanWriteToFile (0 ms) 64: [ RUN ] MatioTest.CanConvertToExistingRealMatrix 64: Converted a 4x3 matrix with 4 levels to reals 64: [ OK ] MatioTest.CanConvertToExistingRealMatrix (0 ms) 64: [ RUN ] MatioTest.CanConvertToNewRealMatrix 64: Converted a 4x3 matrix with 4 levels to reals 64: [ OK ] MatioTest.CanConvertToNewRealMatrix (0 ms) 64: [ RUN ] MatioTest.CanReadSingleMatrixAfterWriting 64: 33% 66%100% 33% 66%100%[ OK ] MatioTest.CanReadSingleMatrixAfterWriting (3 ms) 64: [----------] 4 tests from MatioTest (3 ms total) 64: 64: [----------] 3 tests from MrcSerializer 64: [ RUN ] MrcSerializer.DefaultHeaderValuesAreSet 64: [ OK ] MrcSerializer.DefaultHeaderValuesAreSet (0 ms) 64: [ RUN ] MrcSerializer.DefaultHeaderHasRightSerialSize 64: [ OK ] MrcSerializer.DefaultHeaderHasRightSerialSize (0 ms) 64: [ RUN ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip 64: [ OK ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip (0 ms) 64: [----------] 3 tests from MrcSerializer (0 ms total) 64: 64: [----------] 4 tests from MrcDensityMap 64: [ RUN ] MrcDensityMap.RoundTripIsIdempotent 64: [ OK ] MrcDensityMap.RoundTripIsIdempotent (0 ms) 64: [ RUN ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent 64: [ OK ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent (0 ms) 64: [ RUN ] MrcDensityMap.ReadsCoordinateTransformationFromFile 64: [ OK ] MrcDensityMap.ReadsCoordinateTransformationFromFile (0 ms) 64: [ RUN ] MrcDensityMap.ReadsDensityDataFromFile 64: [ OK ] MrcDensityMap.ReadsDensityDataFromFile (0 ms) 64: [----------] 4 tests from MrcDensityMap (1 ms total) 64: 64: [----------] 8 tests from MrcDensityMapHeaderTest 64: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader 64: [ OK ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader (0 ms) 64: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsCorrect 64: [ OK ] MrcDensityMapHeaderTest.DataSizeIsCorrect (0 ms) 64: [ RUN ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid 64: [ OK ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid (0 ms) 64: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven 64: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven (0 ms) 64: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined 64: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined (0 ms) 64: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues 64: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues (0 ms) 64: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectExtents 64: [ OK ] MrcDensityMapHeaderTest.GetsCorrectExtents (0 ms) 64: [ RUN ] MrcDensityMapHeaderTest.IsSane 64: [ OK ] MrcDensityMapHeaderTest.IsSane (0 ms) 64: [----------] 8 tests from MrcDensityMapHeaderTest (0 ms total) 64: 64: [----------] 10 tests from ReadTest 64: [ RUN ] ReadTest.get_eint_ReadsInteger 64: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms) 64: [ RUN ] ReadTest.get_eint_WarnsAboutFloat 64: 64: ERROR 1 [file unknown]: 64: Right hand side '0.8' for parameter 'test' in parameter file is not an 64: integer value 64: 64: 64: [ OK ] ReadTest.get_eint_WarnsAboutFloat (0 ms) 64: [ RUN ] ReadTest.get_eint_WarnsAboutString 64: 64: ERROR 1 [file unknown]: 64: Right hand side 'hello' for parameter 'test' in parameter file is not an 64: integer value 64: 64: 64: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms) 64: [ RUN ] ReadTest.get_eint64_ReadsInteger 64: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms) 64: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat 64: 64: ERROR 1 [file unknown]: 64: Right hand side '0.8' for parameter 'test' in parameter file is not an 64: integer value 64: 64: 64: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (0 ms) 64: [ RUN ] ReadTest.get_eint64_WarnsAboutString 64: 64: ERROR 1 [file unknown]: 64: Right hand side 'hello' for parameter 'test' in parameter file is not an 64: integer value 64: 64: 64: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms) 64: [ RUN ] ReadTest.get_ereal_ReadsInteger 64: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms) 64: [ RUN ] ReadTest.get_ereal_ReadsFloat 64: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms) 64: [ RUN ] ReadTest.get_ereal_WarnsAboutString 64: 64: ERROR 1 [file unknown]: 64: Right hand side 'hello' for parameter 'test' in parameter file is not a 64: real value 64: 64: 64: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms) 64: [ RUN ] ReadTest.setStringEntry_ReturnsCorrectString 64: [ OK ] ReadTest.setStringEntry_ReturnsCorrectString (0 ms) 64: [----------] 10 tests from ReadTest (0 ms total) 64: 64: [----------] 3 tests from TimeControlTest 64: [ RUN ] TimeControlTest.UnSetHasNoValue 64: [ OK ] TimeControlTest.UnSetHasNoValue (0 ms) 64: [ RUN ] TimeControlTest.CanSetValue 64: [ OK ] TimeControlTest.CanSetValue (0 ms) 64: [ RUN ] TimeControlTest.CanUnsetValueAgain 64: [ OK ] TimeControlTest.CanUnsetValueAgain (0 ms) 64: [----------] 3 tests from TimeControlTest (0 ms total) 64: 64: [----------] 1 test from FileIOXdrSerializerTest 64: [ RUN ] FileIOXdrSerializerTest.SizeIsCorrect 64: [ OK ] FileIOXdrSerializerTest.SizeIsCorrect (0 ms) 64: [----------] 1 test from FileIOXdrSerializerTest (0 ms total) 64: 64: [----------] 1 test from TngTest 64: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal 64: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms) 64: [----------] 1 test from TngTest (0 ms total) 64: 64: [----------] 4 tests from XvgioTest 64: [ RUN ] XvgioTest.readXvgIntWorks 64: [ OK ] XvgioTest.readXvgIntWorks (0 ms) 64: [ RUN ] XvgioTest.readXvgRealWorks 64: [ OK ] XvgioTest.readXvgRealWorks (0 ms) 64: [ RUN ] XvgioTest.readXvgIgnoreCommentLineWorks 64: [ OK ] XvgioTest.readXvgIgnoreCommentLineWorks (0 ms) 64: [ RUN ] XvgioTest.readXvgDeprecatedWorks 64: [ OK ] XvgioTest.readXvgDeprecatedWorks (0 ms) 64: [----------] 4 tests from XvgioTest (0 ms total) 64: 64: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest 64: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 64: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (1 ms) 64: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 64: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (0 ms) 64: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 64: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (0 ms) 64: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 64: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (1 ms) 64: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (3 ms total) 64: 64: [----------] 360 tests from FileTypeMatch/FileTypeTest 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/0 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/0 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/1 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/1 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/2 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/2 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/3 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/3 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/4 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/4 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/5 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/5 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/6 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/6 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/7 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/7 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/8 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/8 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/9 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/9 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/10 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/10 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/11 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/11 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/12 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/12 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/13 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/13 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/14 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/14 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/15 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/15 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/16 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/16 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/17 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/17 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/18 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/18 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/19 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/19 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/20 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/20 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/21 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/21 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/22 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/22 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/23 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/23 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/24 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/24 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/25 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/25 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/26 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/26 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/27 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/27 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/28 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/28 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/29 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/29 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/30 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/30 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/31 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/31 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/32 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/32 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/33 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/33 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/34 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/34 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/35 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/35 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/36 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/36 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/37 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/37 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/38 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/38 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/39 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/39 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/40 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/40 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/41 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/41 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/42 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/42 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/43 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/43 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/44 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/44 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/45 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/45 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/46 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/46 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/47 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/47 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/48 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/48 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/49 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/49 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/50 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/50 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/51 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/51 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/52 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/52 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/53 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/53 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/54 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/54 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/55 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/55 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/56 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/56 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/57 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/57 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/58 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/58 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/59 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/59 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/60 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/60 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/61 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/61 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/62 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/62 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/63 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/63 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/64 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/64 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/65 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/65 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/66 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/66 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/67 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/67 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/68 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/68 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/69 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/69 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/70 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/70 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/71 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/71 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/72 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/72 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/73 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/73 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/74 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/74 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/75 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/75 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/76 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/76 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/77 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/77 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/78 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/78 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/79 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/79 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/80 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/80 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/81 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/81 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/82 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/82 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/83 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/83 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/84 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/84 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/85 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/85 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/86 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/86 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/87 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/87 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/88 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/88 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/89 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/89 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/90 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/90 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/91 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/91 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/92 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/92 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/93 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/93 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/94 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/94 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/95 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/95 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/96 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/96 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/97 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/97 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/98 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/98 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/99 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/99 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/100 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/100 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/101 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/101 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/102 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/102 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/103 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/103 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/104 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/104 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/105 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/105 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/106 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/106 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/107 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/107 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/108 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/108 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/109 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/109 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/110 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/110 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/111 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/111 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/112 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/112 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/113 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/113 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/114 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/114 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/115 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/115 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/116 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/116 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/117 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/117 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/118 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/118 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/119 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/119 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/120 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/120 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/121 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/121 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/122 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/122 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/123 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/123 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/124 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/124 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/125 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/125 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/126 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/126 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/127 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/127 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/128 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/128 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/129 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/129 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/130 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/130 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/131 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/131 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/132 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/132 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/133 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/133 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/134 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/134 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/135 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/135 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/136 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/136 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/137 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/137 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/138 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/138 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/139 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/139 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/140 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/140 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/141 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/141 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/142 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/142 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/143 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/143 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/144 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/144 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/145 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/145 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/146 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/146 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/147 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/147 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/148 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/148 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/149 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/149 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/150 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/150 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/151 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/151 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/152 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/152 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/153 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/153 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/154 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/154 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/155 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/155 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/156 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/156 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/157 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/157 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/158 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/158 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/159 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/159 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/160 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/160 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/161 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/161 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/162 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/162 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/163 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/163 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/164 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/164 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/165 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/165 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/166 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/166 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/167 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/167 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/168 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/168 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/169 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/169 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/170 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/170 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/171 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/171 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/172 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/172 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/173 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/173 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/174 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/174 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/175 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/175 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/176 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/176 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/177 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/177 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/178 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/178 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/179 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/179 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/0 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/0 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/1 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/1 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/2 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/2 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/3 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/3 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/4 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/4 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/5 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/5 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/6 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/6 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/7 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/7 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/8 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/8 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/9 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/9 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/10 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/10 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/11 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/11 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/12 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/12 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/13 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/13 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/14 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/14 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/15 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/15 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/16 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/16 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/17 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/17 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/18 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/18 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/19 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/19 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/20 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/20 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/21 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/21 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/22 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/22 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/23 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/23 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/24 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/24 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/25 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/25 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/26 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/26 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/27 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/27 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/28 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/28 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/29 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/29 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/30 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/30 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/31 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/31 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/32 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/32 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/33 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/33 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/34 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/34 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/35 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/35 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/36 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/36 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/37 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/37 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/38 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/38 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/39 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/39 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/40 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/40 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/41 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/41 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/42 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/42 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/43 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/43 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/44 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/44 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/45 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/45 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/46 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/46 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/47 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/47 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/48 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/48 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/49 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/49 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/50 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/50 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/51 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/51 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/52 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/52 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/53 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/53 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/54 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/54 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/55 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/55 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/56 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/56 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/57 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/57 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/58 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/58 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/59 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/59 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/60 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/60 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/61 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/61 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/62 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/62 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/63 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/63 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/64 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/64 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/65 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/65 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/66 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/66 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/67 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/67 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/68 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/68 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/69 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/69 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/70 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/70 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/71 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/71 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/72 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/72 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/73 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/73 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/74 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/74 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/75 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/75 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/76 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/76 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/77 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/77 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/78 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/78 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/79 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/79 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/80 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/80 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/81 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/81 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/82 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/82 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/83 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/83 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/84 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/84 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/85 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/85 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/86 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/86 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/87 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/87 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/88 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/88 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/89 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/89 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/90 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/90 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/91 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/91 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/92 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/92 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/93 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/93 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/94 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/94 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/95 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/95 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/96 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/96 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/97 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/97 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/98 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/98 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/99 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/99 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/100 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/100 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/101 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/101 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/102 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/102 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/103 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/103 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/104 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/104 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/105 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/105 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/106 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/106 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/107 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/107 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/108 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/108 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/109 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/109 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/110 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/110 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/111 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/111 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/112 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/112 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/113 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/113 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/114 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/114 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/115 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/115 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/116 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/116 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/117 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/117 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/118 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/118 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/119 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/119 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/120 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/120 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/121 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/121 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/122 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/122 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/123 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/123 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/124 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/124 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/125 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/125 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/126 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/126 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/127 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/127 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/128 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/128 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/129 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/129 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/130 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/130 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/131 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/131 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/132 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/132 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/133 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/133 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/134 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/134 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/135 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/135 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/136 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/136 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/137 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/137 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/138 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/138 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/139 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/139 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/140 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/140 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/141 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/141 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/142 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/142 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/143 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/143 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/144 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/144 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/145 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/145 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/146 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/146 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/147 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/147 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/148 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/148 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/149 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/149 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/150 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/150 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/151 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/151 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/152 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/152 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/153 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/153 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/154 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/154 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/155 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/155 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/156 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/156 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/157 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/157 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/158 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/158 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/159 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/159 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/160 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/160 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/161 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/161 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/162 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/162 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/163 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/163 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/164 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/164 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/165 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/165 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/166 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/166 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/167 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/167 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/168 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/168 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/169 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/169 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/170 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/170 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/171 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/171 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/172 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/172 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/173 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/173 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/174 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/174 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/175 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/175 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/176 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/176 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/177 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/177 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/178 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/178 (0 ms) 64: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/179 64: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/179 (0 ms) 64: [----------] 360 tests from FileTypeMatch/FileTypeTest (2 ms total) 64: 64: [----------] 4 tests from XvgReadTimeSeries/XvgioTest 64: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/0 64: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/0 (0 ms) 64: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/1 64: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/1 (0 ms) 64: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/2 64: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/2 (0 ms) 64: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/3 64: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/3 (0 ms) 64: [----------] 4 tests from XvgReadTimeSeries/XvgioTest (1 ms total) 64: 64: [----------] Global test environment tear-down 64: [==========] 421 tests from 17 test suites ran. (16 ms total) 64: [ PASSED ] 421 tests. 64/94 Test #64: FileIOTests .................................. Passed 0.44 sec test 65 Start 65: SelectionUnitTests 65: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/selection-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/SelectionUnitTests.xml" 65: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/selection/tests 65: Test timeout computed to be: 30 65: [==========] Running 201 tests from 11 test suites. 65: [----------] Global test environment set-up. 65: [----------] 1 test from IndexGroupTest 65: [ RUN ] IndexGroupTest.RemovesDuplicates 65: [ OK ] IndexGroupTest.RemovesDuplicates (0 ms) 65: [----------] 1 test from IndexGroupTest (0 ms total) 65: 65: [----------] 15 tests from IndexBlockTest 65: [ RUN ] IndexBlockTest.CreatesUnknownBlock 65: [ OK ] IndexBlockTest.CreatesUnknownBlock (0 ms) 65: [ RUN ] IndexBlockTest.CreatesAtomBlock 65: [ OK ] IndexBlockTest.CreatesAtomBlock (0 ms) 65: [ RUN ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology 65: [ OK ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology (0 ms) 65: [ RUN ] IndexBlockTest.CreatesResidueBlocksForComplexTopology 65: [ OK ] IndexBlockTest.CreatesResidueBlocksForComplexTopology (0 ms) 65: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology 65: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology (0 ms) 65: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology 65: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology (0 ms) 65: [ RUN ] IndexBlockTest.CreatesSingleBlock 65: [ OK ] IndexBlockTest.CreatesSingleBlock (0 ms) 65: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksPositive 65: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksPositive (0 ms) 65: [ RUN ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive 65: [ OK ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive (0 ms) 65: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksNegative 65: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksNegative (0 ms) 65: [ RUN ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial 65: [ OK ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial (0 ms) 65: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive 65: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive (0 ms) 65: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative 65: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative (0 ms) 65: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive 65: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive (0 ms) 65: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative 65: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative (0 ms) 65: [----------] 15 tests from IndexBlockTest (1 ms total) 65: 65: [----------] 11 tests from IndexMapTest 65: [ RUN ] IndexMapTest.InitializesAtomBlock 65: [ OK ] IndexMapTest.InitializesAtomBlock (0 ms) 65: [ RUN ] IndexMapTest.InitializesOrgIdGroupAtom 65: [ OK ] IndexMapTest.InitializesOrgIdGroupAtom (0 ms) 65: [ RUN ] IndexMapTest.InitializesOrgIdGroupSingle 65: [ OK ] IndexMapTest.InitializesOrgIdGroupSingle (0 ms) 65: [ RUN ] IndexMapTest.InitializesOrgIdGroupResidue 65: [ OK ] IndexMapTest.InitializesOrgIdGroupResidue (0 ms) 65: [ RUN ] IndexMapTest.InitializesOrgIdGroupMolecule 65: [ OK ] IndexMapTest.InitializesOrgIdGroupMolecule (0 ms) 65: [ RUN ] IndexMapTest.InitializesOrgIdGroupAll 65: [ OK ] IndexMapTest.InitializesOrgIdGroupAll (0 ms) 65: [ RUN ] IndexMapTest.InitializesMoleculeBlock 65: [ OK ] IndexMapTest.InitializesMoleculeBlock (0 ms) 65: [ RUN ] IndexMapTest.MapsSingleBlock 65: [ OK ] IndexMapTest.MapsSingleBlock (0 ms) 65: [ RUN ] IndexMapTest.MapsResidueBlocks 65: [ OK ] IndexMapTest.MapsResidueBlocks (0 ms) 65: [ RUN ] IndexMapTest.MapsResidueBlocksWithMask 65: [ OK ] IndexMapTest.MapsResidueBlocksWithMask (0 ms) 65: [ RUN ] IndexMapTest.HandlesMultipleRequests 65: [ OK ] IndexMapTest.HandlesMultipleRequests (0 ms) 65: [----------] 11 tests from IndexMapTest (1 ms total) 65: 65: [----------] 3 tests from IndexGroupsAndNamesTest 65: [ RUN ] IndexGroupsAndNamesTest.containsNames 65: [ OK ] IndexGroupsAndNamesTest.containsNames (0 ms) 65: [ RUN ] IndexGroupsAndNamesTest.throwsWhenNameMissing 65: [ OK ] IndexGroupsAndNamesTest.throwsWhenNameMissing (0 ms) 65: [ RUN ] IndexGroupsAndNamesTest.groupIndicesCorrect 65: [ OK ] IndexGroupsAndNamesTest.groupIndicesCorrect (0 ms) 65: [----------] 3 tests from IndexGroupsAndNamesTest (0 ms total) 65: 65: [----------] 15 tests from NeighborhoodSearchTest 65: [ RUN ] NeighborhoodSearchTest.SimpleSearch 65: [ OK ] NeighborhoodSearchTest.SimpleSearch (14 ms) 65: [ RUN ] NeighborhoodSearchTest.SimpleSearchXY 65: [ OK ] NeighborhoodSearchTest.SimpleSearchXY (13 ms) 65: [ RUN ] NeighborhoodSearchTest.GridSearchBox 65: [ OK ] NeighborhoodSearchTest.GridSearchBox (2 ms) 65: [ RUN ] NeighborhoodSearchTest.GridSearchTriclinic 65: [ OK ] NeighborhoodSearchTest.GridSearchTriclinic (8 ms) 65: [ RUN ] NeighborhoodSearchTest.GridSearch2DPBC 65: [ OK ] NeighborhoodSearchTest.GridSearch2DPBC (4 ms) 65: [ RUN ] NeighborhoodSearchTest.GridSearchNoPBC 65: [ OK ] NeighborhoodSearchTest.GridSearchNoPBC (1 ms) 65: [ RUN ] NeighborhoodSearchTest.GridSearchXYBox 65: [ OK ] NeighborhoodSearchTest.GridSearchXYBox (2 ms) 65: [ RUN ] NeighborhoodSearchTest.SimpleSelfPairsSearch 65: [ OK ] NeighborhoodSearchTest.SimpleSelfPairsSearch (0 ms) 65: [ RUN ] NeighborhoodSearchTest.GridSelfPairsSearch 65: [ OK ] NeighborhoodSearchTest.GridSelfPairsSearch (46 ms) 65: [ RUN ] NeighborhoodSearchTest.HandlesConcurrentSearches 65: [ OK ] NeighborhoodSearchTest.HandlesConcurrentSearches (0 ms) 65: [ RUN ] NeighborhoodSearchTest.HandlesNoPBC 65: [ OK ] NeighborhoodSearchTest.HandlesNoPBC (0 ms) 65: [ RUN ] NeighborhoodSearchTest.HandlesNullPBC 65: [ OK ] NeighborhoodSearchTest.HandlesNullPBC (0 ms) 65: [ RUN ] NeighborhoodSearchTest.HandlesSkippingPairs 65: [ OK ] NeighborhoodSearchTest.HandlesSkippingPairs (0 ms) 65: [ RUN ] NeighborhoodSearchTest.SimpleSearchExclusions 65: [ OK ] NeighborhoodSearchTest.SimpleSearchExclusions (3 ms) 65: [ RUN ] NeighborhoodSearchTest.GridSearchExclusions 65: [ OK ] NeighborhoodSearchTest.GridSearchExclusions (0 ms) 65: [----------] 15 tests from NeighborhoodSearchTest (98 ms total) 65: 65: [----------] 13 tests from PositionCalculationTest 65: [ RUN ] PositionCalculationTest.ComputesAtomPositions 65: [ OK ] PositionCalculationTest.ComputesAtomPositions (0 ms) 65: [ RUN ] PositionCalculationTest.ComputesAtomPositionsWithRepeatedIndex 65: [ OK ] PositionCalculationTest.ComputesAtomPositionsWithRepeatedIndex (0 ms) 65: [ RUN ] PositionCalculationTest.ComputesResidueCOGPositions 65: [ OK ] PositionCalculationTest.ComputesResidueCOGPositions (0 ms) 65: [ RUN ] PositionCalculationTest.ComputesResidueCOMPositions 65: [ OK ] PositionCalculationTest.ComputesResidueCOMPositions (0 ms) 65: [ RUN ] PositionCalculationTest.ComputesGroupCOGPositions 65: [ OK ] PositionCalculationTest.ComputesGroupCOGPositions (0 ms) 65: [ RUN ] PositionCalculationTest.ComputesGroupCOMPositions 65: [ OK ] PositionCalculationTest.ComputesGroupCOMPositions (0 ms) 65: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteWhole 65: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteWhole (0 ms) 65: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteMax 65: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteMax (0 ms) 65: [ RUN ] PositionCalculationTest.ComputesPositionMask 65: [ OK ] PositionCalculationTest.ComputesPositionMask (0 ms) 65: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms 65: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms (0 ms) 65: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms2 65: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms2 (0 ms) 65: [ RUN ] PositionCalculationTest.HandlesIdenticalStaticCalculations 65: [ OK ] PositionCalculationTest.HandlesIdenticalStaticCalculations (0 ms) 65: [ RUN ] PositionCalculationTest.HandlesOverlappingStaticCalculations 65: [ OK ] PositionCalculationTest.HandlesOverlappingStaticCalculations (0 ms) 65: [----------] 13 tests from PositionCalculationTest (2 ms total) 65: 65: [----------] 33 tests from SelectionCollectionTest 65: [ RUN ] SelectionCollectionTest.HandlesNoSelections 65: [ OK ] SelectionCollectionTest.HandlesNoSelections (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType 65: [ OK ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesVelocityAndForceRequests 65: [ OK ] SelectionCollectionTest.HandlesVelocityAndForceRequests (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry 65: [ OK ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry (0 ms) 65: [ RUN ] SelectionCollectionTest.ParsesSelectionsFromFile 65: [ OK ] SelectionCollectionTest.ParsesSelectionsFromFile (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesAtypicalWhitespace 65: [ OK ] SelectionCollectionTest.HandlesAtypicalWhitespace (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesInvalidRegularExpressions 65: [ OK ] SelectionCollectionTest.HandlesInvalidRegularExpressions (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue 65: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue2 65: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue2 (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue3 65: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue3 (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 65: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 65: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 65: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 65: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReference 65: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReference (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed 65: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup 65: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed 65: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 65: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 (0 ms) 65: [ RUN ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo 65: [ OK ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo (0 ms) 65: [ RUN ] SelectionCollectionTest.RecoversFromMissingAtomTypes 65: [ OK ] SelectionCollectionTest.RecoversFromMissingAtomTypes (0 ms) 65: [ RUN ] SelectionCollectionTest.RecoversFromMissingPDBInfo 65: [ OK ] SelectionCollectionTest.RecoversFromMissingPDBInfo (0 ms) 65: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation 65: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation (0 ms) 65: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation2 65: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation2 (0 ms) 65: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation3 65: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation3 (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets 65: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 65: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 65: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 (0 ms) 65: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 65: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 (0 ms) 65: [ RUN ] SelectionCollectionTest.RetrieveValidSelection 65: [ OK ] SelectionCollectionTest.RetrieveValidSelection (0 ms) 65: [ RUN ] SelectionCollectionTest.RetrieveInvalidSelection 65: [ OK ] SelectionCollectionTest.RetrieveInvalidSelection (0 ms) 65: [ RUN ] SelectionCollectionTest.CanCopyEmptyCollection 65: [ OK ] SelectionCollectionTest.CanCopyEmptyCollection (0 ms) 65: [ RUN ] SelectionCollectionTest.CopiedSelectionListsAreHandledSeparately 65: [ OK ] SelectionCollectionTest.CopiedSelectionListsAreHandledSeparately (0 ms) 65: [----------] 33 tests from SelectionCollectionTest (9 ms total) 65: 65: [----------] 14 tests from SelectionCollectionInteractiveTest 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesBasicInput 65: [ OK ] SelectionCollectionInteractiveTest.HandlesBasicInput (0 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesContinuation 65: [ OK ] SelectionCollectionInteractiveTest.HandlesContinuation (0 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput 65: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput (0 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput 65: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput (0 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups 65: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups (0 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections 65: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections (0 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus 65: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus (0 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus 65: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus (0 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus 65: [ OK ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus (0 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline 65: [ OK ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline (0 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesEmptySelections 65: [ OK ] SelectionCollectionInteractiveTest.HandlesEmptySelections (0 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine 65: [ OK ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine (0 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput 65: [ OK ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput (0 ms) 65: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively 65: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively (0 ms) 65: [----------] 14 tests from SelectionCollectionInteractiveTest (4 ms total) 65: 65: [----------] 70 tests from SelectionCollectionDataTest 65: [ RUN ] SelectionCollectionDataTest.HandlesAllNone 65: [ OK ] SelectionCollectionDataTest.HandlesAllNone (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesAtomnr 65: [ OK ] SelectionCollectionDataTest.HandlesAtomnr (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesResnr 65: [ OK ] SelectionCollectionDataTest.HandlesResnr (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesResIndex 65: [ OK ] SelectionCollectionDataTest.HandlesResIndex (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesMolIndex 65: [ OK ] SelectionCollectionDataTest.HandlesMolIndex (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesAtomname 65: [ OK ] SelectionCollectionDataTest.HandlesAtomname (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesPdbAtomname 65: [ OK ] SelectionCollectionDataTest.HandlesPdbAtomname (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesAtomtype 65: [ OK ] SelectionCollectionDataTest.HandlesAtomtype (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesChain 65: [ OK ] SelectionCollectionDataTest.HandlesChain (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesMass 65: [ OK ] SelectionCollectionDataTest.HandlesMass (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesCharge 65: [ OK ] SelectionCollectionDataTest.HandlesCharge (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesAltLoc 65: [ OK ] SelectionCollectionDataTest.HandlesAltLoc (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesInsertCode 65: [ OK ] SelectionCollectionDataTest.HandlesInsertCode (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesOccupancy 65: [ OK ] SelectionCollectionDataTest.HandlesOccupancy (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesBeta 65: [ OK ] SelectionCollectionDataTest.HandlesBeta (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesResname 65: [ OK ] SelectionCollectionDataTest.HandlesResname (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesCoordinateKeywords 65: [ OK ] SelectionCollectionDataTest.HandlesCoordinateKeywords (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesSameResidue 65: [ OK ] SelectionCollectionDataTest.HandlesSameResidue (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesSameResidueName 65: [ OK ] SelectionCollectionDataTest.HandlesSameResidueName (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesPositionKeywords 65: [ OK ] SelectionCollectionDataTest.HandlesPositionKeywords (1 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesDistanceKeyword 65: [ OK ] SelectionCollectionDataTest.HandlesDistanceKeyword (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesMinDistanceKeyword 65: [ OK ] SelectionCollectionDataTest.HandlesMinDistanceKeyword (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesWithinKeyword 65: [ OK ] SelectionCollectionDataTest.HandlesWithinKeyword (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword 65: [ OK ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword (2 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesPermuteModifier 65: [ OK ] SelectionCollectionDataTest.HandlesPermuteModifier (1 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesPlusModifier 65: [ OK ] SelectionCollectionDataTest.HandlesPlusModifier (1 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesMergeModifier 65: [ OK ] SelectionCollectionDataTest.HandlesMergeModifier (1 ms) 65: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndCharges 65: [ OK ] SelectionCollectionDataTest.ComputesMassesAndCharges (1 ms) 65: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology 65: [ OK ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets 65: [ OK ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesSelectionNames 65: [ OK ] SelectionCollectionDataTest.HandlesSelectionNames (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections 65: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed 65: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections 65: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections (1 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed 65: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositions 65: [ OK ] SelectionCollectionDataTest.HandlesConstantPositions (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers 65: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesWithinConstantPositions 65: [ OK ] SelectionCollectionDataTest.HandlesWithinConstantPositions (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges 65: [ OK ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingRealRanges 65: [ OK ] SelectionCollectionDataTest.HandlesOverlappingRealRanges (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode 65: [ OK ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesWildcardMatching 65: [ OK ] SelectionCollectionDataTest.HandlesWildcardMatching (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesRegexMatching 65: [ OK ] SelectionCollectionDataTest.HandlesRegexMatching (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesBasicBoolean 65: [ OK ] SelectionCollectionDataTest.HandlesBasicBoolean (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters 65: [ OK ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions 65: [ OK ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame 65: [ OK ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords 65: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods 65: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositions 65: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositions (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic 65: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesNumericComparisons 65: [ OK ] SelectionCollectionDataTest.HandlesNumericComparisons (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesArithmeticExpressions 65: [ OK ] SelectionCollectionDataTest.HandlesArithmeticExpressions (1 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesNumericVariables 65: [ OK ] SelectionCollectionDataTest.HandlesNumericVariables (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesComplexNumericVariables 65: [ OK ] SelectionCollectionDataTest.HandlesComplexNumericVariables (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariables 65: [ OK ] SelectionCollectionDataTest.HandlesPositionVariables (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariableInModifier 65: [ OK ] SelectionCollectionDataTest.HandlesPositionVariableInModifier (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionInVariable 65: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionInVariable (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables 65: [ OK ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis 65: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables 65: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables 65: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesUnusedVariables 65: [ OK ] SelectionCollectionDataTest.HandlesUnusedVariables (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups 65: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups 65: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups (0 ms) 65: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 65: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 (0 ms) 65: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWorksPreCompilation 65: [ OK ] SelectionCollectionDataTest.CopiedSelectionWorksPreCompilation (1 ms) 65: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation 65: [ OK ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation (1 ms) 65: [ RUN ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent 65: [ OK ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent (1 ms) 65: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation 65: [ OK ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation (1 ms) 65: [----------] 70 tests from SelectionCollectionDataTest (50 ms total) 65: 65: [----------] 17 tests from SelectionOptionTest 65: [ RUN ] SelectionOptionTest.ParsesSimpleSelection 65: [ OK ] SelectionOptionTest.ParsesSimpleSelection (0 ms) 65: [ RUN ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired 65: [ OK ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired (0 ms) 65: [ RUN ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired 65: [ OK ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired (0 ms) 65: [ RUN ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired 65: [ OK ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired (0 ms) 65: [ RUN ] SelectionOptionTest.ChecksEmptySelections 65: [ OK ] SelectionOptionTest.ChecksEmptySelections (0 ms) 65: [ RUN ] SelectionOptionTest.ChecksEmptyDelayedSelections 65: [ OK ] SelectionOptionTest.ChecksEmptyDelayedSelections (0 ms) 65: [ RUN ] SelectionOptionTest.HandlesTooManySelections 65: [ OK ] SelectionOptionTest.HandlesTooManySelections (0 ms) 65: [ RUN ] SelectionOptionTest.HandlesTooFewSelections 65: [ OK ] SelectionOptionTest.HandlesTooFewSelections (0 ms) 65: [ RUN ] SelectionOptionTest.HandlesDefaultSelectionText 65: [ OK ] SelectionOptionTest.HandlesDefaultSelectionText (0 ms) 65: [ RUN ] SelectionOptionTest.HandlesAdjuster 65: [ OK ] SelectionOptionTest.HandlesAdjuster (0 ms) 65: [ RUN ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster 65: [ OK ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster (0 ms) 65: [ RUN ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster 65: [ OK ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster (0 ms) 65: [ RUN ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster 65: [ OK ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster (0 ms) 65: [ RUN ] SelectionOptionTest.HandlesDelayedRequiredSelection 65: [ OK ] SelectionOptionTest.HandlesDelayedRequiredSelection (0 ms) 65: [ RUN ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections 65: [ OK ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections (0 ms) 65: [ RUN ] SelectionOptionTest.HandlesDelayedOptionalSelection 65: [ OK ] SelectionOptionTest.HandlesDelayedOptionalSelection (0 ms) 65: [ RUN ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster 65: [ OK ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster (0 ms) 65: [----------] 17 tests from SelectionOptionTest (4 ms total) 65: 65: [----------] 9 tests from SelectionFileOptionTest 65: [ RUN ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile 65: [ OK ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile (0 ms) 65: [ RUN ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions 65: [ OK ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions (0 ms) 65: [ RUN ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile 65: [ OK ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile (0 ms) 65: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFile 65: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFile (0 ms) 65: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet 65: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet (0 ms) 65: [ RUN ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile 65: [ OK ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile (0 ms) 65: [ RUN ] SelectionFileOptionTest.GivesErrorWithNoFile 65: [ OK ] SelectionFileOptionTest.GivesErrorWithNoFile (0 ms) 65: [ RUN ] SelectionFileOptionTest.GivesErrorWithNonExistentFile 65: [ OK ] SelectionFileOptionTest.GivesErrorWithNonExistentFile (0 ms) 65: [ RUN ] SelectionFileOptionTest.GivesErrorWithMultipleFiles 65: [ OK ] SelectionFileOptionTest.GivesErrorWithMultipleFiles (0 ms) 65: [----------] 9 tests from SelectionFileOptionTest (2 ms total) 65: 65: [----------] Global test environment tear-down 65: [==========] 201 tests from 11 test suites ran. (176 ms total) 65: [ PASSED ] 201 tests. 65/94 Test #65: SelectionUnitTests ........................... Passed 0.53 sec test 66 Start 66: MdrunOutputTests 66: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/mdrun-output-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/MdrunOutputTests.xml" 66: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests 66: Test timeout computed to be: 600 66: [==========] Running 12 tests from 5 test suites. 66: [----------] Global test environment set-up. 66: [----------] 1 test from MdrunTest 66: [ RUN ] MdrunTest.WritesHelp 66: [ OK ] MdrunTest.WritesHelp (81 ms) 66: [----------] 1 test from MdrunTest (81 ms total) 66: 66: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput 66: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group rest is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 2 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 1 steps, 0.0 ps. 66: Setting the LD random seed to 1778253303 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.062 0.031 199.2 66: (ns/day) (hour/ns) 66: Performance: 5.557 4.319 66: Reading frame 0 time 0.000 66: # Atoms 6 66: Reading frame 1 time 0.001 Last frame 1 time 0.001 66: 66: 66: Item #frames Timestep (ps) 66: Step 2 0.001 66: Time 2 0.001 66: Lambda 0 66: Coords 2 0.001 66: Velocities 0 66: Forces 0 66: Box 2 0.001 66: Checking file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.xtc 66: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 (41 ms) 66: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group rest is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 2 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 1 steps, 0.0 ps. 66: Setting the LD random seed to -723089 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.021 0.010 198.2 66: (ns/day) (hour/ns) 66: Performance: 16.596 1.446 66: Reading frame 0 time 0.000 66: # Atoms 6 66: Reading frame 1 time 0.001 Last frame 1 time 0.001 66: 66: 66: Item #frames Timestep (ps) 66: Step 2 0.001 66: Time 2 0.001 66: Lambda 0 66: Coords 2 0.001 66: Velocities 0 66: Forces 0 66: Box 2 0.001 66: Checking file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.xtc 66: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 (17 ms) 66: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group rest is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 66: NVE simulation: will use the initial temperature of 2573.591 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 2 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 1 steps, 0.0 ps. 66: Setting the LD random seed to -16777217 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.024 0.012 198.7 66: (ns/day) (hour/ns) 66: Performance: 14.265 1.682 66: Reading frame 0 time 0.000 66: # Atoms 3 66: Reading frame 1 time 0.001 Last frame 1 time 0.001 66: 66: 66: Item #frames Timestep (ps) 66: Step 2 0.001 66: Time 2 0.001 66: Lambda 0 66: Coords 2 0.001 66: Velocities 0 66: Forces 0 66: Box 2 0.001 66: Checking file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.xtc 66: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 (19 ms) 66: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput (78 ms total) 66: 66: [----------] 2 tests from Argon12/OutputFiles 66: [ RUN ] Argon12/OutputFiles.FilesArePresent/0 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 66: NVE simulation: will use the initial temperature of 68.810 K for 66: determining the Verlet buffer size 66: 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.048 0.024 199.4 66: (ns/day) (hour/ns) 66: Performance: 61.300 0.392 66: [ OK ] Argon12/OutputFiles.FilesArePresent/0 (33 ms) 66: [ RUN ] Argon12/OutputFiles.FilesArePresent/1 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 66: NVE simulation: will use the initial temperature of 68.810 K for 66: determining the Verlet buffer size 66: 66: 66: There were 3 NOTEs 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 16 steps, 0.0 ps. 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.025 0.013 198.7 66: (ns/day) (hour/ns) 66: Performance: 115.123 0.208 66: [ OK ] Argon12/OutputFiles.FilesArePresent/1 (19 ms) 66: [----------] 2 tests from Argon12/OutputFiles (52 ms total) 66: 66: [----------] 3 tests from MdrunCanWrite/Trajectories 66: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 66: Number of degrees of freedom in T-Coupling group System is 12.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There was 1 NOTE 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 66: 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc-and-methanol' 66: 6 steps, 0.0 ps. 66: Setting the LD random seed to -1136722498 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.035 0.018 199.1 66: (ns/day) (hour/ns) 66: Performance: 34.476 0.696 66: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 (27 ms) 66: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 66: Number of degrees of freedom in T-Coupling group System is 12.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There was 1 NOTE 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 66: 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc-and-methanol' 66: 6 steps, 0.0 ps. 66: Setting the LD random seed to -554180901 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: NOTE: 39 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.041 0.021 198.8 66: (ns/day) (hour/ns) 66: Performance: 29.220 0.821 66: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 (33 ms) 66: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 66: Number of degrees of freedom in T-Coupling group System is 12.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There was 1 NOTE 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 66: 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc-and-methanol' 66: 6 steps, 0.0 ps. 66: Setting the LD random seed to 2080047063 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.041 0.021 199.2 66: (ns/day) (hour/ns) 66: Performance: 29.375 0.817 66: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 (32 ms) 66: [----------] 3 tests from MdrunCanWrite/Trajectories (93 ms total) 66: 66: [----------] 3 tests from MdrunCanWrite/NptTrajectories 66: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 66: Number of degrees of freedom in T-Coupling group System is 12.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There was 1 NOTE 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 66: 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc-and-methanol' 66: 2 steps, 0.0 ps. 66: Setting the LD random seed to -3174437 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.025 0.012 198.8 66: (ns/day) (hour/ns) 66: Performance: 20.743 1.157 66: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 (23 ms) 66: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 66: 66: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: 66: The Berendsen barostat does not generate any strictly correct ensemble, 66: and should not be used for new production simulations (in our opinion). 66: We recommend using the C-rescale barostat instead. 66: 66: Number of degrees of freedom in T-Coupling group System is 12.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There was 1 NOTE 66: 66: There was 1 WARNING 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 66: 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc-and-methanol' 66: 2 steps, 0.0 ps. 66: Setting the LD random seed to 2033379187 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.016 0.008 198.1 66: (ns/day) (hour/ns) 66: Performance: 32.321 0.743 66: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 (18 ms) 66: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 66: Number of degrees of freedom in T-Coupling group System is 12.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There was 1 NOTE 66: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 66: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 66: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 66: 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc-and-methanol' 66: 2 steps, 0.0 ps. 66: Setting the LD random seed to -269607689 66: 66: Generated 8 of the 10 non-bonded parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'Methanol' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.026 0.013 198.8 66: (ns/day) (hour/ns) 66: Performance: 19.766 1.214 66: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 (32 ms) 66: [----------] 3 tests from MdrunCanWrite/NptTrajectories (73 ms total) 66: 66: [----------] Global test environment tear-down 66: [==========] 12 tests from 5 test suites ran. (681 ms total) 66: [ PASSED ] 12 tests. 66/94 Test #66: MdrunOutputTests ............................. Passed 1.03 sec test 67 Start 67: MdrunModulesTests 67: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/mdrun-modules-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/MdrunModulesTests.xml" 67: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests 67: Test timeout computed to be: 600 67: [==========] Running 15 tests from 3 test suites. 67: [----------] Global test environment set-up. 67: [----------] 9 tests from DensityFittingTest 67: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct 67: Number of degrees of freedom in T-Coupling group rest is 33.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Using 1 MPI process 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Steepest Descents: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 2 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Steepest Descents did not converge to Fmax < 10 in 3 steps. 67: Potential Energy = -3.8565254e+03 67: Maximum force = 4.5099883e+03 on atom 3 67: Norm of force = 1.6816849e+03 67: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to 392980446 67: 67: Generated 1 of the 1 non-bonded parameter combinations 67: 67: Excluding 1 bonded neighbours molecule type 'Argon' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct (8 ms) 67: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation 67: Number of degrees of freedom in T-Coupling group rest is 33.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Using 1 MPI process 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Steepest Descents: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 2 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Steepest Descents did not converge to Fmax < 10 in 3 steps. 67: Potential Energy = -9.8207725e+03 67: Maximum force = 7.3954834e+03 on atom 2 67: Norm of force = 2.7825089e+03 67: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to 2096856494 67: 67: Generated 1 of the 1 non-bonded parameter combinations 67: 67: Excluding 1 bonded neighbours molecule type 'Argon' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation (6 ms) 67: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff 67: [ OK ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff (0 ms) 67: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix 67: Number of degrees of freedom in T-Coupling group rest is 33.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Overriding nsteps with value passed on the command line: 4 steps 67: 67: Using 1 MPI process 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Steepest Descents: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 4 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Steepest Descents did not converge to Fmax < 10 in 5 steps. 67: Potential Energy = -1.0954993e+04 67: Maximum force = 7.4724790e+03 on atom 2 67: Norm of force = 2.7758003e+03 67: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Setting the LD random seed to 2067690738 67: 67: Generated 1 of the 1 non-bonded parameter combinations 67: 67: Excluding 1 bonded neighbours molecule type 'Argon' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix (6 ms) 67: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff 67: [ OK ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff (0 ms) 67: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix 67: Number of degrees of freedom in T-Coupling group rest is 33.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Using 1 MPI process 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Steepest Descents: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 2 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Steepest Descents did not converge to Fmax < 10 in 3 steps. 67: Potential Energy = -3.8565254e+03 67: Maximum force = 4.5099883e+03 on atom 3 67: Norm of force = 1.6816849e+03 67: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -1344815873 67: 67: Generated 1 of the 1 non-bonded parameter combinations 67: 67: Excluding 1 bonded neighbours molecule type 'Argon' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix (5 ms) 67: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy 67: Number of degrees of freedom in T-Coupling group rest is 33.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Using 1 MPI process 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Steepest Descents: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 2 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Steepest Descents did not converge to Fmax < 10 in 3 steps. 67: Potential Energy = -2.7138664e+04 67: Maximum force = 6.7827656e+03 on atom 2 67: Norm of force = 1.9608866e+03 67: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to 1799281591 67: 67: Generated 1 of the 1 non-bonded parameter combinations 67: 67: Excluding 1 bonded neighbours molecule type 'Argon' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy (6 ms) 67: [ RUN ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch 67: [ OK ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch (0 ms) 67: [ RUN ] DensityFittingTest.CheckpointWorks 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (2) 67: 67: Number of degrees of freedom in T-Coupling group rest is 33.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: 67: NVE simulation: will use the initial temperature of 68.810 K for 67: determining the Verlet buffer size 67: 67: 67: There were 2 NOTEs 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI process 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Argon' 67: 2 steps, 0.0 ps. 67: Setting the LD random seed to 2137998335 67: 67: Generated 1 of the 1 non-bonded parameter combinations 67: 67: Excluding 1 bonded neighbours molecule type 'Argon' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 67: 67: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 68.8096 K 67: 67: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.160 0.080 199.8 67: (ns/day) (hour/ns) 67: Performance: 3.242 7.402 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Overriding nsteps with value passed on the command line: 4 steps, 0.004 ps 67: Can not increase nstlist because an NVE ensemble is used 67: 67: Using 1 MPI process 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Argon' 67: 6 steps, 0.0 ps (continuing from step 2, 0.0 ps). 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.020 0.010 199.0 67: (ns/day) (hour/ns) 67: Performance: 43.490 0.552 67: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Last energy frame read 1 time 0.002 [ OK ] DensityFittingTest.CheckpointWorks (99 ms) 67: [----------] 9 tests from DensityFittingTest (133 ms total) 67: 67: [----------] 4 tests from MimicTest 67: [ RUN ] MimicTest.OneQuantumMol 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Number of degrees of freedom in T-Coupling group rest is 21.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 67: NVE simulation with an initial temperature of zero: will use a Verlet 67: buffer of 10%. Check your energy drift! 67: 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 3 NOTEs 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI process 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro' 67: 67: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 67: Reading frame 0 time 0.000 Last frame 0 time 0.000 67: 67: NOTE: 28 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.001 0.000 189.5 67: (ns/day) (hour/ns) 67: Performance: 256.286 0.094 67: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -51019860 67: 67: Generated 10 of the 10 non-bonded parameter combinations 67: 67: Generated 10 of the 10 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MimicTest.OneQuantumMol (7 ms) 67: [ RUN ] MimicTest.AllQuantumMol 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Number of degrees of freedom in T-Coupling group rest is 21.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 67: NVE simulation with an initial temperature of zero: will use a Verlet 67: buffer of 10%. Check your energy drift! 67: 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 3 NOTEs 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI process 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro' 67: 67: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 67: Reading frame 0 time 0.000 Last frame 0 time 0.000 67: 67: NOTE: 28 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.000 0.000 184.7 67: (ns/day) (hour/ns) 67: Performance: 341.232 0.070 67: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -1660948513 67: 67: Generated 10 of the 10 non-bonded parameter combinations 67: 67: Generated 10 of the 10 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MimicTest.AllQuantumMol (5 ms) 67: [ RUN ] MimicTest.TwoQuantumMol 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Number of degrees of freedom in T-Coupling group rest is 21.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 67: NVE simulation with an initial temperature of zero: will use a Verlet 67: buffer of 10%. Check your energy drift! 67: 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 3 NOTEs 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI process 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro' 67: 67: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 67: Reading frame 0 time 0.000 Last frame 0 time 0.000 67: 67: NOTE: 28 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.000 0.000 188.1 67: (ns/day) (hour/ns) 67: Performance: 353.549 0.068 67: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -1346430722 67: 67: Generated 10 of the 10 non-bonded parameter combinations 67: 67: Generated 10 of the 10 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MimicTest.TwoQuantumMol (5 ms) 67: [ RUN ] MimicTest.BondCuts 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Number of degrees of freedom in T-Coupling group rest is 66.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 67: NVE simulation: will use the initial temperature of 300.368 K for 67: determining the Verlet buffer size 67: 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 3 NOTEs 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 1 MPI process 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 67: 67: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 67: Reading frame 0 time 0.000 Last frame 0 time 0.000 67: 67: NOTE: 30 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.001 0.001 193.6 67: (ns/day) (hour/ns) 67: Performance: 140.515 0.171 67: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -1130823941 67: 67: Generated 2211 of the 2211 non-bonded parameter combinations 67: 67: Generated 2211 of the 2211 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 67: 67: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 67: 67: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MimicTest.BondCuts (17 ms) 67: [----------] 4 tests from MimicTest (35 ms total) 67: 67: [----------] 2 tests from WithIntegrator/ImdTest 67: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/0 67: Generating 1-4 interactions: fudge = 1 67: 67: NOTE 1 [file glycine_vacuo.top, line 12]: 67: The bond in molecule-type Glycine between atoms 1 N and 2 H1 has an 67: estimated oscillational period of 1.0e-02 ps, which is less than 10 times 67: the time step of 2.0e-03 ps. 67: Maybe you forgot to change the constraints mdp option. 67: 67: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). 67: Number of degrees of freedom in T-Coupling group System is 27.00 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 2 NOTEs 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Changing nstlist from 10 to 25, rlist from 1.071 to 1.232 67: 67: Using 1 MPI process 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: IMD: Enabled. This simulation will accept incoming IMD connections. 67: IMD: Pulling from IMD remote is enabled (-imdpull). 67: IMD: Setting port for connection requests to 0. 67: IMD: Setting up incoming socket. 67: IMD: Listening for IMD connection on port 42091. 67: IMD: -imdwait not set, starting simulation. 67: starting mdrun 'Glycine' 67: 2 steps, 0.0 ps. 67: Setting the LD random seed to 798989039 67: 67: Generated 20503 of the 20503 non-bonded parameter combinations 67: 67: Generated 17396 of the 20503 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Glycine' 67: 67: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/glycine_vacuo.gro', all velocities are zero 67: 67: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 67: 67: Calculated rlist for 1x1 atom pair-list as 1.093 nm, buffer size 0.093 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 1.071 nm, buffer size 0.071 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.022 0.011 198.4 67: (ns/day) (hour/ns) 67: Performance: 47.668 0.503 67: [ OK ] WithIntegrator/ImdTest.ImdCanRun/0 (121 ms) 67: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/1 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: 67: Setting tcoupl from 'V-rescale' to 'no'. Temperature coupling does not 67: apply to steep. 67: 67: Generating 1-4 interactions: fudge = 1 67: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). 67: Number of degrees of freedom in T-Coupling group System is 27.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 2 NOTEs 67: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 67: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 67: Using 1 MPI process 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: IMD: Enabled. This simulation will accept incoming IMD connections. 67: IMD: Pulling from IMD remote is enabled (-imdpull). 67: IMD: Setting port for connection requests to 0. 67: IMD: Setting up incoming socket. 67: IMD: Listening for IMD connection on port 57229. 67: IMD: -imdwait not set, starting simulation. 67: 67: Steepest Descents: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 2 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Steepest Descents did not converge to Fmax < 10 in 3 steps. 67: Potential Energy = 1.1977064e+03 67: Maximum force = 1.7794877e+04 on atom 9 67: Norm of force = 7.8732901e+03 67: Setting the LD random seed to -207788099 67: 67: Generated 20503 of the 20503 non-bonded parameter combinations 67: 67: Generated 17396 of the 20503 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Glycine' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] WithIntegrator/ImdTest.ImdCanRun/1 (118 ms) 67: [----------] 2 tests from WithIntegrator/ImdTest (239 ms total) 67: 67: [----------] Global test environment tear-down 67: [==========] 15 tests from 3 test suites ran. (620 ms total) 67: [ PASSED ] 15 tests. 67/94 Test #67: MdrunModulesTests ............................ Passed 0.95 sec test 68 Start 68: MdrunIOTests 68: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/mdrun-io-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/MdrunIOTests.xml" 68: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests 68: Test timeout computed to be: 600 68: [==========] Running 76 tests from 13 test suites. 68: [----------] Global test environment set-up. 68: [----------] 9 tests from GromppTest 68: [ RUN ] GromppTest.EmptyMdpFileWorks 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 68: For a correct single-point energy evaluation with nsteps = 0, use 68: continuation = yes to avoid constraining the input coordinates. 68: 68: Number of degrees of freedom in T-Coupling group rest is 12.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 68: NVE simulation: will use the initial temperature of 1046.791 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Setting the LD random seed to -168315985 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] GromppTest.EmptyMdpFileWorks (6 ms) 68: [ RUN ] GromppTest.SimulatedAnnealingWorks 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 68: For a correct single-point energy evaluation with nsteps = 0, use 68: continuation = yes to avoid constraining the input coordinates. 68: 68: Simulated annealing for group rest: Periodic, 4 timepoints 68: Time (ps) Temperature (K) 68: 0.0 298.0 68: 2.0 320.0 68: 4.0 320.0 68: 6.0 298.0 68: Number of degrees of freedom in T-Coupling group rest is 12.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 68: NVE simulation: will use the initial temperature of 1046.791 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Setting the LD random seed to -1107624481 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] GromppTest.SimulatedAnnealingWorks (4 ms) 68: [ RUN ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 68: For a correct single-point energy evaluation with nsteps = 0, use 68: continuation = yes to avoid constraining the input coordinates. 68: 68: Simulated annealing for group Methanol: Single, 3 timepoints 68: Time (ps) Temperature (K) 68: 0.0 298.0 68: 3.0 280.0 68: 6.0- 270.0 68: Simulated annealing for group SOL: Periodic, 4 timepoints 68: Time (ps) Temperature (K) 68: 0.0 298.0 68: 2.0 320.0 68: 4.0 320.0 68: 6.0 298.0 68: Number of degrees of freedom in T-Coupling group Methanol is 7.20 68: Number of degrees of freedom in T-Coupling group SOL is 4.80 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 68: NVE simulation: will use the initial temperature of 1046.791 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Setting the LD random seed to -268509701 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups (3 ms) 68: [ RUN ] GromppTest.DeathTestHandlesNoMaxwarnError 68: [ OK ] GromppTest.DeathTestHandlesNoMaxwarnError (0 ms) 68: [ RUN ] GromppTest.HandlesMaxwarn 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 68: For a correct single-point energy evaluation with nsteps = 0, use 68: continuation = yes to avoid constraining the input coordinates. 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 68: The Berendsen thermostat does not generate the correct kinetic energy 68: distribution, and should not be used for new production simulations (in 68: our opinion). We would recommend the V-rescale thermostat. 68: 68: Number of degrees of freedom in T-Coupling group System is 12.00 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 2 NOTEs 68: 68: There was 1 WARNING 68: Setting the LD random seed to -76103698 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] GromppTest.HandlesMaxwarn (3 ms) 68: [ RUN ] GromppTest.MaxwarnShouldBePositive 68: [ OK ] GromppTest.MaxwarnShouldBePositive (0 ms) 68: [ RUN ] GromppTest.ValidTransformationCoord 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 68: For a correct single-point energy evaluation with nsteps = 0, use 68: continuation = yes to avoid constraining the input coordinates. 68: 68: Pull group 1 'SOL' has 3 atoms 68: Pull group 2 'Methanol' has 3 atoms 68: Number of degrees of freedom in T-Coupling group rest is 12.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 68: NVE simulation: will use the initial temperature of 1046.791 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 3 5 68: 2 3 2 0.613 nm 0.000 nm 68: 1 3 5 68: 2 3 2 0.613 nm 0.000 nm 68: 68: There were 3 NOTEs 68: Setting the LD random seed to -457179161 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] GromppTest.ValidTransformationCoord (6 ms) 68: [ RUN ] GromppTest.InvalidTransformationCoord 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 68: For a correct single-point energy evaluation with nsteps = 0, use 68: continuation = yes to avoid constraining the input coordinates. 68: 68: Pull group 1 'SOL' has 3 atoms 68: Pull group 2 'Methanol' has 3 atoms 68: Number of degrees of freedom in T-Coupling group rest is 12.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 68: NVE simulation: will use the initial temperature of 1046.791 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 3 5 68: 2 3 2 0.613 nm 0.000 nm 68: 1 3 5 68: 2 3 2 Setting the LD random seed to -413185166 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: [ OK ] GromppTest.InvalidTransformationCoord (5 ms) 68: [ RUN ] GromppTest.RejectCRescaleAndAnisotropic 68: [ OK ] GromppTest.RejectCRescaleAndAnisotropic (0 ms) 68: [----------] 9 tests from GromppTest (31 ms total) 68: 68: [----------] 6 tests from MdrunTerminationTest 68: [ RUN ] MdrunTerminationTest.CheckpointRestartAppendsByDefault 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There was 1 NOTE 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 2 steps, 0.0 ps. 68: Setting the LD random seed to -59171 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.015 0.008 198.3 68: (ns/day) (hour/ns) 68: Performance: 33.477 0.717 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Setting nsteps to 4 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 68: Input file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 2 68: Runtime for the run 0.002 ps 68: Run end step 2 68: Run end time 0.002 ps 68: 68: 68: Output file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 4 68: Runtime for the run 0.004 ps 68: Run end step 4 68: Run end time 0.004 ps 68: 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.011 0.005 197.9 68: (ns/day) (hour/ns) 68: Performance: 48.111 0.499 68: [ OK ] MdrunTerminationTest.CheckpointRestartAppendsByDefault (26 ms) 68: [ RUN ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There was 1 NOTE 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 10 to 1, rlist from 1.032 to 1 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 100 steps, 0.1 ps. 68: 68: Step 3: Run time exceeded 0.000 hours, will terminate the run within 200 steps 68: Setting the LD random seed to -277615590 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: NOTE: 21 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.030 0.015 199.0 68: (ns/day) (hour/ns) 68: Performance: 586.717 0.041 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Setting nsteps to 102 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 102 steps, 0.1 ps (continuing from step 100, 0.1 ps). 68: Input file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 100 68: Runtime for the run 0.1 ps 68: Run end step 100 68: Run end time 0.1 ps 68: 68: 68: Output file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 102 68: Runtime for the run 0.102 ps 68: Run end step 102 68: Run end time 0.102 ps 68: 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.015 0.008 197.9 68: (ns/day) (hour/ns) 68: Performance: 34.404 0.698 68: [ OK ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (34 ms) 68: [ RUN ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There was 1 NOTE 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 2 steps, 0.0 ps. 68: Setting the LD random seed to -556336964 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.012 0.006 197.7 68: (ns/day) (hour/ns) 68: Performance: 41.331 0.581 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Setting nsteps to 4 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 68: Input file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 2 68: Runtime for the run 0.002 ps 68: Run end step 2 68: Run end time 0.002 ps 68: 68: 68: Output file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 4 68: Runtime for the run 0.004 ps 68: Run end step 4 68: Run end time 0.004 ps 68: 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.013 0.007 198.6 68: (ns/day) (hour/ns) 68: Performance: 39.756 0.604 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Setting nsteps to 6 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 6 steps, 0.0 ps (continuing from step 4, 0.0 ps). 68: Input file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 4 68: Runtime for the run 0.004 ps 68: Run end step 4 68: Run end time 0.004 ps 68: 68: 68: Output file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 6 68: Runtime for the run 0.006 ps 68: Run end step 6 68: Run end time 0.006 ps 68: 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.017 0.009 198.9 68: (ns/day) (hour/ns) 68: Performance: 29.933 0.802 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Setting nsteps to 8 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps (continuing from step 6, 0.0 ps). 68: Input file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 6 68: Runtime for the run 0.006 ps 68: Run end step 6 68: Run end time 0.006 ps 68: 68: 68: Output file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 8 68: Runtime for the run 0.008 ps 68: Run end step 8 68: Run end time 0.008 ps 68: 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.017 0.009 198.9 68: (ns/day) (hour/ns) 68: Performance: 29.934 0.802 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: NOTE: 29 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.000 0.000 180.4 68: (ns/day) (hour/ns) 68: Performance: 386.753 0.062 68: [ OK ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend (53 ms) 68: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There was 1 NOTE 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 2 steps, 0.0 ps. 68: Setting the LD random seed to -268682758 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.012 0.006 197.9 68: (ns/day) (hour/ns) 68: Performance: 43.500 0.552 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Setting nsteps to 4 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 4 steps, 0.0 ps. 68: Input file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 2 68: Runtime for the run 0.002 ps 68: Run end step 2 68: Run end time 0.002 ps 68: 68: 68: Output file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 4 68: Runtime for the run 0.004 ps 68: Run end step 4 68: Run end time 0.004 ps 68: 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.014 0.007 198.0 68: (ns/day) (hour/ns) 68: Performance: 59.994 0.400 68: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile (25 ms) 68: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There was 1 NOTE 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 2 steps, 0.0 ps. 68: Setting the LD random seed to 2063597022 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.012 0.006 197.7 68: (ns/day) (hour/ns) 68: Performance: 43.422 0.553 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Setting nsteps to 4 68: Input file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 2 68: Runtime for the run 0.002 ps 68: Run end step 2 68: Run end time 0.002 ps 68: 68: 68: Output file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 4 68: Runtime for the run 0.004 ps 68: Run end step 4 68: Run end time 0.004 ps 68: 68: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile (14 ms) 68: [ RUN ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There was 1 NOTE 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 2 steps, 0.0 ps. 68: Setting the LD random seed to -174852882 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.016 0.008 197.7 68: (ns/day) (hour/ns) 68: Performance: 31.672 0.758 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Setting nsteps to 4 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 68: Input file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 2 68: Runtime for the run 0.002 ps 68: Run end step 2 68: Run end time 0.002 ps 68: 68: 68: Output file: 68: Run start step 0 68: Run start time 0 ps 68: Step to be made during run 4 68: Runtime for the run 0.004 ps 68: Run end step 4 68: Run end time 0.004 ps 68: 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.018 0.009 198.9 68: (ns/day) (hour/ns) 68: Performance: 28.263 0.849 68: [ OK ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles (29 ms) 68: [----------] 6 tests from MdrunTerminationTest (184 ms total) 68: 68: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks 68: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.026 0.013 198.8 68: (ns/day) (hour/ns) 68: Performance: 112.730 0.213 68: trr version: GMX_trn_file (single precision) 68: 68: 68: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 (20 ms) 68: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.019 0.009 198.4 68: (ns/day) (hour/ns) 68: Performance: 154.855 0.155 68: 68: 68: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 (20 ms) 68: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks (40 ms total) 68: 68: [----------] 24 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.021 0.010 198.3 68: (ns/day) (hour/ns) 68: Performance: 140.968 0.170 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.017 0.009 198.4 68: (ns/day) (hour/ns) 68: Performance: 89.119 0.269 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.017 0.009 198.7 68: (ns/day) (hour/ns) 68: Performance: 88.538 0.271 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (46 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.024 0.012 198.8 68: (ns/day) (hour/ns) 68: Performance: 121.667 0.197 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.018 0.009 198.6 68: (ns/day) (hour/ns) 68: Performance: 87.271 0.275 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.016 0.008 198.1 68: (ns/day) (hour/ns) 68: Performance: 94.833 0.253 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (47 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.017 0.009 199.0 68: (ns/day) (hour/ns) 68: Performance: 169.443 0.142 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.017 0.009 198.9 68: (ns/day) (hour/ns) 68: Performance: 88.647 0.271 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.019 0.010 198.0 68: (ns/day) (hour/ns) 68: Performance: 79.850 0.301 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (42 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.022 0.011 199.0 68: (ns/day) (hour/ns) 68: Performance: 135.487 0.177 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.023 0.012 199.2 68: (ns/day) (hour/ns) 68: Performance: 67.074 0.358 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.024 0.012 198.4 68: (ns/day) (hour/ns) 68: Performance: 65.251 0.368 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (49 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.020 0.010 198.8 68: (ns/day) (hour/ns) 68: Performance: 142.950 0.168 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.021 0.011 199.0 68: (ns/day) (hour/ns) 68: Performance: 72.705 0.330 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.021 0.010 199.0 68: (ns/day) (hour/ns) 68: Performance: 74.207 0.323 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (49 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.709 to 0.733 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.711 nm, buffer size 0.011 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.711 nm, buffer size 0.011 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.033 0.016 199.0 68: (ns/day) (hour/ns) 68: Performance: 89.356 0.269 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.709 to 0.733 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.020 0.010 199.0 68: (ns/day) (hour/ns) 68: Performance: 78.936 0.304 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.709 to 0.733 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.022 0.011 199.0 68: (ns/day) (hour/ns) 68: Performance: 69.733 0.344 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (57 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.024 0.012 199.0 68: (ns/day) (hour/ns) 68: Performance: 120.468 0.199 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.020 0.010 198.8 68: (ns/day) (hour/ns) 68: Performance: 75.473 0.318 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.022 0.011 198.9 68: (ns/day) (hour/ns) 68: Performance: 68.844 0.349 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (52 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.022 0.011 198.9 68: (ns/day) (hour/ns) 68: Performance: 132.551 0.181 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.023 0.012 198.8 68: (ns/day) (hour/ns) 68: Performance: 67.324 0.356 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.029 0.014 199.1 68: (ns/day) (hour/ns) 68: Performance: 54.329 0.442 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (55 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.030 0.015 198.6 68: (ns/day) (hour/ns) 68: Performance: 98.816 0.243 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.032 0.016 199.1 68: (ns/day) (hour/ns) 68: Performance: 48.678 0.493 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.020 0.010 198.6 68: (ns/day) (hour/ns) 68: Performance: 76.396 0.314 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (68 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.040 0.020 199.2 68: (ns/day) (hour/ns) 68: Performance: 73.557 0.326 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.026 0.013 198.9 68: (ns/day) (hour/ns) 68: Performance: 58.394 0.411 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.029 0.014 199.0 68: (ns/day) (hour/ns) 68: Performance: 53.678 0.447 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (70 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.139 0.070 199.8 68: (ns/day) (hour/ns) 68: Performance: 21.042 1.141 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.032 0.016 199.3 68: (ns/day) (hour/ns) 68: Performance: 49.140 0.488 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.030 0.015 198.7 68: (ns/day) (hour/ns) 68: Performance: 51.600 0.465 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_secondpart.part0002.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (118 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.144 0.072 199.8 68: (ns/day) (hour/ns) 68: Performance: 20.366 1.178 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.022 0.011 199.0 68: (ns/day) (hour/ns) 68: Performance: 70.277 0.342 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.025 0.013 198.8 68: (ns/day) (hour/ns) 68: Performance: 60.949 0.394 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_secondpart.part0002.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (121 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/12 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.026 0.013 198.9 68: (ns/day) (hour/ns) 68: Performance: 111.506 0.215 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.028 0.014 199.0 68: (ns/day) (hour/ns) 68: Performance: 55.463 0.433 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.019 0.010 198.3 68: (ns/day) (hour/ns) 68: Performance: 79.533 0.302 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_secondpart.part0002.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/12 (58 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/13 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.73 to 0.811 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.024 0.012 198.8 68: (ns/day) (hour/ns) 68: Performance: 121.504 0.198 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.73 to 0.811 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.018 0.009 198.6 68: (ns/day) (hour/ns) 68: Performance: 83.951 0.286 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.73 to 0.811 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.023 0.012 198.9 68: (ns/day) (hour/ns) 68: Performance: 67.516 0.355 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_secondpart.part0002.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/13 (60 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/14 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.760 nm, buffer size 0.060 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.760 nm, buffer size 0.060 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.036 0.018 199.0 68: (ns/day) (hour/ns) 68: Performance: 81.297 0.295 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.021 0.011 198.7 68: (ns/day) (hour/ns) 68: Performance: 73.834 0.325 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.018 0.009 198.5 68: (ns/day) (hour/ns) 68: Performance: 87.861 0.273 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_secondpart.part0002.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/14 (59 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/15 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 25, rlist from 0.752 to 0.89 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.757 nm, buffer size 0.057 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.752 nm, buffer size 0.052 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.757 nm, buffer size 0.057 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.752 nm, buffer size 0.052 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.036 0.018 199.2 68: (ns/day) (hour/ns) 68: Performance: 81.481 0.295 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 25, rlist from 0.752 to 0.89 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.018 0.009 198.5 68: (ns/day) (hour/ns) 68: Performance: 88.025 0.273 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 25, rlist from 0.752 to 0.89 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.020 0.010 198.7 68: (ns/day) (hour/ns) 68: Performance: 79.020 0.304 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_secondpart.part0002.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/15 (60 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/16 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 68: NVE simulation: will use the initial temperature of 456.887 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 6 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 68: NVE simulation: will use the initial temperature of 456.887 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 6 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.031 0.016 198.9 68: (ns/day) (hour/ns) 68: Performance: 93.789 0.256 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.034 0.017 198.9 68: (ns/day) (hour/ns) 68: Performance: 45.923 0.523 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.101 0.051 199.6 68: (ns/day) (hour/ns) 68: Performance: 15.375 1.561 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_secondpart.part0002.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/16 (131 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/17 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 68: NVE simulation: will use the initial temperature of 456.887 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 6 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 68: NVE simulation: will use the initial temperature of 456.887 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 6 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.022 0.011 198.5 68: (ns/day) (hour/ns) 68: Performance: 129.924 0.185 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.019 0.010 198.2 68: (ns/day) (hour/ns) 68: Performance: 81.031 0.296 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.020 0.010 198.1 68: (ns/day) (hour/ns) 68: Performance: 77.771 0.309 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_secondpart.part0002.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/17 (78 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/18 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 68: NVE simulation: will use the initial temperature of 456.887 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 6 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 68: NVE simulation: will use the initial temperature of 456.887 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 6 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.023 0.012 197.6 68: (ns/day) (hour/ns) 68: Performance: 125.406 0.191 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.036 0.018 199.1 68: (ns/day) (hour/ns) 68: Performance: 42.821 0.560 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.022 0.011 198.5 68: (ns/day) (hour/ns) 68: Performance: 69.613 0.345 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_secondpart.part0002.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/18 (86 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/19 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 68: NVE simulation: will use the initial temperature of 456.887 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 6 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 68: NVE simulation: will use the initial temperature of 456.887 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 6 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.030 0.015 198.8 68: (ns/day) (hour/ns) 68: Performance: 96.849 0.248 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.028 0.014 198.8 68: (ns/day) (hour/ns) 68: Performance: 55.117 0.435 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.041 0.021 199.1 68: (ns/day) (hour/ns) 68: Performance: 37.592 0.638 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_secondpart.part0002.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/19 (101 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/20 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.040 0.020 199.1 68: (ns/day) (hour/ns) 68: Performance: 72.591 0.331 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.060 0.030 199.4 68: (ns/day) (hour/ns) 68: Performance: 25.819 0.930 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.034 0.017 198.9 68: (ns/day) (hour/ns) 68: Performance: 45.943 0.522 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_secondpart.part0002.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/20 (164 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/21 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 80, rlist from 0.741 to 0.841 68: 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.747 nm, buffer size 0.047 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.747 nm, buffer size 0.047 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.038 0.019 199.2 68: (ns/day) (hour/ns) 68: Performance: 76.569 0.313 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 80, rlist from 0.741 to 0.841 68: 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.200 0.100 199.8 68: (ns/day) (hour/ns) 68: Performance: 7.754 3.095 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 80, rlist from 0.741 to 0.841 68: 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.039 0.020 199.1 68: (ns/day) (hour/ns) 68: Performance: 39.647 0.605 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_secondpart.part0002.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/21 (392 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/22 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.029 0.015 198.9 68: (ns/day) (hour/ns) 68: Performance: 99.701 0.241 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.048 0.024 199.3 68: (ns/day) (hour/ns) 68: Performance: 32.343 0.742 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.024 0.012 198.3 68: (ns/day) (hour/ns) 68: Performance: 63.205 0.380 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_secondpart.part0002.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/22 (137 ms) 68: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/23 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 5 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 25, rlist from 0.724 to 0.793 68: 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.728 nm, buffer size 0.028 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.724 nm, buffer size 0.024 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.728 nm, buffer size 0.028 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.724 nm, buffer size 0.024 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.632 0.316 199.9 68: (ns/day) (hour/ns) 68: Performance: 4.644 5.168 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 25, rlist from 0.724 to 0.793 68: 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.028 0.014 198.8 68: (ns/day) (hour/ns) 68: Performance: 54.242 0.442 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 25, rlist from 0.724 to 0.793 68: 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.042 0.021 199.1 68: (ns/day) (hour/ns) 68: Performance: 37.082 0.647 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_secondpart.part0002.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/23 (479 ms) 68: [----------] 24 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact (2593 ms total) 68: 68: [----------] 8 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact 68: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 294.908 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 294.908 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps. 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.040 0.020 198.9 68: (ns/day) (hour/ns) 68: Performance: 73.204 0.328 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.054 0.027 199.0 68: (ns/day) (hour/ns) 68: Performance: 28.728 0.835 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.033 0.017 190.5 68: (ns/day) (hour/ns) 68: Performance: 45.139 0.532 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (116 ms) 68: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 294.908 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 294.908 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps. 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.051 0.026 199.2 68: (ns/day) (hour/ns) 68: Performance: 57.415 0.418 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.037 0.018 198.6 68: (ns/day) (hour/ns) 68: Performance: 42.300 0.567 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.033 0.017 198.9 68: (ns/day) (hour/ns) 68: Performance: 46.898 0.512 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (110 ms) 68: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: NVE simulation: will use the initial temperature of 294.908 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: NVE simulation: will use the initial temperature of 294.908 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps. 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.046 0.023 199.4 68: (ns/day) (hour/ns) 68: Performance: 63.634 0.377 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.542 0.271 199.9 68: (ns/day) (hour/ns) 68: Performance: 2.870 8.363 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.050 0.025 198.6 68: (ns/day) (hour/ns) 68: Performance: 30.802 0.779 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (395 ms) 68: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: NVE simulation: will use the initial temperature of 294.908 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: NVE simulation: will use the initial temperature of 294.908 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 4 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps. 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.048 0.024 199.3 68: (ns/day) (hour/ns) 68: Performance: 61.056 0.393 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.042 0.021 199.4 68: (ns/day) (hour/ns) 68: Performance: 36.705 0.654 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.053 0.027 198.8 68: (ns/day) (hour/ns) 68: Performance: 29.205 0.822 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (118 ms) 68: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/4 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps. 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.732 nm, buffer size 0.032 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.732 nm, buffer size 0.032 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.037 0.018 199.0 68: (ns/day) (hour/ns) 68: Performance: 79.940 0.300 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.046 0.023 198.1 68: (ns/day) (hour/ns) 68: Performance: 33.765 0.711 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.035 0.018 198.3 68: (ns/day) (hour/ns) 68: Performance: 44.428 0.540 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (146 ms) 68: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/5 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.728 to 0.806 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps. 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.059 0.030 199.2 68: (ns/day) (hour/ns) 68: Performance: 49.428 0.486 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.728 to 0.806 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.031 0.015 197.8 68: (ns/day) (hour/ns) 68: Performance: 50.191 0.478 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.728 to 0.806 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.038 0.019 198.8 68: (ns/day) (hour/ns) 68: Performance: 41.014 0.585 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (356 ms) 68: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/6 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps. 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.041 0.021 198.3 68: (ns/day) (hour/ns) 68: Performance: 71.539 0.335 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.042 0.021 198.3 68: (ns/day) (hour/ns) 68: Performance: 37.118 0.647 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.036 0.018 198.5 68: (ns/day) (hour/ns) 68: Performance: 42.441 0.565 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (152 ms) 68: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/7 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 20, rlist from 0.749 to 0.842 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps. 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.042 0.021 198.8 68: (ns/day) (hour/ns) 68: Performance: 70.285 0.341 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 20, rlist from 0.749 to 0.842 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.038 0.019 198.2 68: (ns/day) (hour/ns) 68: Performance: 40.612 0.591 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 20, rlist from 0.749 to 0.843 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.046 0.023 198.7 68: (ns/day) (hour/ns) 68: Performance: 33.825 0.710 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (172 ms) 68: [----------] 8 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact (1568 ms total) 68: 68: [----------] 8 tests from NVT/MdrunNoAppendContinuationIsExact 68: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.024 0.012 198.6 68: (ns/day) (hour/ns) 68: Performance: 123.906 0.194 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.027 0.014 199.0 68: (ns/day) (hour/ns) 68: Performance: 57.421 0.418 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.027 0.014 198.6 68: (ns/day) (hour/ns) 68: Performance: 57.064 0.421 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (59 ms) 68: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.029 0.014 199.0 68: (ns/day) (hour/ns) 68: Performance: 102.000 0.235 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.032 0.016 199.2 68: (ns/day) (hour/ns) 68: Performance: 48.504 0.495 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.028 0.014 198.8 68: (ns/day) (hour/ns) 68: Performance: 55.265 0.434 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (65 ms) 68: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 68: 1 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 68: 1 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 3 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.026 0.013 198.9 68: (ns/day) (hour/ns) 68: Performance: 110.429 0.217 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.026 0.013 199.0 68: (ns/day) (hour/ns) 68: Performance: 58.661 0.409 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.037 0.019 198.9 68: (ns/day) (hour/ns) 68: Performance: 41.899 0.573 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (64 ms) 68: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 68: 1 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 68: 1 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 3 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.025 0.013 198.9 68: (ns/day) (hour/ns) 68: Performance: 116.398 0.206 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.032 0.016 198.8 68: (ns/day) (hour/ns) 68: Performance: 48.154 0.498 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.030 0.015 198.5 68: (ns/day) (hour/ns) 68: Performance: 50.904 0.471 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (65 ms) 68: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.048 0.024 199.4 68: (ns/day) (hour/ns) 68: Performance: 61.449 0.391 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.059 0.029 199.5 68: (ns/day) (hour/ns) 68: Performance: 26.508 0.905 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.048 0.024 198.8 68: (ns/day) (hour/ns) 68: Performance: 32.458 0.739 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (104 ms) 68: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.049 0.024 199.1 68: (ns/day) (hour/ns) 68: Performance: 59.973 0.400 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.047 0.024 199.2 68: (ns/day) (hour/ns) 68: Performance: 32.677 0.734 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.052 0.026 198.6 68: (ns/day) (hour/ns) 68: Performance: 29.431 0.815 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (115 ms) 68: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.053 0.027 199.3 68: (ns/day) (hour/ns) 68: Performance: 54.997 0.436 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.038 0.019 198.9 68: (ns/day) (hour/ns) 68: Performance: 40.724 0.589 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.044 0.022 198.2 68: (ns/day) (hour/ns) 68: Performance: 35.033 0.685 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (117 ms) 68: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.040 0.020 199.2 68: (ns/day) (hour/ns) 68: Performance: 72.428 0.331 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.047 0.024 199.3 68: (ns/day) (hour/ns) 68: Performance: 32.914 0.729 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.046 0.023 198.6 68: (ns/day) (hour/ns) 68: Performance: 33.815 0.710 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (118 ms) 68: [----------] 8 tests from NVT/MdrunNoAppendContinuationIsExact (712 ms total) 68: 68: [----------] 2 tests from NPH/MdrunNoAppendContinuationIsExact 68: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.045 0.023 199.2 68: (ns/day) (hour/ns) 68: Performance: 65.019 0.369 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.043 0.022 198.9 68: (ns/day) (hour/ns) 68: Performance: 35.603 0.674 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.029 0.015 198.3 68: (ns/day) (hour/ns) 68: Performance: 53.023 0.453 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (91 ms) 68: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 68.810 K for 68: determining the Verlet buffer size 68: 68: 68: There were 3 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.111 0.056 199.7 68: (ns/day) (hour/ns) 68: Performance: 26.454 0.907 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.045 0.022 199.4 68: (ns/day) (hour/ns) 68: Performance: 34.743 0.691 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.040 0.020 198.5 68: (ns/day) (hour/ns) 68: Performance: 38.620 0.621 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (134 ms) 68: [----------] 2 tests from NPH/MdrunNoAppendContinuationIsExact (226 ms total) 68: 68: [----------] 8 tests from NPT/MdrunNoAppendContinuationIsExact 68: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.021 0.011 198.4 68: (ns/day) (hour/ns) 68: Performance: 135.705 0.177 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.030 0.015 198.9 68: (ns/day) (hour/ns) 68: Performance: 51.485 0.466 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.027 0.014 198.5 68: (ns/day) (hour/ns) 68: Performance: 57.112 0.420 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (63 ms) 68: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.044 0.022 199.2 68: (ns/day) (hour/ns) 68: Performance: 67.232 0.357 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.033 0.017 198.8 68: (ns/day) (hour/ns) 68: Performance: 46.637 0.515 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.033 0.017 198.8 68: (ns/day) (hour/ns) 68: Performance: 46.167 0.520 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (73 ms) 68: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 68: 1 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 68: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 68: 1 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 3 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.033 0.017 198.9 68: (ns/day) (hour/ns) 68: Performance: 87.802 0.273 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.036 0.018 199.1 68: (ns/day) (hour/ns) 68: Performance: 43.083 0.557 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.028 0.014 198.7 68: (ns/day) (hour/ns) 68: Performance: 54.616 0.439 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (66 ms) 68: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 68: 1 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 68: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 68: 1 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 3 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.031 0.016 198.5 68: (ns/day) (hour/ns) 68: Performance: 93.478 0.257 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.028 0.014 198.6 68: (ns/day) (hour/ns) 68: Performance: 55.741 0.431 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.033 0.017 198.8 68: (ns/day) (hour/ns) 68: Performance: 46.675 0.514 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (68 ms) 68: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.037 0.019 199.2 68: (ns/day) (hour/ns) 68: Performance: 79.279 0.303 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.059 0.030 199.5 68: (ns/day) (hour/ns) 68: Performance: 26.314 0.912 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.038 0.019 198.6 68: (ns/day) (hour/ns) 68: Performance: 40.926 0.586 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (86 ms) 68: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.035 0.017 199.2 68: (ns/day) (hour/ns) 68: Performance: 84.061 0.286 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.038 0.019 199.2 68: (ns/day) (hour/ns) 68: Performance: 41.011 0.585 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.063 0.032 199.0 68: (ns/day) (hour/ns) 68: Performance: 24.552 0.978 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (95 ms) 68: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 68: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (0 ms) 68: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 2 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.055 0.028 199.3 68: (ns/day) (hour/ns) 68: Performance: 53.005 0.453 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.072 0.036 199.5 68: (ns/day) (hour/ns) 68: Performance: 21.516 1.115 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.060 0.030 199.3 68: (ns/day) (hour/ns) 68: Performance: 25.639 0.936 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (119 ms) 68: [----------] 8 tests from NPT/MdrunNoAppendContinuationIsExact (574 ms total) 68: 68: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact 68: [ RUN ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: MTTK coupling is deprecated and will soon be removed 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: MTTK coupling is deprecated and will soon be removed 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: There were 3 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps. 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.033 0.017 198.8 68: (ns/day) (hour/ns) 68: Performance: 88.068 0.273 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.046 0.023 199.3 68: (ns/day) (hour/ns) 68: Performance: 34.050 0.705 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Argon' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.030 0.015 198.4 68: (ns/day) (hour/ns) 68: Performance: 51.872 0.463 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (79 ms) 68: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact (79 ms total) 68: 68: [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact 68: [ RUN ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Pull group 1 'FirstWaterMolecule' has 3 atoms 68: Pull group 2 'SecondWaterMolecule' has 3 atoms 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 3 2 68: 2 3 5 1.112 nm 1.000 nm 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Pull group 1 'FirstWaterMolecule' has 3 atoms 68: Pull group 2 'SecondWaterMolecule' has 3 atoms 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 3 2 68: 2 3 5 1.112 nm 1.000 nm 68: 68: There were 3 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.170 0.085 199.7 68: (ns/day) (hour/ns) 68: Performance: 17.306 1.387 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.200 0.100 199.8 68: (ns/day) (hour/ns) 68: Performance: 7.775 3.087 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.052 0.026 199.2 68: (ns/day) (hour/ns) 68: Performance: 30.030 0.799 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (247 ms) 68: [ RUN ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/1 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Pull group 1 'FirstWaterMolecule' has 3 atoms 68: Pull group 2 'SecondWaterMolecule' has 3 atoms 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 3 2 68: 2 3 5 1.112 nm 1.000 nm 68: 68: There were 3 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Pull group 1 'FirstWaterMolecule' has 3 atoms 68: Pull group 2 'SecondWaterMolecule' has 3 atoms 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 2573.591 K for 68: determining the Verlet buffer size 68: 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 3 2 68: 2 3 5 1.112 nm 1.000 nm 68: 68: There were 3 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps. 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.042 0.021 199.2 68: (ns/day) (hour/ns) 68: Performance: 69.967 0.343 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.054 0.027 199.4 68: (ns/day) (hour/ns) 68: Performance: 28.808 0.833 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.132 0.066 199.6 68: (ns/day) (hour/ns) 68: Performance: 11.773 2.039 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (138 ms) 68: [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact (386 ms total) 68: 68: [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact 68: [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 68: Setting the AWH bias MC random seed to -142871041 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Pull group 1 'C_&_r_1' has 1 atoms 68: Pull group 2 'N_&_r_2' has 1 atoms 68: Pull group 3 'CA' has 1 atoms 68: Pull group 4 'C_&_r_2' has 1 atoms 68: Pull group 5 'N_&_r_3' has 1 atoms 68: Number of degrees of freedom in T-Coupling group System is 51.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 1 0 68: 2 1 0 179.098 deg 0.000 deg 68: 2 1 0 68: 3 1 0 158.667 deg 0.000 deg 68: 68: There were 3 NOTEs 68: Setting the AWH bias MC random seed to -939532457 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Pull group 1 'C_&_r_1' has 1 atoms 68: Pull group 2 'N_&_r_2' has 1 atoms 68: Pull group 3 'CA' has 1 atoms 68: Pull group 4 'C_&_r_2' has 1 atoms 68: Pull group 5 'N_&_r_3' has 1 atoms 68: Number of degrees of freedom in T-Coupling group System is 51.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 1 0 68: 2 1 0 179.098 deg 0.000 deg 68: 2 1 0 68: 3 1 0 158.667 deg 0.000 deg 68: 68: There were 3 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 16 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.734 0.367 199.9 68: (ns/day) (hour/ns) 68: Performance: 4.001 5.998 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.049 0.025 198.3 68: (ns/day) (hour/ns) 68: Performance: 31.306 0.767 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.042 0.021 198.6 68: (ns/day) (hour/ns) 68: Performance: 36.972 0.649 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (677 ms) 68: [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 68: Setting the AWH bias MC random seed to -622370817 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Pull group 1 'C_&_r_1' has 1 atoms 68: Pull group 2 'N_&_r_2' has 1 atoms 68: Pull group 3 'CA' has 1 atoms 68: Pull group 4 'C_&_r_2' has 1 atoms 68: Pull group 5 'N_&_r_3' has 1 atoms 68: Number of degrees of freedom in T-Coupling group System is 51.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 1 0 68: 2 1 0 179.098 deg 0.000 deg 68: 2 1 0 68: 3 1 0 158.667 deg 0.000 deg 68: 68: There were 3 NOTEs 68: Setting the AWH bias MC random seed to -1283985541 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: Setting nstcalcenergy (100) equal to nstenergy (4) 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Pull group 1 'C_&_r_1' has 1 atoms 68: Pull group 2 'N_&_r_2' has 1 atoms 68: Pull group 3 'CA' has 1 atoms 68: Pull group 4 'C_&_r_2' has 1 atoms 68: Pull group 5 'N_&_r_3' has 1 atoms 68: Number of degrees of freedom in T-Coupling group System is 51.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: Pull group natoms pbc atom distance at start reference at t=0 68: 1 1 0 68: 2 1 0 179.098 deg 0.000 deg 68: 2 1 0 68: 3 1 0 158.667 deg 0.000 deg 68: 68: There were 3 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 16 steps, 0.0 ps. 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.054 0.027 198.7 68: (ns/day) (hour/ns) 68: Performance: 54.203 0.443 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.053 0.027 198.7 68: (ns/day) (hour/ns) 68: Performance: 29.153 0.823 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine-dipeptide' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.181 0.090 199.6 68: (ns/day) (hour/ns) 68: Performance: 8.592 2.793 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (246 ms) 68: [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact (924 ms total) 68: 68: [----------] 1 test from ExpandedEnsemble/MdrunNoAppendContinuationIsExact 68: [ RUN ] ExpandedEnsemble/MdrunNoAppendContinuationIsExact.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 2 NOTEs 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 79.00 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 2 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps. 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Generated 2485 of the 2485 non-bonded parameter combinations 68: 68: Generated 2485 of the 2485 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'nonanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 68: 68: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.240 0.120 199.9 68: (ns/day) (hour/ns) 68: Performance: 12.210 1.966 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 8 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.152 0.076 199.7 68: (ns/day) (hour/ns) 68: Performance: 10.209 2.351 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun '30 atom system in water' 68: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.079 0.040 199.0 68: (ns/day) (hour/ns) 68: Performance: 19.671 1.220 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] ExpandedEnsemble/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (351 ms) 68: [----------] 1 test from ExpandedEnsemble/MdrunNoAppendContinuationIsExact (351 ms total) 68: 68: [----------] 3 tests from Checking/InitialConstraintsTest 68: [ RUN ] Checking/InitialConstraintsTest.Works/0 68: Number of degrees of freedom in T-Coupling group rest is 11.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 68: NVE simulation: will use the initial temperature of 1141.954 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 2 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc-and-methanol' 68: 1 steps, 0.0 ps. 68: Setting the LD random seed to -201335809 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.023 0.012 198.2 68: (ns/day) (hour/ns) 68: Performance: 14.872 1.614 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_spc-and-methanol.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/0 (27 ms) 68: [ RUN ] Checking/InitialConstraintsTest.Works/1 68: Number of degrees of freedom in T-Coupling group rest is 11.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 68: NVE simulation: will use the initial temperature of 1141.954 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 2 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc-and-methanol' 68: 1 steps, 0.0 ps. 68: Setting the LD random seed to -571026292 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.038 0.019 198.8 68: (ns/day) (hour/ns) 68: Performance: 9.060 2.649 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_spc-and-methanol.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/1 (34 ms) 68: [ RUN ] Checking/InitialConstraintsTest.Works/2 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 68: Integrator method md-vv-avek is implemented primarily for validation 68: purposes; for molecular dynamics, you should probably be using md or 68: md-vv 68: 68: Number of degrees of freedom in T-Coupling group rest is 11.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 68: NVE simulation: will use the initial temperature of 1141.954 K for 68: determining the Verlet buffer size 68: 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 3 NOTEs 68: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 68: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc-and-methanol' 68: 1 steps, 0.0 ps. 68: Setting the LD random seed to -805839000 68: 68: Generated 8 of the 10 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'Methanol' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 68: 68: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.061 0.031 199.2 68: (ns/day) (hour/ns) 68: Performance: 5.625 4.267 68: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_spc-and-methanol.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/2 (51 ms) 68: [----------] 3 tests from Checking/InitialConstraintsTest (113 ms total) 68: 68: [----------] Global test environment tear-down 68: [==========] 76 tests from 13 test suites ran. (8774 ms total) 68: [ PASSED ] 76 tests. 68/94 Test #68: MdrunIOTests ................................. Passed 9.12 sec test 69 Start 69: MdrunTestsOneRank 69: Test command: /usr/bin/mpiexec "-n" "1" "/build/reproducible-path/gromacs-2025.0/build/mpi/bin/mdrun-test" "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/MdrunTestsOneRank.xml" 69: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests 69: Test timeout computed to be: 600 69: [==========] Running 29 tests from 8 test suites. 69: [----------] Global test environment set-up. 69: [----------] 1 test from CompelTest 69: [ RUN ] CompelTest.SwapCanRun 69: Setting the LD random seed to -1241535011 69: 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: Generating 1-4 interactions: fudge = 0.5 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Protein' 69: 69: turning all bonds into constraints... 69: 69: Excluding 3 bonded neighbours molecule type 'OCT' 69: 69: turning all bonds into constraints... 69: 69: Excluding 1 bonded neighbours molecule type 'NA' 69: 69: turning all bonds into constraints... 69: 69: Excluding 1 bonded neighbours molecule type 'CL' 69: 69: turning all bonds into constraints... 69: 69: Excluding 3 bonded neighbours molecule type 'Protein' 69: 69: Excluding 3 bonded neighbours molecule type 'OCT' 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning all bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/OctaneSandwich.gro' 69: Split0 group 'Ch0' contains 83 atoms. 69: Split1 group 'Ch1' contains 83 atoms. 69: Solvent group 'SOL' contains 11931 atoms. 69: Swap group 'NA+' contains 19 atoms. 69: Swap group 'CL-' contains 19 atoms. 69: Number of degrees of freedom in T-Coupling group System is 27869.00 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 69: 69: Calculated rlist for 1x1 atom pair-list as 1.316 nm, buffer size 0.316 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 1.262 nm, buffer size 0.262 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 1 Mb of data 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 69: Removing center of mass motion in the presence of position restraints 69: might cause artifacts. When you are using position restraints to 69: equilibrate a macro-molecule, the artifacts are usually negligible. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 2 NOTEs 69: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Update groups can not be used for this system because there are three or more consecutively coupled constraints 69: 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: SWAP: Determining initial numbers of ions per compartment. 69: SWAP: Setting pointers for checkpoint writing 69: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 69: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 69: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 69: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 69: starting mdrun 'Channel_coco in octane membrane' 69: 2 steps, 0.0 ps. 69: 69: Writing final coordinates. 69: 69: NOTE: 36 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.363 0.182 199.8 69: (ns/day) (hour/ns) 69: Performance: 7.126 3.368 69: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps 69: 69: Update groups can not be used for this system because there are three or more consecutively coupled constraints 69: 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: SWAP: Setting pointers for checkpoint writing 69: SWAP: Copying channel fluxes from checkpoint file data 69: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 69: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 69: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 69: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 69: starting mdrun 'Channel_coco in octane membrane' 69: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 69: 69: Writing final coordinates. 69: 69: NOTE: 23 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.276 0.138 199.8 69: (ns/day) (hour/ns) 69: Performance: 9.378 2.559 69: [ OK ] CompelTest.SwapCanRun (1095 ms) 69: [----------] 1 test from CompelTest (1095 ms total) 69: 69: [----------] 6 tests from BondedInteractionsTest 69: [ RUN ] BondedInteractionsTest.NormalBondWorks 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: Setting the LD random seed to 1589628319 69: 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'butane' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 69: 69: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: 69: In moleculetype 'butane' 2 atoms are not bound by a potential or 69: constraint to any other atom in the same moleculetype. Although 69: technically this might not cause issues in a simulation, this often means 69: that the user forgot to add a bond/potential/constraint or put multiple 69: molecules in the same moleculetype definition by mistake. Run with -v to 69: get information for each atom. 69: 69: Number of degrees of freedom in T-Coupling group rest is 9.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 69: NVE simulation with an initial temperature of zero: will use a Verlet 69: buffer of 10%. Check your energy drift! 69: 69: 69: There were 3 NOTEs 69: 69: This run will generate roughly 0 Mb of data 69: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 69: 69: Reading frames from gro file 'A single butane', 4 atoms. 69: Reading frame 0 time 0.000 Last frame 0 time 0.000 69: 69: NOTE: 22 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.001 0.000 190.6 69: (ns/day) (hour/ns) 69: Performance: 242.076 0.099 69: [ OK ] BondedInteractionsTest.NormalBondWorks (7 ms) 69: [ RUN ] BondedInteractionsTest.TabulatedBondWorks 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: 69: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: 69: In moleculetype 'butane' 2 atoms are not bound by a potential or 69: constraint to any other atom in the same moleculetype. Although 69: technically this might not cause issues in a simulation, this often means 69: that the user forgot to add a bond/potential/constraint or put multiple 69: molecules in the same moleculetype definition by mistake. Run with -v to 69: get information for each atom. 69: 69: Number of degrees of freedom in T-Coupling group rest is 9.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 69: NVE simulation with an initial temperature of zero: will use a Verlet 69: buffer of 10%. Check your energy drift! 69: 69: 69: There were 3 NOTEs 69: Setting the LD random seed to 2128704991 69: 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'butane' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 69: 69: This run will generate roughly 0 Mb of data 69: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 69: 69: Reading frames from gro file 'A single butane', 4 atoms. 69: Reading frame 0 time 0.000 Last frame 0 time 0.000 69: 69: NOTE: 22 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.001 0.000 190.0 69: (ns/day) (hour/ns) 69: Performance: 242.076 0.099 69: [ OK ] BondedInteractionsTest.TabulatedBondWorks (6 ms) 69: [ RUN ] BondedInteractionsTest.NormalAngleWorks 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: 69: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: 69: In moleculetype 'butane' 4 atoms are not bound by a potential or 69: constraint to any other atom in the same moleculetype. Although 69: technically this might not cause issues in a simulation, this often means 69: that the user forgot to add a bond/potential/constraint or put multiple 69: molecules in the same moleculetype definition by mistake. Run with -v to 69: get information for each atom. 69: 69: Number of degrees of freedom in T-Coupling group rest is 9.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 69: NVE simulation with an initial temperature of zero: will use a Verlet 69: buffer of 10%. Check your energy drift! 69: 69: 69: There were 3 NOTEs 69: Setting the LD random seed to -89793026 69: 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'butane' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 69: 69: This run will generate roughly 0 Mb of data 69: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 69: 69: Reading frames from gro file 'A single butane', 4 atoms. 69: Reading frame 0 time 0.000 Last frame 0 time 0.000 69: 69: NOTE: 15 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.001 0.000 189.1 69: (ns/day) (hour/ns) 69: Performance: 183.117 0.131 69: [ OK ] BondedInteractionsTest.NormalAngleWorks (8 ms) 69: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: Setting the LD random seed to -1271022035 69: 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'butane' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 69: 69: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: 69: In moleculetype 'butane' 4 atoms are not bound by a potential or 69: constraint to any other atom in the same moleculetype. Although 69: technically this might not cause issues in a simulation, this often means 69: that the user forgot to add a bond/potential/constraint or put multiple 69: molecules in the same moleculetype definition by mistake. Run with -v to 69: get information for each atom. 69: 69: Number of degrees of freedom in T-Coupling group rest is 9.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 69: NVE simulation with an initial temperature of zero: will use a Verlet 69: buffer of 10%. Check your energy drift! 69: 69: 69: There were 3 NOTEs 69: 69: This run will generate roughly 0 Mb of data 69: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 69: 69: Reading frames from gro file 'A single butane', 4 atoms. 69: Reading frame 0 time 0.000 Last frame 0 time 0.000 69: 69: NOTE: 23 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.001 0.000 188.4 69: (ns/day) (hour/ns) 69: Performance: 274.121 0.088 69: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (6 ms) 69: [ RUN ] BondedInteractionsTest.NormalDihedralWorks 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: Setting the LD random seed to 2138177535 69: 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'butane' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 69: 69: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]: 69: In moleculetype 'butane' 4 atoms are not bound by a potential or 69: constraint to any other atom in the same moleculetype. Although 69: technically this might not cause issues in a simulation, this often means 69: that the user forgot to add a bond/potential/constraint or put multiple 69: molecules in the same moleculetype definition by mistake. Run with -v to 69: get information for each atom. 69: 69: Number of degrees of freedom in T-Coupling group rest is 9.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 69: NVE simulation with an initial temperature of zero: will use a Verlet 69: buffer of 10%. Check your energy drift! 69: 69: 69: There were 3 NOTEs 69: 69: This run will generate roughly 0 Mb of data 69: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 69: 69: Reading frames from gro file 'A single butane', 4 atoms. 69: Reading frame 0 time 0.000 Last frame 0 time 0.000 69: 69: NOTE: 21 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.001 0.000 189.7 69: (ns/day) (hour/ns) 69: Performance: 290.375 0.083 69: [ OK ] BondedInteractionsTest.NormalDihedralWorks (6 ms) 69: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: Setting the LD random seed to 2091642777 69: 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'butane' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 69: 69: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]: 69: In moleculetype 'butane' 4 atoms are not bound by a potential or 69: constraint to any other atom in the same moleculetype. Although 69: technically this might not cause issues in a simulation, this often means 69: that the user forgot to add a bond/potential/constraint or put multiple 69: molecules in the same moleculetype definition by mistake. Run with -v to 69: get information for each atom. 69: 69: Number of degrees of freedom in T-Coupling group rest is 9.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 69: NVE simulation with an initial temperature of zero: will use a Verlet 69: buffer of 10%. Check your energy drift! 69: 69: 69: There were 3 NOTEs 69: 69: This run will generate roughly 0 Mb of data 69: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 69: 69: Reading frames from gro file 'A single butane', 4 atoms. 69: Reading frame 0 time 0.000 Last frame 0 time 0.000 69: 69: NOTE: 43 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.001 0.001 190.8 69: (ns/day) (hour/ns) 69: Performance: 170.055 0.141 69: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (8 ms) 69: [----------] 6 tests from BondedInteractionsTest (44 ms total) 69: 69: [----------] 2 tests from BoxDeformationTest 69: [ RUN ] BoxDeformationTest.flowDoesNotAffectEkin 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (10) 69: 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: Setting the LD random seed to -151257161 69: Number of degrees of freedom in T-Coupling group rest is 33.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: There were 3 NOTEs 69: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: Generated 1 of the 1 non-bonded parameter combinations 69: 69: Excluding 1 bonded neighbours molecule type 'Argon' 69: 69: Setting gen_seed to -1110970497 69: 69: Velocities were taken from a Maxwell distribution at 0 K 69: 69: This run will generate roughly 0 Mb of data 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Argon' 69: 0 steps, 0.0 ps. 69: 69: NOTE: 32 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.001 0.000 171.8 69: (ns/day) (hour/ns) 69: Performance: 547.414 0.044 69: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] BoxDeformationTest.flowDoesNotAffectEkin (7 ms) 69: [ RUN ] BoxDeformationTest.EnergiesWithinTolerances 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (10) 69: 69: Setting the LD random seed to -412893537 69: 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: Generating 1-4 interactions: fudge = 0.5 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc216.gro' 69: Number of degrees of freedom in T-Coupling group rest is 1293.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: The largest distance between excluded atoms is 0.152 nm between atom 41 and 42 69: Calculating fourier grid dimensions for X Y Z 69: Using a fourier grid of 16x16x16, spacing 0.116 0.116 0.116 69: 69: Estimate for the relative computational load of the PME mesh part: 0.20 69: 69: This run will generate roughly 0 Mb of data 69: 69: There were 2 NOTEs 69: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 20 steps, 0.0 ps. 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.075 0.037 199.4 69: (ns/day) (hour/ns) 69: Performance: 97.027 0.247 69: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Reading energy frame 2 time 0.040 Last energy frame read 2 time 0.040 [ OK ] BoxDeformationTest.EnergiesWithinTolerances (650 ms) 69: [----------] 2 tests from BoxDeformationTest (658 ms total) 69: 69: [----------] 1 test from PositionRestraintCommTest 69: [ RUN ] PositionRestraintCommTest.PositionRestraintsTwoCOMs 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 69: You have set rlist larger than the interaction cut-off, but you also have 69: verlet-buffer-tolerance > 0. Will set rlist using 69: verlet-buffer-tolerance. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (10) 69: 69: Setting the LD random seed to -210370738 69: 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: Generating 1-4 interactions: fudge = 0.5 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Protein' 69: 69: Excluding 3 bonded neighbours molecule type 'OCT' 69: 69: Excluding 1 bonded neighbours molecule type 'NA' 69: 69: Excluding 1 bonded neighbours molecule type 'CL' 69: 69: Excluding 3 bonded neighbours molecule type 'Protein' 69: 69: Excluding 3 bonded neighbours molecule type 'OCT' 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/OctaneSandwich.gro' 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 69: 13489 atoms are not part of any of the VCM groups 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 69: 13489 atoms are not part of any center of mass motion removal group. 69: This may lead to artifacts. 69: In most cases one should use one group for the whole system. 69: 69: Number of degrees of freedom in T-Coupling group System is 29527.73 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.990 nm, buffer size 0.090 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.965 nm, buffer size 0.065 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: Chain0: 2.207 2.168 7.330 69: Chain1: 2.228 2.186 2.401 69: Chain0: 2.207 2.168 7.330 69: Chain1: 2.228 2.186 2.401 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 69: Removing center of mass motion in the presence of position restraints 69: might cause artifacts. When you are using position restraints to 69: equilibrate a macro-molecule, the artifacts are usually negligible. 69: 69: 69: There were 4 NOTEs 69: 69: There was 1 WARNING 69: 69: This run will generate roughly 1 Mb of data 69: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Changing nstlist from 10 to 20, rlist from 0.965 to 1.066 69: 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Channel_coco in octane membrane' 69: 10 steps, 0.0 ps. 69: 69: Writing final coordinates. 69: 69: NOTE: 15 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.323 0.162 199.8 69: (ns/day) (hour/ns) 69: Performance: 11.748 2.043 69: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Last energy frame read 1 time 0.020 [ OK ] PositionRestraintCommTest.PositionRestraintsTwoCOMs (848 ms) 69: [----------] 1 test from PositionRestraintCommTest (848 ms total) 69: 69: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest 69: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: Setting the LD random seed to -181441 69: Generating 1-4 interactions: fudge = 0.5 69: 69: Generated 2211 of the 2211 non-bonded parameter combinations 69: 69: Generated 2211 of the 2211 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 69: 69: NOTE 2 [file ala.top, line 256]: 69: For energy conservation with LINCS, lincs_iter should be 2 or larger. 69: 69: 69: Number of degrees of freedom in T-Coupling group rest is 54.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 69: Calculating fourier grid dimensions for X Y Z 69: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 69: 69: Estimate for the relative computational load of the PME mesh part: 0.94 69: 69: This run will generate roughly 0 Mb of data 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 69: The optimal PME mesh load for parallel simulations is below 0.5 69: and for highly parallel simulations between 0.25 and 0.33, 69: for higher performance, increase the cut-off and the PME grid spacing. 69: 69: 69: 69: There were 3 NOTEs 69: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'UNNAMED in water' 69: 4 steps, 0.0 ps. 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.041 0.021 198.8 69: (ns/day) (hour/ns) 69: Performance: 20.847 1.151 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: Setting the LD random seed to -8391685 69: 69: Generated 2211 of the 2211 non-bonded parameter combinations 69: Generating 1-4 interactions: fudge = 0.5 69: 69: Generated 2211 of the 2211 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 69: 69: turning H bonds into constraints... 69: 69: NOTE 2 [file ala.top, line 256]: 69: For energy conservation with LINCS, lincs_iter should be 2 or larger. 69: 69: 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 69: Number of degrees of freedom in T-Coupling group rest is 54.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 69: Calculating fourier grid dimensions for X Y Z 69: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 69: 69: Estimate for the relative computational load of the PME mesh part: 0.94 69: 69: This run will generate roughly 0 Mb of data 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 69: The optimal PME mesh load for parallel simulations is below 0.5 69: and for highly parallel simulations between 0.25 and 0.33, 69: for higher performance, increase the cut-off and the PME grid spacing. 69: 69: 69: 69: There were 3 NOTEs 69: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'UNNAMED in water' 69: 4 steps, 0.0 ps. 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.025 0.013 197.5 69: (ns/day) (hour/ns) 69: Performance: 33.654 0.713 69: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 trr version: GMX_trn_file (single precision) 69: 69: 69: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (420 ms) 69: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: Setting the LD random seed to -640155940 69: 69: Generated 2211 of the 2211 non-bonded parameter combinations 69: Generating 1-4 interactions: fudge = 0.5 69: 69: Generated 2211 of the 2211 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 69: 69: turning H bonds into constraints... 69: 69: NOTE 2 [file ala.top, line 256]: 69: For energy conservation with LINCS, lincs_iter should be 2 or larger. 69: 69: 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 69: Number of degrees of freedom in T-Coupling group rest is 54.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 69: Calculating fourier grid dimensions for X Y Z 69: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 69: 69: Estimate for the relative computational load of the PME mesh part: 0.94 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 69: The optimal PME mesh load for parallel simulations is below 0.5 69: and for highly parallel simulations between 0.25 and 0.33, 69: for higher performance, increase the cut-off and the PME grid spacing. 69: 69: 69: 69: There were 3 NOTEs 69: 69: This run will generate roughly 0 Mb of data 69: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'UNNAMED in water' 69: 4 steps, 0.0 ps. 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.047 0.024 199.0 69: (ns/day) (hour/ns) 69: Performance: 18.204 1.318 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: Setting the LD random seed to -1393401922 69: 69: Generated 2211 of the 2211 non-bonded parameter combinations 69: 69: Generated 2211 of the 2211 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 69: 69: turning H bonds into constraints... 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 2 [file ala.top, line 256]: 69: For energy conservation with LINCS, lincs_iter should be 2 or larger. 69: 69: 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 69: Number of degrees of freedom in T-Coupling group rest is 54.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 69: The optimal PME mesh load for parallel simulations is below 0.5 69: and for highly parallel simulations between 0.25 and 0.33, 69: for higher performance, increase the cut-off and the PME grid spacing. 69: 69: 69: 69: There were 3 NOTEs 69: 69: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 69: Calculating fourier grid dimensions for X Y Z 69: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 69: 69: Estimate for the relative computational load of the PME mesh part: 0.94 69: 69: This run will generate roughly 0 Mb of data 69: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 69: Can not increase nstlist because an NVE ensemble is used 69: 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'UNNAMED in water' 69: 4 steps, 0.0 ps. 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.175 0.088 199.7 69: (ns/day) (hour/ns) 69: Performance: 4.929 4.870 69: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 69: 69: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (170 ms) 69: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (591 ms total) 69: 69: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest 69: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: Setting the LD random seed to -71499781 69: Generating 1-4 interactions: fudge = 0.5 69: Pull group 1 'FirstWaterMolecule' has 3 atoms 69: Pull group 2 'SecondWaterMolecule' has 3 atoms 69: Number of degrees of freedom in T-Coupling group rest is 9.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Generated 3 of the 3 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 69: Pull group natoms pbc atom distance at start reference at t=0 69: 1 3 2 69: 2 3 5 1.112 nm 1.000 nm 69: 69: There was 1 NOTE 69: 69: This run will generate roughly 0 Mb of data 69: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 4 steps, 0.0 ps. 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.032 0.016 198.1 69: (ns/day) (hour/ns) 69: Performance: 26.882 0.893 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: Setting the LD random seed to -1411384829 69: Generating 1-4 interactions: fudge = 0.5 69: Pull group 1 'FirstWaterMolecule' has 3 atoms 69: Pull group 2 'SecondWaterMolecule' has 3 atoms 69: Number of degrees of freedom in T-Coupling group rest is 9.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Generated 3 of the 3 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 69: Pull group natoms pbc atom distance at start reference at t=0 69: 1 3 2 69: 2 3 5 1.112 nm 1.000 nm 69: 69: There was 1 NOTE 69: 69: This run will generate roughly 0 Mb of data 69: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 69: Can not increase nstlist because an NVE ensemble is used 69: 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 4 steps, 0.0 ps. 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.037 0.019 198.5 69: (ns/day) (hour/ns) 69: Performance: 23.038 1.042 69: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 69: 69: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (53 ms) 69: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (53 ms total) 69: 69: [----------] 12 tests from FreezeWorks/FreezeGroupTest 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 69: NVE simulation: will use the initial temperature of 246.451 K for 69: determining the Verlet buffer size 69: 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 5 NOTEs 69: 69: There was 1 WARNING 69: 69: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.027 0.014 198.4 69: (ns/day) (hour/ns) 69: Performance: 57.499 0.417 69: 69: 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (32 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 69: NVE simulation: will use the initial temperature of 246.451 K for 69: determining the Verlet buffer size 69: 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 5 NOTEs 69: 69: There was 1 WARNING 69: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.025 0.013 197.4 69: (ns/day) (hour/ns) 69: Performance: 60.815 0.395 69: 69: 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (30 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 69: NVE simulation: will use the initial temperature of 246.451 K for 69: determining the Verlet buffer size 69: 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 5 NOTEs 69: 69: There was 1 WARNING 69: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.022 0.011 198.0 69: (ns/day) (hour/ns) 69: Performance: 71.131 0.337 69: 69: 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (28 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 69: NVE simulation: will use the initial temperature of 246.451 K for 69: determining the Verlet buffer size 69: 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 5 NOTEs 69: 69: There was 1 WARNING 69: 69: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.027 0.014 198.3 69: (ns/day) (hour/ns) 69: Performance: 56.624 0.424 69: 69: 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 (32 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 69: NVE simulation: will use the initial temperature of 246.451 K for 69: determining the Verlet buffer size 69: 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 5 NOTEs 69: 69: There was 1 WARNING 69: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.019 0.010 197.8 69: (ns/day) (hour/ns) 69: Performance: 79.199 0.303 69: 69: 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (27 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 69: ./src/programs/mdrun/tests/freezegroups.cpp:209: Skipped 69: Parrinello-Rahman is not implemented in md-vv. 69: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (0 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: 69: There was 1 WARNING 69: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 69: 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.022 0.011 198.3 69: (ns/day) (hour/ns) 69: Performance: 68.880 0.348 69: 69: 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (35 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: 69: There was 1 WARNING 69: 69: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 69: 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.234 0.117 199.8 69: (ns/day) (hour/ns) 69: Performance: 6.651 3.609 69: 69: 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (142 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: 69: There was 1 WARNING 69: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 69: 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.198 0.099 199.8 69: (ns/day) (hour/ns) 69: Performance: 7.833 3.064 69: 69: 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 (122 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: 69: There was 1 WARNING 69: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 69: 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.022 0.011 198.2 69: (ns/day) (hour/ns) 69: Performance: 71.353 0.336 69: 69: 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 (69 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: 69: There was 1 WARNING 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 69: 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.037 0.019 198.6 69: (ns/day) (hour/ns) 69: Performance: 41.393 0.580 69: 69: 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 (79 ms) 69: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 69: 69: turning H bonds into constraints... 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 69: There are 5 atoms that are fully frozen and part of COMM removal 69: group(s), removing these atoms from the COMM removal group(s) 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 69: There are 3 atoms that are frozen along less then 3 dimensions and part 69: of COMM removal group(s), due to limitations in the code these still 69: contribute to the mass of the COM along frozen dimensions and therefore 69: the COMM correction will be too small. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: 69: There was 1 WARNING 69: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 69: 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine-dipeptide' 69: 8 steps, 0.0 ps. 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.033 0.017 198.7 69: (ns/day) (hour/ns) 69: Performance: 46.565 0.515 69: 69: 69: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 (76 ms) 69: [----------] 12 tests from FreezeWorks/FreezeGroupTest (678 ms total) 69: 69: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest 69: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 69: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: Net Acceleration in X direction, will not be corrected 69: Net Acceleration in Y direction, will not be corrected 69: Net Acceleration in Z direction, will not be corrected 69: 69: There were 3 NOTEs 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Generated 3 of the 3 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Setting gen_seed to 2116810431 69: 69: Velocities were taken from a Maxwell distribution at 0 K 69: 69: This run will generate roughly 0 Mb of data 69: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 8 steps, 0.0 ps. 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.026 0.013 198.3 69: (ns/day) (hour/ns) 69: Performance: 116.532 0.206 69: 69: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (28 ms) 69: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Generated 3 of the 3 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Setting gen_seed to -598073 69: 69: Velocities were taken from a Maxwell distribution at 0 K 69: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 69: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 69: Net Acceleration in X direction, will not be corrected 69: Net Acceleration in Y direction, will not be corrected 69: Net Acceleration in Z direction, will not be corrected 69: 69: There were 3 NOTEs 69: 69: This run will generate roughly 0 Mb of data 69: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Can not increase nstlist because verlet-buffer-tolerance is not set or used 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 8 steps, 0.0 ps. 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.024 0.012 198.2 69: (ns/day) (hour/ns) 69: Performance: 126.741 0.189 69: 69: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (23 ms) 69: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Generated 3 of the 3 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Setting gen_seed to -16933409 69: 69: Velocities were taken from a Maxwell distribution at 0 K 69: 69: This run will generate roughly 0 Mb of data 69: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 69: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: Net Acceleration in X direction, will not be corrected 69: Net Acceleration in Y direction, will not be corrected 69: Net Acceleration in Z direction, will not be corrected 69: 69: There were 3 NOTEs 69: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 8 steps, 0.0 ps. 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.025 0.012 198.3 69: (ns/day) (hour/ns) 69: Performance: 124.906 0.192 69: 69: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 (21 ms) 69: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 69: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 69: < 0 69: 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Generated 3 of the 3 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Setting gen_seed to 2004612719 69: 69: Velocities were taken from a Maxwell distribution at 0 K 69: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 69: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 69: Net Acceleration in X direction, will not be corrected 69: Net Acceleration in Y direction, will not be corrected 69: Net Acceleration in Z direction, will not be corrected 69: 69: There were 3 NOTEs 69: 69: This run will generate roughly 0 Mb of data 69: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 69: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 69: Can not increase nstlist because verlet-buffer-tolerance is not set or used 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 8 steps, 0.0 ps. 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.020 0.010 198.0 69: (ns/day) (hour/ns) 69: Performance: 154.291 0.156 69: 69: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (19 ms) 69: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (92 ms total) 69: 69: [----------] Global test environment tear-down 69: [==========] 29 tests from 8 test suites ran. (4670 ms total) 69: [ PASSED ] 28 tests. 69: [ SKIPPED ] 1 test, listed below: 69: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 69/94 Test #69: MdrunTestsOneRank ............................ Passed 5.15 sec test 70 Start 70: MdrunTestsTwoRanks 70: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2025.0/build/mpi/bin/mdrun-test" "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/MdrunTestsTwoRanks.xml" 70: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests 70: Test timeout computed to be: 600 70: [==========] Running 29 tests from 8 test suites. 70: [----------] Global test environment set-up. 70: [----------] 1 test from CompelTest 70: [ RUN ] CompelTest.SwapCanRun 70: Setting the LD random seed to -403779665 70: 70: Generated 330891 of the 330891 non-bonded parameter combinations 70: Generating 1-4 interactions: fudge = 0.5 70: 70: Generated 330891 of the 330891 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Protein' 70: 70: turning all bonds into constraints... 70: 70: Excluding 3 bonded neighbours molecule type 'OCT' 70: 70: turning all bonds into constraints... 70: 70: Excluding 1 bonded neighbours molecule type 'NA' 70: 70: turning all bonds into constraints... 70: 70: Excluding 1 bonded neighbours molecule type 'CL' 70: 70: turning all bonds into constraints... 70: 70: Excluding 3 bonded neighbours molecule type 'Protein' 70: 70: Excluding 3 bonded neighbours molecule type 'OCT' 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: turning all bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/OctaneSandwich.gro' 70: Split0 group 'Ch0' contains 83 atoms. 70: Split1 group 'Ch1' contains 83 atoms. 70: Solvent group 'SOL' contains 11931 atoms. 70: Swap group 'NA+' contains 19 atoms. 70: Swap group 'CL-' contains 19 atoms. 70: Number of degrees of freedom in T-Coupling group System is 27869.00 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 70: 70: Calculated rlist for 1x1 atom pair-list as 1.316 nm, buffer size 0.316 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 1.262 nm, buffer size 0.262 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 70: Removing center of mass motion in the presence of position restraints 70: might cause artifacts. When you are using position restraints to 70: equilibrate a macro-molecule, the artifacts are usually negligible. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 2 NOTEs 70: 70: This run will generate roughly 1 Mb of data 70: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Update groups can not be used for this system because there are three or more consecutively coupled constraints 70: 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: SWAP: Determining initial numbers of ions per compartment. 70: SWAP: Setting pointers for checkpoint writing 70: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 70: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 70: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 70: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 70: starting mdrun 'Channel_coco in octane membrane' 70: 2 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB was off during the run due to low measured imbalance. 70: Average load imbalance: 11.3%. 70: The balanceable part of the MD step is 13%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 1.5%. 70: 70: 70: NOTE: 7 % of the run time was spent in domain decomposition, 70: 26 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.645 0.161 399.6 70: (ns/day) (hour/ns) 70: Performance: 8.033 2.988 70: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps 70: 70: Update groups can not be used for this system because there are three or more consecutively coupled constraints 70: 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: SWAP: Setting pointers for checkpoint writing 70: SWAP: Copying channel fluxes from checkpoint file data 70: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 70: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 70: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 70: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 70: starting mdrun 'Channel_coco in octane membrane' 70: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 70: 70: Writing final coordinates. 70: 70: NOTE: 19 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.419 0.105 399.2 70: (ns/day) (hour/ns) 70: Performance: 12.343 1.944 70: [ OK ] CompelTest.SwapCanRun (1049 ms) 70: [----------] 1 test from CompelTest (1049 ms total) 70: 70: [----------] 6 tests from BondedInteractionsTest 70: [ RUN ] BondedInteractionsTest.NormalBondWorks 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: Setting the LD random seed to -352370729 70: 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'butane' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 70: 70: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: 70: In moleculetype 'butane' 2 atoms are not bound by a potential or 70: constraint to any other atom in the same moleculetype. Although 70: technically this might not cause issues in a simulation, this often means 70: that the user forgot to add a bond/potential/constraint or put multiple 70: molecules in the same moleculetype definition by mistake. Run with -v to 70: get information for each atom. 70: 70: Number of degrees of freedom in T-Coupling group rest is 9.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 70: NVE simulation with an initial temperature of zero: will use a Verlet 70: buffer of 10%. Check your energy drift! 70: 70: 70: This run will generate roughly 0 Mb of data 70: 70: There were 3 NOTEs 70: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 70: 70: Reading frames from gro file 'A single butane', 4 atoms. 70: Reading frame 0 time 0.000 Last frame 0 time 0.000 70: 70: NOTE: 18 % of the run time was spent in domain decomposition, 70: 18 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 5 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.002 0.000 379.6 70: (ns/day) (hour/ns) 70: Performance: 174.393 0.138 70: [ OK ] BondedInteractionsTest.NormalBondWorks (9 ms) 70: [ RUN ] BondedInteractionsTest.TabulatedBondWorks 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: Setting the LD random seed to -1382075441 70: 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'butane' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 70: 70: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: 70: In moleculetype 'butane' 2 atoms are not bound by a potential or 70: constraint to any other atom in the same moleculetype. Although 70: technically this might not cause issues in a simulation, this often means 70: that the user forgot to add a bond/potential/constraint or put multiple 70: molecules in the same moleculetype definition by mistake. Run with -v to 70: get information for each atom. 70: 70: Number of degrees of freedom in T-Coupling group rest is 9.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 70: NVE simulation with an initial temperature of zero: will use a Verlet 70: buffer of 10%. Check your energy drift! 70: 70: 70: There were 3 NOTEs 70: 70: This run will generate roughly 0 Mb of data 70: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 70: 70: Reading frames from gro file 'A single butane', 4 atoms. 70: Reading frame 0 time 0.000 Last frame 0 time 0.000 70: 70: NOTE: 18 % of the run time was spent in domain decomposition, 70: 18 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.002 0.001 380.5 70: (ns/day) (hour/ns) 70: Performance: 171.180 0.140 70: [ OK ] BondedInteractionsTest.TabulatedBondWorks (9 ms) 70: [ RUN ] BondedInteractionsTest.NormalAngleWorks 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: Setting the LD random seed to -606159267 70: 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'butane' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 70: 70: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: 70: In moleculetype 'butane' 4 atoms are not bound by a potential or 70: constraint to any other atom in the same moleculetype. Although 70: technically this might not cause issues in a simulation, this often means 70: that the user forgot to add a bond/potential/constraint or put multiple 70: molecules in the same moleculetype definition by mistake. Run with -v to 70: get information for each atom. 70: 70: Number of degrees of freedom in T-Coupling group rest is 9.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 70: NVE simulation with an initial temperature of zero: will use a Verlet 70: buffer of 10%. Check your energy drift! 70: 70: 70: There were 3 NOTEs 70: 70: This run will generate roughly 0 Mb of data 70: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 70: 70: Reading frames from gro file 'A single butane', 4 atoms. 70: Reading frame 0 time 0.000 Last frame 0 time 0.000 70: 70: NOTE: 15 % of the run time was spent in domain decomposition, 70: 16 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.002 0.001 380.6 70: (ns/day) (hour/ns) 70: Performance: 142.029 0.169 70: [ OK ] BondedInteractionsTest.NormalAngleWorks (7 ms) 70: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: Setting the LD random seed to -144822337 70: 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'butane' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 70: 70: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: 70: In moleculetype 'butane' 4 atoms are not bound by a potential or 70: constraint to any other atom in the same moleculetype. Although 70: technically this might not cause issues in a simulation, this often means 70: that the user forgot to add a bond/potential/constraint or put multiple 70: molecules in the same moleculetype definition by mistake. Run with -v to 70: get information for each atom. 70: 70: Number of degrees of freedom in T-Coupling group rest is 9.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 70: NVE simulation with an initial temperature of zero: will use a Verlet 70: buffer of 10%. Check your energy drift! 70: 70: 70: There were 3 NOTEs 70: 70: This run will generate roughly 0 Mb of data 70: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 70: 70: Reading frames from gro file 'A single butane', 4 atoms. 70: Reading frame 0 time 0.000 Last frame 0 time 0.000 70: 70: NOTE: 20 % of the run time was spent in domain decomposition, 70: 16 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.002 0.001 380.3 70: (ns/day) (hour/ns) 70: Performance: 172.197 0.139 70: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (9 ms) 70: [ RUN ] BondedInteractionsTest.NormalDihedralWorks 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: Setting the LD random seed to 2099110709 70: 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'butane' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 70: 70: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]: 70: In moleculetype 'butane' 4 atoms are not bound by a potential or 70: constraint to any other atom in the same moleculetype. Although 70: technically this might not cause issues in a simulation, this often means 70: that the user forgot to add a bond/potential/constraint or put multiple 70: molecules in the same moleculetype definition by mistake. Run with -v to 70: get information for each atom. 70: 70: Number of degrees of freedom in T-Coupling group rest is 9.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 70: NVE simulation with an initial temperature of zero: will use a Verlet 70: buffer of 10%. Check your energy drift! 70: 70: 70: This run will generate roughly 0 Mb of data 70: 70: There were 3 NOTEs 70: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 70: 70: Reading frames from gro file 'A single butane', 4 atoms. 70: Reading frame 0 time 0.000 Last frame 0 time 0.000 70: 70: NOTE: 18 % of the run time was spent in domain decomposition, 70: 16 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.002 0.001 379.0 70: (ns/day) (hour/ns) 70: Performance: 169.776 0.141 70: [ OK ] BondedInteractionsTest.NormalDihedralWorks (7 ms) 70: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: Setting the LD random seed to 2146410455 70: 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'butane' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 70: 70: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]: 70: In moleculetype 'butane' 4 atoms are not bound by a potential or 70: constraint to any other atom in the same moleculetype. Although 70: technically this might not cause issues in a simulation, this often means 70: that the user forgot to add a bond/potential/constraint or put multiple 70: molecules in the same moleculetype definition by mistake. Run with -v to 70: get information for each atom. 70: 70: Number of degrees of freedom in T-Coupling group rest is 9.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 70: NVE simulation with an initial temperature of zero: will use a Verlet 70: buffer of 10%. Check your energy drift! 70: 70: 70: There were 3 NOTEs 70: 70: This run will generate roughly 0 Mb of data 70: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/butane1.gro' 70: 70: Reading frames from gro file 'A single butane', 4 atoms. 70: Reading frame 0 time 0.000 Last frame 0 time 0.000 70: 70: NOTE: 17 % of the run time was spent in domain decomposition, 70: 16 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.002 0.001 379.7 70: (ns/day) (hour/ns) 70: Performance: 154.602 0.155 70: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (8 ms) 70: [----------] 6 tests from BondedInteractionsTest (51 ms total) 70: 70: [----------] 2 tests from BoxDeformationTest 70: [ RUN ] BoxDeformationTest.flowDoesNotAffectEkin 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (10) 70: 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: Setting the LD random seed to -1343356931 70: 70: Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: Setting gen_seed to -536939569 70: 70: Velocities were taken from a Maxwell distribution at 0 K 70: 70: This run will generate roughly 0 Mb of data 70: Number of degrees of freedom in T-Coupling group rest is 33.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: There were 3 NOTEs 70: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Argon' 70: 0 steps, 0.0 ps. 70: 70: NOTE: 23 % of the run time was spent in domain decomposition, 70: 24 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.001 0.000 320.7 70: (ns/day) (hour/ns) 70: Performance: 423.227 0.057 70: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] BoxDeformationTest.flowDoesNotAffectEkin (8 ms) 70: [ RUN ] BoxDeformationTest.EnergiesWithinTolerances 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (10) 70: 70: Setting the LD random seed to -1409650757 70: 70: Generated 330891 of the 330891 non-bonded parameter combinations 70: Generating 1-4 interactions: fudge = 0.5 70: 70: Generated 330891 of the 330891 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc216.gro' 70: Number of degrees of freedom in T-Coupling group rest is 1293.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: The largest distance between excluded atoms is 0.152 nm between atom 41 and 42 70: Calculating fourier grid dimensions for X Y Z 70: Using a fourier grid of 16x16x16, spacing 0.116 0.116 0.116 70: 70: Estimate for the relative computational load of the PME mesh part: 0.20 70: 70: This run will generate roughly 0 Mb of data 70: 70: There were 2 NOTEs 70: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 20 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB was off during the run due to low measured imbalance. 70: Average load imbalance: 3.1%. 70: The balanceable part of the MD step is 35%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 1.1%. 70: 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.155 0.039 397.9 70: (ns/day) (hour/ns) 70: Performance: 92.932 0.258 70: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Reading energy frame 2 time 0.040 Last energy frame read 2 time 0.040 [ OK ] BoxDeformationTest.EnergiesWithinTolerances (682 ms) 70: [----------] 2 tests from BoxDeformationTest (691 ms total) 70: 70: [----------] 1 test from PositionRestraintCommTest 70: [ RUN ] PositionRestraintCommTest.PositionRestraintsTwoCOMs 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 70: You have set rlist larger than the interaction cut-off, but you also have 70: verlet-buffer-tolerance > 0. Will set rlist using 70: verlet-buffer-tolerance. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (10) 70: 70: Setting the LD random seed to 1928374911 70: 70: Generated 330891 of the 330891 non-bonded parameter combinations 70: Generating 1-4 interactions: fudge = 0.5 70: 70: Generated 330891 of the 330891 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Protein' 70: 70: Excluding 3 bonded neighbours molecule type 'OCT' 70: 70: Excluding 1 bonded neighbours molecule type 'NA' 70: 70: Excluding 1 bonded neighbours molecule type 'CL' 70: 70: Excluding 3 bonded neighbours molecule type 'Protein' 70: 70: Excluding 3 bonded neighbours molecule type 'OCT' 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/OctaneSandwich.gro' 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 70: 13489 atoms are not part of any of the VCM groups 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 70: 13489 atoms are not part of any center of mass motion removal group. 70: This may lead to artifacts. 70: In most cases one should use one group for the whole system. 70: 70: Number of degrees of freedom in T-Coupling group System is 29527.73 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.990 nm, buffer size 0.090 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.965 nm, buffer size 0.065 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: Chain0: 2.207 2.168 7.330 70: Chain1: 2.228 2.186 2.401 70: Chain0: 2.207 2.168 7.330 70: Chain1: 2.228 2.186 2.401 70: 70: This run will generate roughly 1 Mb of data 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 70: Removing center of mass motion in the presence of position restraints 70: might cause artifacts. When you are using position restraints to 70: equilibrate a macro-molecule, the artifacts are usually negligible. 70: 70: 70: There were 4 NOTEs 70: 70: There was 1 WARNING 70: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Changing nstlist from 10 to 20, rlist from 0.965 to 1.066 70: 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Channel_coco in octane membrane' 70: 10 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: NOTE: 10 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: NOTE: 21 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.450 0.113 398.7 70: (ns/day) (hour/ns) 70: Performance: 16.838 1.425 70: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Last energy frame read 1 time 0.020 [ OK ] PositionRestraintCommTest.PositionRestraintsTwoCOMs (950 ms) 70: [----------] 1 test from PositionRestraintCommTest (951 ms total) 70: 70: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest 70: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: Setting the LD random seed to -134230561 70: Generating 1-4 interactions: fudge = 0.5 70: 70: Generated 2211 of the 2211 non-bonded parameter combinations 70: 70: Generated 2211 of the 2211 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 70: 70: turning H bonds into constraints... 70: 70: NOTE 2 [file ala.top, line 256]: 70: For energy conservation with LINCS, lincs_iter should be 2 or larger. 70: 70: 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 70: Number of degrees of freedom in T-Coupling group rest is 54.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 70: The optimal PME mesh load for parallel simulations is below 0.5 70: and for highly parallel simulations between 0.25 and 0.33, 70: for higher performance, increase the cut-off and the PME grid spacing. 70: 70: 70: 70: There were 3 NOTEs 70: Calculating fourier grid dimensions for X Y Z 70: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 70: 70: Estimate for the relative computational load of the PME mesh part: 0.94 70: 70: This run will generate roughly 0 Mb of data 70: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'UNNAMED in water' 70: 4 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: NOTE: 41 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.081 0.021 394.8 70: (ns/day) (hour/ns) 70: Performance: 21.072 1.139 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: Setting the LD random seed to -7408801 70: 70: Generated 2211 of the 2211 non-bonded parameter combinations 70: 70: Generated 2211 of the 2211 1-4 parameter combinations 70: Generating 1-4 interactions: fudge = 0.5 70: 70: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 70: 70: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 70: Calculating fourier grid dimensions for X Y Z 70: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 70: 70: Estimate for the relative computational load of the PME mesh part: 0.94 70: 70: This run will generate roughly 0 Mb of data 70: 70: NOTE 2 [file ala.top, line 256]: 70: For energy conservation with LINCS, lincs_iter should be 2 or larger. 70: 70: 70: Number of degrees of freedom in T-Coupling group rest is 54.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 70: The optimal PME mesh load for parallel simulations is below 0.5 70: and for highly parallel simulations between 0.25 and 0.33, 70: for higher performance, increase the cut-off and the PME grid spacing. 70: 70: 70: 70: There were 3 NOTEs 70: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'UNNAMED in water' 70: 4 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: NOTE: 40 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.060 0.015 396.1 70: (ns/day) (hour/ns) 70: Performance: 28.445 0.844 70: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 trr version: GMX_trn_file (single precision) 70: 70: 70: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 trr version: GMX_trn_file (single precision) 70: 70: 70: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 70: [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (443 ms) 70: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: Setting the LD random seed to -27323010 70: 70: Generated 2211 of the 2211 non-bonded parameter combinations 70: Generating 1-4 interactions: fudge = 0.5 70: 70: Generated 2211 of the 2211 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 70: 70: turning H bonds into constraints... 70: 70: NOTE 2 [file ala.top, line 256]: 70: For energy conservation with LINCS, lincs_iter should be 2 or larger. 70: 70: 70: Number of degrees of freedom in T-Coupling group rest is 54.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 70: The optimal PME mesh load for parallel simulations is below 0.5 70: and for highly parallel simulations between 0.25 and 0.33, 70: for higher performance, increase the cut-off and the PME grid spacing. 70: 70: 70: 70: There were 3 NOTEs 70: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 70: 70: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 70: Calculating fourier grid dimensions for X Y Z 70: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 70: 70: Estimate for the relative computational load of the PME mesh part: 0.94 70: 70: This run will generate roughly 0 Mb of data 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'UNNAMED in water' 70: 4 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: NOTE: 39 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.064 0.016 395.8 70: (ns/day) (hour/ns) 70: Performance: 26.798 0.896 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: Setting the LD random seed to 2080354297 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 2 [file ala.top, line 256]: 70: For energy conservation with LINCS, lincs_iter should be 2 or larger. 70: 70: 70: Number of degrees of freedom in T-Coupling group rest is 54.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 70: The optimal PME mesh load for parallel simulations is below 0.5 70: and for highly parallel simulations between 0.25 and 0.33, 70: for higher performance, increase the cut-off and the PME grid spacing. 70: 70: 70: 70: There were 3 NOTEs 70: 70: Generated 2211 of the 2211 non-bonded parameter combinations 70: 70: Generated 2211 of the 2211 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 70: 70: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 70: Calculating fourier grid dimensions for X Y Z 70: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 70: 70: Estimate for the relative computational load of the PME mesh part: 0.94 70: 70: This run will generate roughly 0 Mb of data 70: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 70: Can not increase nstlist because an NVE ensemble is used 70: 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'UNNAMED in water' 70: 4 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: NOTE: 41 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.048 0.012 394.7 70: (ns/day) (hour/ns) 70: Performance: 35.175 0.682 70: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 70: 70: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 70: 70: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 70: [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (78 ms) 70: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (522 ms total) 70: 70: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest 70: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Pull group 1 'FirstWaterMolecule' has 3 atoms 70: Pull group 2 'SecondWaterMolecule' has 3 atoms 70: Number of degrees of freedom in T-Coupling group rest is 9.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: Pull group natoms pbc atom distance at start reference at t=0 70: 1 3 2 70: 2 3 5 1.112 nm 1.000 nm 70: 70: There was 1 NOTE 70: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: Setting the LD random seed to 2146814719 70: 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Generated 3 of the 3 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 70: 70: This run will generate roughly 0 Mb of data 70: starting mdrun 'spc2' 70: 4 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: NOTE: 49 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.090 0.023 396.5 70: (ns/day) (hour/ns) 70: Performance: 19.110 1.256 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Pull group 1 'FirstWaterMolecule' has 3 atoms 70: Pull group 2 'SecondWaterMolecule' has 3 atoms 70: Number of degrees of freedom in T-Coupling group rest is 9.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: Pull group natoms pbc atom distance at start reference at t=0 70: 1 3 2 70: 2 3 5 1.112 nm 1.000 nm 70: 70: There was 1 NOTE 70: Setting the LD random seed to -36082322 70: 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Generated 3 of the 3 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2.gro' 70: 70: This run will generate roughly 0 Mb of data 70: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 70: Can not increase nstlist because an NVE ensemble is used 70: 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 4 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: NOTE: 48 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.078 0.020 396.3 70: (ns/day) (hour/ns) 70: Performance: 21.832 1.099 70: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 70: 70: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 70: 70: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 70: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 70: [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (63 ms) 70: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (63 ms total) 70: 70: [----------] 12 tests from FreezeWorks/FreezeGroupTest 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 70: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 70: NVE simulation: will use the initial temperature of 246.451 K for 70: determining the Verlet buffer size 70: 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: 70: There was 1 WARNING 70: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB was off during the run due to low measured imbalance. 70: Average load imbalance: 8.6%. 70: The balanceable part of the MD step is 51%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 4.4%. 70: 70: 70: NOTE: 45 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.058 0.015 395.7 70: (ns/day) (hour/ns) 70: Performance: 52.601 0.456 70: 70: 70: 70: 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (37 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: Generating 1-4 interactions: fudge = 0.5 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 70: NVE simulation: will use the initial temperature of 246.451 K for 70: determining the Verlet buffer size 70: 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: 70: There was 1 WARNING 70: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB was off during the run due to low measured imbalance. 70: Average load imbalance: 6.6%. 70: The balanceable part of the MD step is 46%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 3.1%. 70: 70: 70: NOTE: 43 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.047 0.012 393.7 70: (ns/day) (hour/ns) 70: Performance: 64.836 0.370 70: 70: 70: 70: 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (39 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 70: NVE simulation: will use the initial temperature of 246.451 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: 70: There was 1 WARNING 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB was off during the run due to low measured imbalance. 70: Average load imbalance: 4.3%. 70: The balanceable part of the MD step is 54%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 2.3%. 70: 70: 70: NOTE: 44 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.043 0.011 394.4 70: (ns/day) (hour/ns) 70: Performance: 70.619 0.340 70: 70: 70: 70: 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (33 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: Generating 1-4 interactions: fudge = 0.5 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 70: NVE simulation: will use the initial temperature of 246.451 K for 70: determining the Verlet buffer size 70: 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: 70: There was 1 WARNING 70: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB was off during the run due to low measured imbalance. 70: Average load imbalance: 4.8%. 70: The balanceable part of the MD step is 51%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 2.5%. 70: 70: 70: NOTE: 44 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.050 0.013 394.2 70: (ns/day) (hour/ns) 70: Performance: 60.798 0.395 70: 70: 70: 70: 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 (37 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: Generating 1-4 interactions: fudge = 0.5 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 70: NVE simulation: will use the initial temperature of 246.451 K for 70: determining the Verlet buffer size 70: 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 5 NOTEs 70: 70: There was 1 WARNING 70: 70: This run will generate roughly 0 Mb of data 70: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB was off during the run due to low measured imbalance. 70: Average load imbalance: 7.3%. 70: The balanceable part of the MD step is 51%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 3.7%. 70: 70: 70: NOTE: 43 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.048 0.012 395.3 70: (ns/day) (hour/ns) 70: Performance: 63.396 0.379 70: 70: 70: 70: 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (38 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 70: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (0 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: Generating 1-4 interactions: fudge = 0.5 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 4 NOTEs 70: 70: There was 1 WARNING 70: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 70: 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: NOTE: 43 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.051 0.013 395.7 70: (ns/day) (hour/ns) 70: Performance: 60.099 0.399 70: 70: 70: 70: 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (45 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 70: Generating 1-4 interactions: fudge = 0.5 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 4 NOTEs 70: 70: There was 1 WARNING 70: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 70: 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: NOTE: 42 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.053 0.013 395.6 70: (ns/day) (hour/ns) 70: Performance: 58.301 0.412 70: 70: 70: 70: 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (45 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: Generating 1-4 interactions: fudge = 0.5 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vacuo.gro' 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 4 NOTEs 70: 70: There was 1 WARNING 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 70: 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: NOTE: 44 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.058 0.015 396.5 70: (ns/day) (hour/ns) 70: Performance: 53.457 0.449 70: 70: 70: 70: 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 (45 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 4 NOTEs 70: 70: There was 1 WARNING 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 70: 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: NOTE: 44 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.040 0.010 395.2 70: (ns/day) (hour/ns) 70: Performance: 77.562 0.309 70: 70: 70: 70: 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 (79 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: Generating 1-4 interactions: fudge = 0.5 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 4 NOTEs 70: 70: There was 1 WARNING 70: 70: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 70: 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: NOTE: 44 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.043 0.011 394.9 70: (ns/day) (hour/ns) 70: Performance: 71.457 0.336 70: 70: 70: 70: 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 (80 ms) 70: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 70: 70: turning H bonds into constraints... 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 70: There are 5 atoms that are fully frozen and part of COMM removal 70: group(s), removing these atoms from the COMM removal group(s) 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 70: There are 3 atoms that are frozen along less then 3 dimensions and part 70: of COMM removal group(s), due to limitations in the code these still 70: contribute to the mass of the COM along frozen dimensions and therefore 70: the COMM correction will be too small. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 70: 70: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: 70: This run will generate roughly 0 Mb of data 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: There were 4 NOTEs 70: 70: There was 1 WARNING 70: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 70: 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'Alanine-dipeptide' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: NOTE: 46 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.082 0.021 392.3 70: (ns/day) (hour/ns) 70: Performance: 37.323 0.643 70: 70: 70: 70: 70: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 (95 ms) 70: [----------] 12 tests from FreezeWorks/FreezeGroupTest (581 ms total) 70: 70: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest 70: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Generated 3 of the 3 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Setting gen_seed to -1075847317 70: 70: Velocities were taken from a Maxwell distribution at 0 K 70: 70: This run will generate roughly 0 Mb of data 70: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 70: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: Net Acceleration in X direction, will not be corrected 70: Net Acceleration in Y direction, will not be corrected 70: Net Acceleration in Z direction, will not be corrected 70: 70: There were 3 NOTEs 70: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB was off during the run due to low measured imbalance. 70: Average load imbalance: 4.4%. 70: The balanceable part of the MD step is 22%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 1.0%. 70: 70: 70: NOTE: 46 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.045 0.011 396.7 70: (ns/day) (hour/ns) 70: Performance: 135.757 0.177 70: 70: 70: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (22 ms) 70: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Generated 3 of the 3 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Setting gen_seed to -178438337 70: 70: Velocities were taken from a Maxwell distribution at 0 K 70: 70: This run will generate roughly 0 Mb of data 70: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 70: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 70: Net Acceleration in X direction, will not be corrected 70: Net Acceleration in Y direction, will not be corrected 70: Net Acceleration in Z direction, will not be corrected 70: 70: There were 3 NOTEs 70: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Can not increase nstlist because verlet-buffer-tolerance is not set or used 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB was off during the run due to low measured imbalance. 70: Average load imbalance: 8.2%. 70: The balanceable part of the MD step is 21%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 1.7%. 70: 70: 70: NOTE: 46 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.049 0.012 395.9 70: (ns/day) (hour/ns) 70: Performance: 125.092 0.192 70: 70: 70: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (25 ms) 70: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Generated 3 of the 3 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Setting gen_seed to -1635263521 70: 70: Velocities were taken from a Maxwell distribution at 0 K 70: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 70: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: Net Acceleration in X direction, will not be corrected 70: Net Acceleration in Y direction, will not be corrected 70: Net Acceleration in Z direction, will not be corrected 70: 70: There were 3 NOTEs 70: 70: This run will generate roughly 0 Mb of data 70: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB was off during the run due to low measured imbalance. 70: Average load imbalance: 1.3%. 70: The balanceable part of the MD step is 19%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 0.2%. 70: 70: 70: NOTE: 45 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.051 0.013 396.5 70: (ns/day) (hour/ns) 70: Performance: 119.817 0.200 70: 70: 70: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 (21 ms) 70: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 70: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 70: < 0 70: 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 70: Setting nstcalcenergy (100) equal to nstenergy (4) 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Generated 3 of the 3 non-bonded parameter combinations 70: 70: Generated 3 of the 3 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Setting gen_seed to 1870659580 70: 70: Velocities were taken from a Maxwell distribution at 0 K 70: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 70: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 70: Net Acceleration in X direction, will not be corrected 70: Net Acceleration in Y direction, will not be corrected 70: Net Acceleration in Z direction, will not be corrected 70: 70: There were 3 NOTEs 70: 70: This run will generate roughly 0 Mb of data 70: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 70: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 70: Can not increase nstlist because verlet-buffer-tolerance is not set or used 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc2' 70: 8 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: 70: Dynamic load balancing report: 70: DLB was off during the run due to low measured imbalance. 70: Average load imbalance: 0.3%. 70: The balanceable part of the MD step is 46%, load imbalance is computed from this. 70: Part of the total run time spent waiting due to load imbalance: 0.2%. 70: 70: 70: NOTE: 45 % of the run time was spent communicating energies, 70: you might want to increase some nst* mdp options 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.045 0.011 396.1 70: (ns/day) (hour/ns) 70: Performance: 138.257 0.174 70: 70: 70: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (19 ms) 70: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (89 ms total) 70: 70: [----------] Global test environment tear-down 70: [==========] 29 tests from 8 test suites ran. (4669 ms total) 70: [ PASSED ] 28 tests. 70: [ SKIPPED ] 1 test, listed below: 70: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 70/94 Test #70: MdrunTestsTwoRanks ........................... Passed 5.13 sec test 71 Start 71: MdrunSingleRankAlgorithmsTests 71: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/mdrun-single-rank-algorithms-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/MdrunSingleRankAlgorithmsTests.xml" 71: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests 71: Test timeout computed to be: 600 71: [==========] Running 5 tests from 3 test suites. 71: [----------] Global test environment set-up. 71: [----------] 1 test from DispersionCorrectionTest 71: [ RUN ] DispersionCorrectionTest.DispersionCorrectionCanRun 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 30.00 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]: 71: There are 9 non-linear virtual site constructions. Their contribution to 71: the energy error is approximated. In most cases this does not affect the 71: error significantly. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 2 NOTEs 71: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 71: Changing nstlist from 10 to 40, rlist from 1.023 to 1.158 71: 71: Update groups can not be used for this system because an incompatible virtual site type is used 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'Alanine dipeptide in vacuo' 71: 200 steps, 0.4 ps. 71: Setting the LD random seed to 1072135871 71: 71: Generated 2145 of the 2145 non-bonded parameter combinations 71: 71: Generated 2145 of the 2145 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 71: 71: turning H bonds into constraints... 71: 71: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 71: 71: Cleaning up constraints and constant bonded interactions with virtual sites 71: 71: Converted 3 Bonds with virtual sites to connections, 7 left 71: 71: Removed 18 Angles with virtual sites, 21 left 71: 71: Removed 10 Proper Dih.s with virtual sites, 44 left 71: 71: Converted 12 Constraints with virtual sites to connections, 0 left 71: 71: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 71: 71: Calculated rlist for 1x1 atom pair-list as 1.038 nm, buffer size 0.038 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 1.023 nm, buffer size 0.023 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.549 0.275 199.9 71: (ns/day) (hour/ns) 71: Performance: 126.494 0.190 71: [ OK ] DispersionCorrectionTest.DispersionCorrectionCanRun (366 ms) 71: [----------] 1 test from DispersionCorrectionTest (366 ms total) 71: 71: [----------] 1 test from OriresTest 71: [ RUN ] OriresTest.OriresCanRun 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 518.00 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There was 1 NOTE 71: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 71: Changing nstlist from 10 to 25, rlist from 1.07 to 1.203 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-1' 71: 10 steps, 0.0 ps. 71: Setting the LD random seed to 1912045462 71: 71: Generated 2145 of the 2145 non-bonded parameter combinations 71: 71: Generated 2145 of the 2145 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/orires_1lvz.gro' 71: 71: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 71: 71: Calculated rlist for 1x1 atom pair-list as 1.093 nm, buffer size 0.093 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 1.070 nm, buffer size 0.070 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.686 0.343 199.9 71: (ns/day) (hour/ns) 71: Performance: 5.541 4.331 71: [ OK ] OriresTest.OriresCanRun (1265 ms) 71: [----------] 1 test from OriresTest (1266 ms total) 71: 71: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest 71: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 71: Number of degrees of freedom in T-Coupling group rest is 10.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]: 71: NVE simulation with an initial temperature of zero: will use a Verlet 71: buffer of 10%. Check your energy drift! 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]: 71: The optimal PME mesh load for parallel simulations is below 0.5 71: and for highly parallel simulations between 0.25 and 0.33, 71: for higher performance, increase the cut-off and the PME grid spacing. 71: 71: 71: 71: There were 2 NOTEs 71: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'Dipoles' 71: 20 steps, 0.1 ps. 71: Setting the LD random seed to -85984261 71: 71: Generated 1 of the 1 non-bonded parameter combinations 71: 71: Excluding 1 bonded neighbours molecule type 'Dipole' 71: 71: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/dipoles.gro', all velocities are zero 71: 71: Searching the wall atom type(s) 71: 71: The largest distance between excluded atoms is 0.344 nm between atom 1 and 2 71: Calculating fourier grid dimensions for X Y Z 71: Using a fourier grid of 20x20x40, spacing 0.200 0.200 0.200 71: 71: Estimate for the relative computational load of the PME mesh part: 1.00 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.059 0.030 199.1 71: (ns/day) (hour/ns) 71: Performance: 152.852 0.157 71: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Last energy frame read 5 time 0.050 trr version: GMX_trn_file (single precision) 71: 71: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 (811 ms) 71: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 71: Test system 'epsilon-surface-constraint' cannot run with 1 ranks. 71: The supported numbers are > 1. 71: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 (0 ms) 71: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 71: With epsilon_surface > 0 all molecules should be neutral. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 71: With epsilon_surface > 0 you can only use domain decomposition when there 71: are only small molecules with all bonds constrained (mdrun will check for 71: this). 71: 71: Number of degrees of freedom in T-Coupling group rest is 9.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 71: NVE simulation with an initial temperature of zero: will use a Verlet 71: buffer of 10%. Check your energy drift! 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 71: The optimal PME mesh load for parallel simulations is below 0.5 71: and for highly parallel simulations between 0.25 and 0.33, 71: for higher performance, increase the cut-off and the PME grid spacing. 71: 71: 71: 71: There were 4 NOTEs 71: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 71: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'Dipoles' 71: 20 steps, 0.1 ps. 71: Setting the LD random seed to 2121891547 71: 71: Generated 1 of the 1 non-bonded parameter combinations 71: 71: Excluding 1 bonded neighbours molecule type 'Dipole' 71: 71: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/dipoles.gro', all velocities are zero 71: 71: The largest distance between excluded atoms is 0.344 nm between atom 1 and 2 71: Calculating fourier grid dimensions for X Y Z 71: Using a fourier grid of 20x20x20, spacing 0.200 0.200 0.200 71: 71: Estimate for the relative computational load of the PME mesh part: 1.00 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.074 0.037 199.4 71: (ns/day) (hour/ns) 71: Performance: 121.665 0.197 71: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Last energy frame read 5 time 0.050 71: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 (265 ms) 71: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest (1076 ms total) 71: 71: [----------] Global test environment tear-down 71: [==========] 5 tests from 3 test suites ran. (2902 ms total) 71: [ PASSED ] 5 tests. 71/94 Test #71: MdrunSingleRankAlgorithmsTests ............... Passed 3.25 sec test 72 Start 72: Minimize1RankTests 72: Test command: /usr/bin/mpiexec "-n" "1" "/build/reproducible-path/gromacs-2025.0/build/mpi/bin/minimize-test" "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/Minimize1RankTests.xml" 72: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests 72: Test timeout computed to be: 600 72: [==========] Running 12 tests from 2 test suites. 72: [----------] Global test environment set-up. 72: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 72: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Generated 330891 of the 330891 non-bonded parameter combinations 72: Generating 1-4 interactions: fudge = 0.5 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: Number of degrees of freedom in T-Coupling group System is 27.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 4 NOTEs 72: 72: This run will generate roughly 0 Mb of data 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Using 1 MPI process 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Steepest Descents: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: 72: Energy minimization reached the maximum number of steps before the forces 72: reached the requested precision Fmax < 10. 72: 72: writing lowest energy coordinates. 72: 72: Steepest Descents did not converge to Fmax < 10 in 5 steps. 72: Potential Energy = -4.7991047e+01 72: Maximum force = 1.8629713e+02 on atom 13 72: Norm of force = 8.7721867e+01 72: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (618 ms) 72: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Generated 330891 of the 330891 non-bonded parameter combinations 72: Generating 1-4 interactions: fudge = 0.5 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: Number of degrees of freedom in T-Coupling group System is 27.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 4 NOTEs 72: 72: This run will generate roughly 0 Mb of data 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Using 1 MPI process 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Polak-Ribiere Conjugate Gradients: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: F-max = 3.02331e+02 on atom 3 72: F-Norm = 1.18024e+02 72: 72: 72: Energy minimization reached the maximum number of steps before the forces 72: reached the requested precision Fmax < 10. 72: 72: writing lowest energy coordinates. 72: 72: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 72: Potential Energy = -5.5862484e+01 72: Maximum force = 4.2726132e+02 on atom 13 72: Norm of force = 1.8452547e+02 72: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (592 ms) 72: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Generated 20503 of the 20503 non-bonded parameter combinations 72: Generating 1-4 interactions: fudge = 1 72: 72: Generated 17396 of the 20503 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Glycine' 72: 72: turning H bonds into constraints... 72: Number of degrees of freedom in T-Coupling group System is 22.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 4 NOTEs 72: 72: This run will generate roughly 0 Mb of data 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Using 1 MPI process 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Steepest Descents: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: 72: Energy minimization reached the maximum number of steps before the forces 72: reached the requested precision Fmax < 10. 72: 72: writing lowest energy coordinates. 72: 72: Steepest Descents did not converge to Fmax < 10 in 5 steps. 72: Potential Energy = 3.1937714e+02 72: Maximum force = 9.9988643e+03 on atom 9 72: Norm of force = 4.6166996e+03 72: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (101 ms) 72: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Generated 20503 of the 20503 non-bonded parameter combinations 72: Generating 1-4 interactions: fudge = 1 72: 72: Generated 17396 of the 20503 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Glycine' 72: 72: turning H bonds into constraints... 72: 72: NOTE 3 [file glycine_vacuo.top, line 12]: 72: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 72: 72: Number of degrees of freedom in T-Coupling group System is 22.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 5 NOTEs 72: 72: This run will generate roughly 0 Mb of data 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Using 1 MPI process 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Polak-Ribiere Conjugate Gradients: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: F-max = 2.41575e+04 on atom 10 72: F-Norm = 1.18451e+04 72: 72: 72: Energy minimization reached the maximum number of steps before the forces 72: reached the requested precision Fmax < 10. 72: 72: writing lowest energy coordinates. 72: 72: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 72: Potential Energy = 1.5174426e+02 72: Maximum force = 7.4208862e+03 on atom 9 72: Norm of force = 3.5692992e+03 72: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (95 ms) 72: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Generated 2145 of the 2145 non-bonded parameter combinations 72: 72: Generated 2145 of the 2145 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 72: 72: turning all bonds into constraints... 72: 72: NOTE 3 [file unknown]: 72: You are using constraints on all bonds, whereas the forcefield has been 72: parametrized only with constraints involving hydrogen atoms. We suggest 72: using constraints = h-bonds instead, this will also improve performance. 72: 72: 72: Cleaning up constraints and constant bonded interactions with virtual sites 72: 72: Removed 18 Angles with virtual sites, 21 left 72: 72: Removed 10 Proper Dih.s with virtual sites, 44 left 72: 72: Converted 15 Constraints with virtual sites to connections, 7 left 72: Number of degrees of freedom in T-Coupling group System is 23.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 5 NOTEs 72: 72: This run will generate roughly 0 Mb of data 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Update groups can not be used for this system because an incompatible virtual site type is used 72: 72: Using 1 MPI process 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Steepest Descents: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: 72: Energy minimization reached the maximum number of steps before the forces 72: reached the requested precision Fmax < 10. 72: 72: writing lowest energy coordinates. 72: 72: Steepest Descents did not converge to Fmax < 10 in 5 steps. 72: Potential Energy = -1.5698431e+02 72: Maximum force = 4.5699695e+02 on atom 17 72: Norm of force = 1.8327127e+02 72: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (24 ms) 72: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Generating 1-4 interactions: fudge = 0.5 72: Generated 2145 of the 2145 non-bonded parameter combinations 72: 72: Generated 2145 of the 2145 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 72: 72: turning all bonds into constraints... 72: 72: NOTE 3 [file unknown]: 72: You are using constraints on all bonds, whereas the forcefield has been 72: parametrized only with constraints involving hydrogen atoms. We suggest 72: using constraints = h-bonds instead, this will also improve performance. 72: 72: 72: NOTE 4 [file unknown]: 72: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 72: 72: 72: Cleaning up constraints and constant bonded interactions with virtual sites 72: 72: Removed 18 Angles with virtual sites, 21 left 72: 72: Removed 10 Proper Dih.s with virtual sites, 44 left 72: 72: Converted 15 Constraints with virtual sites to connections, 7 left 72: Number of degrees of freedom in T-Coupling group System is 23.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 6 NOTEs 72: 72: This run will generate roughly 0 Mb of data 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Update groups can not be used for this system because an incompatible virtual site type is used 72: 72: Using 1 MPI process 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Polak-Ribiere Conjugate Gradients: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: F-max = 1.06801e+03 on atom 28 72: F-Norm = 4.26922e+02 72: 72: 72: Energy minimization reached the maximum number of steps before the forces 72: reached the requested precision Fmax < 10. 72: 72: writing lowest energy coordinates. 72: 72: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 72: Potential Energy = -1.6941071e+02 72: Maximum force = 2.1830020e+02 on atom 17 72: Norm of force = 7.9207704e+01 72: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (20 ms) 72: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (1455 ms total) 72: 72: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 72: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Generated 1 of the 1 non-bonded parameter combinations 72: 72: Excluding 1 bonded neighbours molecule type 'Argon' 72: Number of degrees of freedom in T-Coupling group System is 33.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 3 NOTEs 72: 72: This run will generate roughly 0 Mb of data 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Using 1 MPI process 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Steepest Descents: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: 72: writing lowest energy coordinates. 72: 72: Steepest Descents converged to Fmax < 10 in 1 steps 72: Potential Energy = -9.7425687e-01 72: Maximum force = 4.0132279e+00 on atom 1 72: Norm of force = 1.6383933e+00 72: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Number of degrees of freedom in T-Coupling group System is 33.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 3 NOTEs 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (7 ms) 72: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 72: Generated 1 of the 1 non-bonded parameter combinations 72: 72: Excluding 1 bonded neighbours molecule type 'Argon' 72: 72: This run will generate roughly 0 Mb of data 72: Using 1 MPI process 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Polak-Ribiere Conjugate Gradients: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: F-max = 4.01323e+00 on atom 1 72: F-Norm = 1.63839e+00 72: 72: 72: writing lowest energy coordinates. 72: 72: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 72: Potential Energy = -9.9064195e-01 72: Maximum force = 2.5781672e+00 on atom 1 72: Norm of force = 1.0525324e+00 72: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (6 ms) 72: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: 72: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 72: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 72: 72: Number of degrees of freedom in T-Coupling group System is 33.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 3 NOTEs 72: 72: There was 1 WARNING 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Using 1 MPI process 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Low-Memory BFGS Minimizer: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: Using 10 BFGS correction steps. 72: 72: F-max = 4.01323e+00 on atom 1 72: F-Norm = 1.63839e+00 72: 72: 72: writing lowest energy coordinates. 72: 72: Low-Memory BFGS Minimizer converged to Fmax < 10 in -1 steps 72: Potential Energy = -9.9064195e-01 72: Maximum force = 2.5781672e+00 on atom 1 72: Norm of force = 1.0525324e+00 72: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file 72: Generated 1 of the 1 non-bonded parameter combinations 72: 72: Excluding 1 bonded neighbours molecule type 'Argon' 72: 72: This run will generate roughly 0 Mb of data 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (6 ms) 72: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Generated 20503 of the 20503 non-bonded parameter combinations 72: Generating 1-4 interactions: fudge = 1 72: 72: Generated 17396 of the 20503 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Glycine' 72: Number of degrees of freedom in T-Coupling group System is 27.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 4 NOTEs 72: 72: This run will generate roughly 0 Mb of data 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Using 1 MPI process 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Steepest Descents: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: 72: Energy minimization reached the maximum number of steps before the forces 72: reached the requested precision Fmax < 10. 72: 72: writing lowest energy coordinates. 72: 72: Steepest Descents did not converge to Fmax < 10 in 5 steps. 72: Potential Energy = 3.1939697e+02 72: Maximum force = 9.9704248e+03 on atom 9 72: Norm of force = 4.6227540e+03 72: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (98 ms) 72: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Generated 20503 of the 20503 non-bonded parameter combinations 72: Generating 1-4 interactions: fudge = 1 72: 72: Generated 17396 of the 20503 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Glycine' 72: Number of degrees of freedom in T-Coupling group System is 27.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 4 NOTEs 72: 72: This run will generate roughly 0 Mb of data 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Using 1 MPI process 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Polak-Ribiere Conjugate Gradients: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: F-max = 2.41672e+04 on atom 10 72: F-Norm = 1.19357e+04 72: 72: 72: Energy minimization reached the maximum number of steps before the forces 72: reached the requested precision Fmax < 10. 72: 72: writing lowest energy coordinates. 72: 72: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 72: Potential Energy = 1.5625757e+02 72: Maximum force = 7.5018242e+03 on atom 9 72: Norm of force = 3.6139019e+03 72: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (103 ms) 72: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: 72: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 72: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 72: 72: Generating 1-4 interactions: fudge = 1 72: Generated 20503 of the 20503 non-bonded parameter combinations 72: 72: Generated 17396 of the 20503 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Glycine' 72: Number of degrees of freedom in T-Coupling group System is 27.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 72: COM removal frequency is set to (4). 72: Other settings require a global communication frequency of 100. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 100. 72: 72: 72: There were 4 NOTEs 72: 72: There was 1 WARNING 72: 72: This run will generate roughly 0 Mb of data 72: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 72: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 72: Using 1 MPI process 72: Using 2 OpenMP threads 72: 72: 72: NOTE: The number of threads is not equal to the number of (logical) cpus 72: and the -pin option is set to auto: will not pin threads to cpus. 72: This can lead to significant performance degradation. 72: Consider using -pin on (and -pinoffset in case you run multiple jobs). 72: 72: Low-Memory BFGS Minimizer: 72: Tolerance (Fmax) = 1.00000e+01 72: Number of steps = 4 72: Using 10 BFGS correction steps. 72: 72: F-max = 2.41672e+04 on atom 10 72: F-Norm = 1.19357e+04 72: 72: 72: Energy minimization has stopped, but the forces have not converged to the 72: requested precision Fmax < 10 (which may not be possible for your system). It 72: stopped because the algorithm tried to make a new step whose size was too 72: small, or there was no change in the energy since last step. Either way, we 72: regard the minimization as converged to within the available machine 72: precision, given your starting configuration and EM parameters. 72: 72: Double precision normally gives you higher accuracy, but this is often not 72: needed for preparing to run molecular dynamics. 72: 72: writing lowest energy coordinates. 72: 72: Low-Memory BFGS Minimizer converged to machine precision in 0 steps, 72: but did not reach the requested Fmax < 10. 72: Potential Energy = 5.6111731e+02 72: Maximum force = 1.2685497e+04 on atom 10 72: Norm of force = 6.0643635e+03 72: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (105 ms) 72: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (327 ms total) 72: 72: [----------] Global test environment tear-down 72: [==========] 12 tests from 2 test suites ran. (1929 ms total) 72: [ PASSED ] 12 tests. 72/94 Test #72: Minimize1RankTests ........................... Passed 2.41 sec test 73 Start 73: Minimize2RankTests 73: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2025.0/build/mpi/bin/minimize-test" "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/Minimize2RankTests.xml" 73: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests 73: Test timeout computed to be: 600 73: [==========] Running 12 tests from 2 test suites. 73: [----------] Global test environment set-up. 73: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 73: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Generated 330891 of the 330891 non-bonded parameter combinations 73: Generating 1-4 interactions: fudge = 0.5 73: 73: Generated 330891 of the 330891 1-4 parameter combinations 73: 73: Excluding 2 bonded neighbours molecule type 'SOL' 73: Number of degrees of freedom in T-Coupling group System is 27.00 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 4 NOTEs 73: 73: This run will generate roughly 0 Mb of data 73: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 73: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 73: Using 2 MPI processes 73: Using 2 OpenMP threads per MPI process 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: 73: Steepest Descents: 73: Tolerance (Fmax) = 1.00000e+01 73: Number of steps = 4 73: 73: Energy minimization reached the maximum number of steps before the forces 73: reached the requested precision Fmax < 10. 73: 73: writing lowest energy coordinates. 73: 73: Steepest Descents did not converge to Fmax < 10 in 5 steps. 73: Potential Energy = -4.7991032e+01 73: Maximum force = 1.8629765e+02 on atom 13 73: Norm of force = 8.7722064e+01 73: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (633 ms) 73: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Generated 330891 of the 330891 non-bonded parameter combinations 73: Generating 1-4 interactions: fudge = 0.5 73: 73: Generated 330891 of the 330891 1-4 parameter combinations 73: 73: Excluding 2 bonded neighbours molecule type 'SOL' 73: Number of degrees of freedom in T-Coupling group System is 27.00 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: This run will generate roughly 0 Mb of data 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 4 NOTEs 73: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 73: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 73: Using 2 MPI processes 73: Using 2 OpenMP threads per MPI process 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: 73: Polak-Ribiere Conjugate Gradients: 73: Tolerance (Fmax) = 1.00000e+01 73: Number of steps = 4 73: F-max = 3.02331e+02 on atom 3 73: F-Norm = 1.18024e+02 73: 73: 73: Energy minimization reached the maximum number of steps before the forces 73: reached the requested precision Fmax < 10. 73: 73: writing lowest energy coordinates. 73: 73: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 73: Potential Energy = -5.5862144e+01 73: Maximum force = 4.2727667e+02 on atom 13 73: Norm of force = 1.8453053e+02 73: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (601 ms) 73: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Generated 20503 of the 20503 non-bonded parameter combinations 73: Generating 1-4 interactions: fudge = 1 73: 73: Generated 17396 of the 20503 1-4 parameter combinations 73: 73: Excluding 3 bonded neighbours molecule type 'Glycine' 73: 73: turning H bonds into constraints... 73: Number of degrees of freedom in T-Coupling group System is 22.00 73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 4 NOTEs 73: 73: This run will generate roughly 0 Mb of data 73: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 73: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 73: Using 2 MPI processes 73: Using 2 OpenMP threads per MPI process 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: 73: Steepest Descents: 73: Tolerance (Fmax) = 1.00000e+01 73: Number of steps = 4 73: 73: Energy minimization reached the maximum number of steps before the forces 73: reached the requested precision Fmax < 10. 73: 73: writing lowest energy coordinates. 73: 73: Steepest Descents did not converge to Fmax < 10 in 5 steps. 73: Potential Energy = 3.1937704e+02 73: Maximum force = 9.9988633e+03 on atom 9 73: Norm of force = 4.6166993e+03 73: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (104 ms) 73: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 73: Generated 20503 of the 20503 non-bonded parameter combinations 73: Generating 1-4 interactions: fudge = 1 73: 73: Generated 17396 of the 20503 1-4 parameter combinations 73: 73: Excluding 3 bonded neighbours molecule type 'Glycine' 73: 73: turning H bonds into constraints... 73: 73: NOTE 3 [file glycine_vacuo.top, line 12]: 73: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 73: 73: Number of degrees of freedom in T-Coupling group System is 22.00 73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 5 NOTEs 73: 73: This run will generate roughly 0 Mb of data 73: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 73: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 73: Using 2 MPI processes 73: Using 2 OpenMP threads per MPI process 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: 73: Polak-Ribiere Conjugate Gradients: 73: Tolerance (Fmax) = 1.00000e+01 73: Number of steps = 4 73: F-max = 2.41575e+04 on atom 10 73: F-Norm = 1.18451e+04 73: 73: 73: Energy minimization reached the maximum number of steps before the forces 73: reached the requested precision Fmax < 10. 73: 73: writing lowest energy coordinates. 73: 73: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 73: Potential Energy = 1.5174426e+02 73: Maximum force = 7.4208862e+03 on atom 9 73: Norm of force = 3.5692992e+03 73: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (149 ms) 73: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Generated 2145 of the 2145 non-bonded parameter combinations 73: Generating 1-4 interactions: fudge = 0.5 73: 73: Generated 2145 of the 2145 1-4 parameter combinations 73: 73: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 73: 73: turning all bonds into constraints... 73: 73: NOTE 3 [file unknown]: 73: You are using constraints on all bonds, whereas the forcefield has been 73: parametrized only with constraints involving hydrogen atoms. We suggest 73: using constraints = h-bonds instead, this will also improve performance. 73: 73: 73: Cleaning up constraints and constant bonded interactions with virtual sites 73: 73: Removed 18 Angles with virtual sites, 21 left 73: 73: Removed 10 Proper Dih.s with virtual sites, 44 left 73: 73: Converted 15 Constraints with virtual sites to connections, 7 left 73: Number of degrees of freedom in T-Coupling group System is 23.00 73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 5 NOTEs 73: 73: This run will generate roughly 0 Mb of data 73: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 73: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 73: Update groups can not be used for this system because an incompatible virtual site type is used 73: 73: Using 2 MPI processes 73: Using 2 OpenMP threads per MPI process 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: 73: Steepest Descents: 73: Tolerance (Fmax) = 1.00000e+01 73: Number of steps = 4 73: 73: Energy minimization reached the maximum number of steps before the forces 73: reached the requested precision Fmax < 10. 73: 73: writing lowest energy coordinates. 73: 73: Steepest Descents did not converge to Fmax < 10 in 5 steps. 73: Potential Energy = -1.5698425e+02 73: Maximum force = 4.5699695e+02 on atom 17 73: Norm of force = 1.8327127e+02 73: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (41 ms) 73: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Generated 2145 of the 2145 non-bonded parameter combinations 73: Generating 1-4 interactions: fudge = 0.5 73: 73: Generated 2145 of the 2145 1-4 parameter combinations 73: 73: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 73: 73: turning all bonds into constraints... 73: 73: NOTE 3 [file unknown]: 73: You are using constraints on all bonds, whereas the forcefield has been 73: parametrized only with constraints involving hydrogen atoms. We suggest 73: using constraints = h-bonds instead, this will also improve performance. 73: 73: 73: NOTE 4 [file unknown]: 73: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 73: 73: 73: Cleaning up constraints and constant bonded interactions with virtual sites 73: 73: Removed 18 Angles with virtual sites, 21 left 73: 73: Removed 10 Proper Dih.s with virtual sites, 44 left 73: 73: Converted 15 Constraints with virtual sites to connections, 7 left 73: Number of degrees of freedom in T-Coupling group System is 23.00 73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 73: 73: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: This run will generate roughly 0 Mb of data 73: 73: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 6 NOTEs 73: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 73: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 73: Update groups can not be used for this system because an incompatible virtual site type is used 73: 73: Using 2 MPI processes 73: Using 2 OpenMP threads per MPI process 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: 73: Polak-Ribiere Conjugate Gradients: 73: Tolerance (Fmax) = 1.00000e+01 73: Number of steps = 4 73: F-max = 1.06801e+03 on atom 28 73: F-Norm = 4.26922e+02 73: 73: 73: Energy minimization reached the maximum number of steps before the forces 73: reached the requested precision Fmax < 10. 73: 73: writing lowest energy coordinates. 73: 73: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 73: Potential Energy = -1.6941101e+02 73: Maximum force = 2.1832886e+02 on atom 17 73: Norm of force = 7.9206610e+01 73: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file 73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (44 ms) 73: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (1576 ms total) 73: 73: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 73: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Generated 1 of the 1 non-bonded parameter combinations 73: 73: Excluding 1 bonded neighbours molecule type 'Argon' 73: Number of degrees of freedom in T-Coupling group System is 33.00 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 3 NOTEs 73: 73: This run will generate roughly 0 Mb of data 73: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 73: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 73: Using 2 MPI processes 73: Using 2 OpenMP threads per MPI process 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: 73: Steepest Descents: 73: Tolerance (Fmax) = 1.00000e+01 73: Number of steps = 4 73: 73: writing lowest energy coordinates. 73: 73: Steepest Descents converged to Fmax < 10 in 1 steps 73: Potential Energy = -9.7425687e-01 73: Maximum force = 4.0132279e+00 on atom 3 73: Norm of force = 1.6383933e+00 73: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 73: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (15 ms) 73: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Generated 1 of the 1 non-bonded parameter combinations 73: 73: Excluding 1 bonded neighbours molecule type 'Argon' 73: 73: This run will generate roughly 0 Mb of data 73: Number of degrees of freedom in T-Coupling group System is 33.00 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 3 NOTEs 73: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 73: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 73: Using 2 MPI processes 73: Using 2 OpenMP threads per MPI process 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: 73: Polak-Ribiere Conjugate Gradients: 73: Tolerance (Fmax) = 1.00000e+01 73: Number of steps = 4 73: F-max = 4.01323e+00 on atom 3 73: F-Norm = 1.63839e+00 73: 73: 73: writing lowest energy coordinates. 73: 73: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 73: Potential Energy = -9.9064195e-01 73: Maximum force = 2.5781672e+00 on atom 3 73: Norm of force = 1.0525324e+00 73: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (10 ms) 73: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: 73: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 73: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 73: 73: Generated 1 of the 1 non-bonded parameter combinations 73: 73: Excluding 1 bonded neighbours molecule type 'Argon' 73: Number of degrees of freedom in T-Coupling group System is 33.00 73: 73: This run will generate roughly 0 Mb of data 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 3 NOTEs 73: 73: There was 1 WARNING 73: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (6 ms) 73: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Generated 20503 of the 20503 non-bonded parameter combinations 73: Generating 1-4 interactions: fudge = 1 73: 73: Generated 17396 of the 20503 1-4 parameter combinations 73: 73: Excluding 3 bonded neighbours molecule type 'Glycine' 73: Number of degrees of freedom in T-Coupling group System is 27.00 73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 4 NOTEs 73: 73: This run will generate roughly 0 Mb of data 73: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 73: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 73: Using 2 MPI processes 73: Using 2 OpenMP threads per MPI process 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: 73: Steepest Descents: 73: Tolerance (Fmax) = 1.00000e+01 73: Number of steps = 4 73: 73: Energy minimization reached the maximum number of steps before the forces 73: reached the requested precision Fmax < 10. 73: 73: writing lowest energy coordinates. 73: 73: Steepest Descents did not converge to Fmax < 10 in 5 steps. 73: Potential Energy = 3.1939685e+02 73: Maximum force = 9.9704248e+03 on atom 9 73: Norm of force = 4.6227568e+03 73: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (124 ms) 73: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Generated 20503 of the 20503 non-bonded parameter combinations 73: Generating 1-4 interactions: fudge = 1 73: 73: Generated 17396 of the 20503 1-4 parameter combinations 73: 73: Excluding 3 bonded neighbours molecule type 'Glycine' 73: Number of degrees of freedom in T-Coupling group System is 27.00 73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 4 NOTEs 73: 73: This run will generate roughly 0 Mb of data 73: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 73: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 73: Using 2 MPI processes 73: Using 2 OpenMP threads per MPI process 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: 73: Polak-Ribiere Conjugate Gradients: 73: Tolerance (Fmax) = 1.00000e+01 73: Number of steps = 4 73: F-max = 2.41672e+04 on atom 10 73: F-Norm = 1.19357e+04 73: 73: 73: Energy minimization reached the maximum number of steps before the forces 73: reached the requested precision Fmax < 10. 73: 73: writing lowest energy coordinates. 73: 73: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 73: Potential Energy = 1.5625761e+02 73: Maximum force = 7.5018237e+03 on atom 9 73: Norm of force = 3.6139019e+03 73: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 73: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (120 ms) 73: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: 73: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 73: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 73: 73: Generated 20503 of the 20503 non-bonded parameter combinations 73: Generating 1-4 interactions: fudge = 1 73: 73: Generated 17396 of the 20503 1-4 parameter combinations 73: 73: Excluding 3 bonded neighbours molecule type 'Glycine' 73: Number of degrees of freedom in T-Coupling group System is 27.00 73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 73: COM removal frequency is set to (4). 73: Other settings require a global communication frequency of 100. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 100. 73: 73: 73: There were 4 NOTEs 73: 73: There was 1 WARNING 73: 73: This run will generate roughly 0 Mb of data 73: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (120 ms) 73: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (397 ms total) 73: 73: [----------] Global test environment tear-down 73: [==========] 12 tests from 2 test suites ran. (2140 ms total) 73: [ PASSED ] 12 tests. 73/94 Test #73: Minimize2RankTests ........................... Passed 2.62 sec test 74 Start 74: MdrunNonIntegratorTests 74: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/mdrun-non-integrator-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/MdrunNonIntegratorTests.xml" 74: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests 74: Test timeout computed to be: 600 74: [==========] Running 46 tests from 3 test suites. 74: [----------] Global test environment set-up. 74: [----------] 1 test from NonbondedBenchTest 74: [ RUN ] NonbondedBenchTest.BasicEndToEndTest 74: SIMD width: 4 74: System size: 3000 atoms 74: Cut-off radius: 1 nm 74: Number of threads: 1 74: Number of iterations: 1 74: Compute energies: no 74: Ewald excl. corr.: analytical 74: 74: Coulomb LJ comb. SIMD Mcycles Mcycles/it. pairs/cycle 74: total useful 74: Ewald all geom. 4xM 14.915 14.9152 0.0798 0.0422 74: [ OK ] NonbondedBenchTest.BasicEndToEndTest (21 ms) 74: [----------] 1 test from NonbondedBenchTest (21 ms total) 74: 74: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 NOTEs 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.033 0.017 199.1 74: (ns/day) (hour/ns) 74: Performance: 88.288 0.272 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.trr' 74: 74: trr version: GMX_trn_file (single precision) 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 35 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.001 195.6 74: (ns/day) (hour/ns) 74: Performance: 1897.903 0.013 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim2.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 (28 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 NOTEs 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.025 0.013 198.8 74: (ns/day) (hour/ns) 74: Performance: 117.093 0.205 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 35 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.001 0.001 195.3 74: (ns/day) (hour/ns) 74: Performance: 1993.075 0.012 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim2.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 (22 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 NOTEs 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.712 to 0.744 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.028 0.014 199.1 74: (ns/day) (hour/ns) 74: Performance: 104.742 0.229 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.712 to 0.744 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 30 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.001 195.8 74: (ns/day) (hour/ns) 74: Performance: 1816.213 0.013 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim2.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 (24 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 NOTEs 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.026 0.013 199.1 74: (ns/day) (hour/ns) 74: Performance: 112.231 0.214 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 33 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.001 194.9 74: (ns/day) (hour/ns) 74: Performance: 1869.112 0.013 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim2.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 (23 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 27.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 74: NVE simulation: will use the initial temperature of 398.997 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 16 steps, 0.0 ps. 74: Generated 330891 of the 330891 non-bonded parameter combinations 74: 74: Generated 330891 of the 330891 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.035 0.018 199.0 74: (ns/day) (hour/ns) 74: Performance: 83.919 0.286 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 15 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.004 0.002 197.8 74: (ns/day) (hour/ns) 74: Performance: 709.828 0.034 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim2.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 (665 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 27.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 74: NVE simulation: will use the initial temperature of 398.997 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 16 steps, 0.0 ps. 74: Generated 330891 of the 330891 non-bonded parameter combinations 74: 74: Generated 330891 of the 330891 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.045 0.023 199.4 74: (ns/day) (hour/ns) 74: Performance: 64.794 0.370 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 31 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.001 0.001 195.6 74: (ns/day) (hour/ns) 74: Performance: 2043.315 0.012 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim2.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 (567 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 27.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.735 to 0.831 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 16 steps, 0.0 ps. 74: Generated 330891 of the 330891 non-bonded parameter combinations 74: 74: Generated 330891 of the 330891 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.738 nm, buffer size 0.038 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.041 0.020 199.3 74: (ns/day) (hour/ns) 74: Performance: 72.117 0.333 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.735 to 0.831 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 28 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.001 195.8 74: (ns/day) (hour/ns) 74: Performance: 1827.527 0.013 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim2.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 (603 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 27.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 16 steps, 0.0 ps. 74: Generated 330891 of the 330891 non-bonded parameter combinations 74: 74: Generated 330891 of the 330891 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.041 0.021 199.2 74: (ns/day) (hour/ns) 74: Performance: 71.329 0.336 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 26 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.001 195.8 74: (ns/day) (hour/ns) 74: Performance: 1815.143 0.013 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim2.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 (584 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: 74: NOTE 3 [file unknown]: 74: You are using constraints on all bonds, whereas the forcefield has been 74: parametrized only with constraints involving hydrogen atoms. We suggest 74: using constraints = h-bonds instead, this will also improve performance. 74: 74: Number of degrees of freedom in T-Coupling group System is 23.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 74: NVE simulation: will use the initial temperature of 456.887 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 74: There are 9 non-linear virtual site constructions. Their contribution to 74: the energy error is approximated. In most cases this does not affect the 74: error significantly. 74: 74: 74: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 6 NOTEs 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Update groups can not be used for this system because an incompatible virtual site type is used 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'Alanine dipeptide in vacuo' 74: 16 steps, 0.0 ps. 74: Generated 2145 of the 2145 non-bonded parameter combinations 74: 74: Generated 2145 of the 2145 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 74: 74: turning all bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 74: 74: Cleaning up constraints and constant bonded interactions with virtual sites 74: 74: Removed 18 Angles with virtual sites, 21 left 74: 74: Removed 10 Proper Dih.s with virtual sites, 44 left 74: 74: Converted 15 Constraints with virtual sites to connections, 7 left 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.030 0.015 198.8 74: (ns/day) (hour/ns) 74: Performance: 95.746 0.251 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Update groups can not be used for this system because an incompatible virtual site type is used 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 25 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.001 195.9 74: (ns/day) (hour/ns) 74: Performance: 1348.051 0.018 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim2.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 (38 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: 74: NOTE 3 [file unknown]: 74: You are using constraints on all bonds, whereas the forcefield has been 74: parametrized only with constraints involving hydrogen atoms. We suggest 74: using constraints = h-bonds instead, this will also improve performance. 74: 74: Number of degrees of freedom in T-Coupling group System is 23.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 74: NVE simulation: will use the initial temperature of 456.887 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 74: There are 9 non-linear virtual site constructions. Their contribution to 74: the energy error is approximated. In most cases this does not affect the 74: error significantly. 74: 74: 74: NOTE 6 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 6 NOTEs 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Update groups can not be used for this system because an incompatible virtual site type is used 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'Alanine dipeptide in vacuo' 74: 16 steps, 0.0 ps. 74: Generated 2145 of the 2145 non-bonded parameter combinations 74: 74: Generated 2145 of the 2145 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 74: 74: turning all bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 74: 74: Cleaning up constraints and constant bonded interactions with virtual sites 74: 74: Removed 18 Angles with virtual sites, 21 left 74: 74: Removed 10 Proper Dih.s with virtual sites, 44 left 74: 74: Converted 15 Constraints with virtual sites to connections, 7 left 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.030 0.015 198.8 74: (ns/day) (hour/ns) 74: Performance: 98.980 0.242 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Update groups can not be used for this system because an incompatible virtual site type is used 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 26 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.001 196.5 74: (ns/day) (hour/ns) 74: Performance: 1256.239 0.019 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim2.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 (38 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: 74: NOTE 3 [file unknown]: 74: You are using constraints on all bonds, whereas the forcefield has been 74: parametrized only with constraints involving hydrogen atoms. We suggest 74: using constraints = h-bonds instead, this will also improve performance. 74: 74: Number of degrees of freedom in T-Coupling group System is 23.00 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 74: There are 9 non-linear virtual site constructions. Their contribution to 74: the energy error is approximated. In most cases this does not affect the 74: error significantly. 74: 74: 74: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 5 NOTEs 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 80, rlist from 0.748 to 0.865 74: 74: Update groups can not be used for this system because an incompatible virtual site type is used 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'Alanine dipeptide in vacuo' 74: 16 steps, 0.0 ps. 74: Generated 2145 of the 2145 non-bonded parameter combinations 74: 74: Generated 2145 of the 2145 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 74: 74: turning all bonds into constraints... 74: 74: Cleaning up constraints and constant bonded interactions with virtual sites 74: 74: Removed 18 Angles with virtual sites, 21 left 74: 74: Removed 10 Proper Dih.s with virtual sites, 44 left 74: 74: Converted 15 Constraints with virtual sites to connections, 7 left 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.027 0.014 198.9 74: (ns/day) (hour/ns) 74: Performance: 107.659 0.223 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 80, rlist from 0.748 to 0.865 74: 74: Update groups can not be used for this system because an incompatible virtual site type is used 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 26 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.001 195.2 74: (ns/day) (hour/ns) 74: Performance: 1121.740 0.021 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim2.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 (166 ms) 74: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: 74: NOTE 3 [file unknown]: 74: You are using constraints on all bonds, whereas the forcefield has been 74: parametrized only with constraints involving hydrogen atoms. We suggest 74: using constraints = h-bonds instead, this will also improve performance. 74: 74: Number of degrees of freedom in T-Coupling group System is 23.00 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 74: There are 9 non-linear virtual site constructions. Their contribution to 74: the energy error is approximated. In most cases this does not affect the 74: error significantly. 74: 74: 74: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 5 NOTEs 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 25, rlist from 0.729 to 0.81 74: 74: Update groups can not be used for this system because an incompatible virtual site type is used 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'Alanine dipeptide in vacuo' 74: 16 steps, 0.0 ps. 74: Generated 2145 of the 2145 non-bonded parameter combinations 74: 74: Generated 2145 of the 2145 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 74: 74: turning all bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 74: 74: Cleaning up constraints and constant bonded interactions with virtual sites 74: 74: Removed 18 Angles with virtual sites, 21 left 74: 74: Removed 10 Proper Dih.s with virtual sites, 44 left 74: 74: Converted 15 Constraints with virtual sites to connections, 7 left 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.027 0.014 198.8 74: (ns/day) (hour/ns) 74: Performance: 108.223 0.222 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 25, rlist from 0.729 to 0.81 74: 74: Update groups can not be used for this system because an incompatible virtual site type is used 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 27 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.001 193.5 74: (ns/day) (hour/ns) 74: Performance: 1150.867 0.021 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim2.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 (85 ms) 74: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest (2850 ms total) 74: 74: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.029 0.015 198.6 74: (ns/day) (hour/ns) 74: Performance: 100.703 0.238 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 23 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.001 184.3 74: (ns/day) (hour/ns) 74: Performance: 1055.438 0.023 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim2.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 (38 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.033 0.017 198.7 74: (ns/day) (hour/ns) 74: Performance: 88.272 0.272 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 23 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.001 183.8 74: (ns/day) (hour/ns) 74: Performance: 1015.929 0.024 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim2.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 (39 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.027 0.014 198.4 74: (ns/day) (hour/ns) 74: Performance: 108.291 0.222 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 23 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.001 184.1 74: (ns/day) (hour/ns) 74: Performance: 1046.652 0.023 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim2.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 (36 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.025 0.013 198.5 74: (ns/day) (hour/ns) 74: Performance: 114.496 0.210 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 23 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.001 182.0 74: (ns/day) (hour/ns) 74: Performance: 1062.354 0.023 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim2.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 (36 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.039 0.020 198.9 74: (ns/day) (hour/ns) 74: Performance: 74.939 0.320 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 14 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.005 0.003 190.8 74: (ns/day) (hour/ns) 74: Performance: 556.010 0.043 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim2.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 (48 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.048 0.024 199.1 74: (ns/day) (hour/ns) 74: Performance: 60.419 0.397 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 14 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.005 0.003 188.2 74: (ns/day) (hour/ns) 74: Performance: 527.945 0.045 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim2.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 (56 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.039 0.020 198.8 74: (ns/day) (hour/ns) 74: Performance: 74.498 0.322 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 12 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.006 0.003 193.0 74: (ns/day) (hour/ns) 74: Performance: 436.426 0.055 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim2.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 (47 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.039 0.020 198.8 74: (ns/day) (hour/ns) 74: Performance: 74.542 0.322 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 25 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.002 183.0 74: (ns/day) (hour/ns) 74: Performance: 932.434 0.026 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim2.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 (44 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.031 0.016 198.5 74: (ns/day) (hour/ns) 74: Performance: 93.464 0.257 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 24 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.002 181.3 74: (ns/day) (hour/ns) 74: Performance: 946.473 0.025 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim2.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 (40 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.029 0.014 198.5 74: (ns/day) (hour/ns) 74: Performance: 102.252 0.235 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 23 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.001 183.9 74: (ns/day) (hour/ns) 74: Performance: 1050.221 0.023 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim2.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 (38 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.028 0.014 198.5 74: (ns/day) (hour/ns) 74: Performance: 104.685 0.229 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 25 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.001 183.5 74: (ns/day) (hour/ns) 74: Performance: 990.927 0.024 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim2.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 (37 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.038 0.019 199.3 74: (ns/day) (hour/ns) 74: Performance: 76.242 0.315 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 24 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.001 181.6 74: (ns/day) (hour/ns) 74: Performance: 1096.191 0.022 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim2.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 (42 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.045 0.022 199.3 74: (ns/day) (hour/ns) 74: Performance: 65.726 0.365 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 27 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.002 182.5 74: (ns/day) (hour/ns) 74: Performance: 920.453 0.026 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim2.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 (46 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.042 0.021 199.2 74: (ns/day) (hour/ns) 74: Performance: 68.890 0.348 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 25 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.002 181.6 74: (ns/day) (hour/ns) 74: Performance: 906.770 0.026 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim2.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 (45 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.037 0.019 199.3 74: (ns/day) (hour/ns) 74: Performance: 78.877 0.304 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 23 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.001 182.2 74: (ns/day) (hour/ns) 74: Performance: 996.054 0.024 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim2.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 (42 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.036 0.018 199.3 74: (ns/day) (hour/ns) 74: Performance: 82.245 0.292 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 25 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.001 181.3 74: (ns/day) (hour/ns) 74: Performance: 1045.941 0.023 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim2.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 (41 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.038 0.019 199.3 74: (ns/day) (hour/ns) 74: Performance: 77.237 0.311 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 21 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.002 182.5 74: (ns/day) (hour/ns) 74: Performance: 883.113 0.027 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim2.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 (42 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.036 0.018 199.3 74: (ns/day) (hour/ns) 74: Performance: 81.541 0.294 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 22 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.002 186.8 74: (ns/day) (hour/ns) 74: Performance: 911.465 0.026 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim2.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 (46 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.043 0.022 199.3 74: (ns/day) (hour/ns) 74: Performance: 67.973 0.353 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 12 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.005 0.003 191.1 74: (ns/day) (hour/ns) 74: Performance: 549.758 0.044 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim2.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 (48 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.049 0.025 193.7 74: (ns/day) (hour/ns) 74: Performance: 58.214 0.412 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 22 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.001 175.3 74: (ns/day) (hour/ns) 74: Performance: 982.708 0.024 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim2.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 (56 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.047 0.024 199.4 74: (ns/day) (hour/ns) 74: Performance: 62.045 0.387 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 21 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.002 179.8 74: (ns/day) (hour/ns) 74: Performance: 902.651 0.027 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim2.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 (55 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 74: NVE simulation: will use the initial temperature of 294.908 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 4 NOTEs 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.046 0.023 199.4 74: (ns/day) (hour/ns) 74: Performance: 63.373 0.379 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 12 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.004 0.002 176.8 74: (ns/day) (hour/ns) 74: Performance: 623.226 0.039 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim2.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 (52 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.043 0.022 199.0 74: (ns/day) (hour/ns) 74: Performance: 68.129 0.352 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 16 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 146.1 74: (ns/day) (hour/ns) 74: Performance: 871.988 0.028 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim2.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 (69 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.040 0.020 198.9 74: (ns/day) (hour/ns) 74: Performance: 73.247 0.328 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.007 0.004 189.7 74: (ns/day) (hour/ns) 74: Performance: 410.050 0.059 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim2.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 (75 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.186 0.093 199.8 74: (ns/day) (hour/ns) 74: Performance: 15.801 1.519 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 20 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.002 180.8 74: (ns/day) (hour/ns) 74: Performance: 873.100 0.027 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim2.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 (144 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.032 0.016 198.5 74: (ns/day) (hour/ns) 74: Performance: 90.149 0.266 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 18 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.002 181.1 74: (ns/day) (hour/ns) 74: Performance: 806.360 0.030 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim2.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 (64 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.046 0.023 198.0 74: (ns/day) (hour/ns) 74: Performance: 63.611 0.377 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 20 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.002 178.3 74: (ns/day) (hour/ns) 74: Performance: 915.529 0.026 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim2.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 (73 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.028 0.014 198.2 74: (ns/day) (hour/ns) 74: Performance: 102.414 0.234 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 20 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.002 178.2 74: (ns/day) (hour/ns) 74: Performance: 925.431 0.026 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim2.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 (64 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.047 0.024 199.0 74: (ns/day) (hour/ns) 74: Performance: 62.183 0.386 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.007 0.004 189.6 74: (ns/day) (hour/ns) 74: Performance: 396.409 0.061 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim2.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 (77 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.040 0.020 198.6 74: (ns/day) (hour/ns) 74: Performance: 72.083 0.333 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 10 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.006 0.003 188.8 74: (ns/day) (hour/ns) 74: Performance: 442.635 0.054 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim2.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 (78 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.042 0.021 198.9 74: (ns/day) (hour/ns) 74: Performance: 68.994 0.348 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.009 0.005 190.7 74: (ns/day) (hour/ns) 74: Performance: 320.580 0.075 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim2.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 (79 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.046 0.023 198.9 74: (ns/day) (hour/ns) 74: Performance: 63.012 0.381 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: NOTE: 19 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.002 178.6 74: (ns/day) (hour/ns) 74: Performance: 884.761 0.027 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim2.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 (82 ms) 74: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 79.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun '30 atom system in water' 74: 16 steps, 0.0 ps. 74: Generated 2485 of the 2485 non-bonded parameter combinations 74: 74: Generated 2485 of the 2485 1-4 parameter combinations 74: 74: Excluding 3 bonded neighbours molecule type 'nonanol' 74: 74: turning H bonds into constraints... 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: turning H bonds into constraints... 74: 74: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.038 0.019 198.7 74: (ns/day) (hour/ns) 74: Performance: 77.076 0.311 74: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 74: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 74: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 74: 74: Using 1 MPI process 74: Using 2 OpenMP threads 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.trr' 74: 74: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.013 0.007 192.6 74: (ns/day) (hour/ns) 74: Performance: 212.882 0.113 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim2.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 74: 74: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 (84 ms) 74: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest (1882 ms total) 74: 74: [----------] Global test environment tear-down 74: [==========] 46 tests from 3 test suites ran. (4902 ms total) 74: [ PASSED ] 46 tests. 74/94 Test #74: MdrunNonIntegratorTests ...................... Passed 5.25 sec test 75 Start 75: MdrunTpiTests 75: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/mdrun-tpi-test "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/MdrunTpiTests.xml" 75: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests 75: Test timeout computed to be: 600 75: [==========] Running 3 tests from 1 test suite. 75: [----------] Global test environment set-up. 75: [----------] 3 tests from Simple/TpiTest 75: [ RUN ] Simple/TpiTest.ReproducesOutput/0 75: Generating 1-4 interactions: fudge = 0.5 75: Number of degrees of freedom in T-Coupling group System is 1308.00 75: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 75: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 75: TPI is not implemented for GPUs. 75: 75: Using 1 MPI process 75: Using 1 OpenMP thread 75: 75: 75: NOTE: Thread affinity was not set. 75: Reading frames from gro file '216 water molecules', 648 atoms. 75: Reading frame 0 time 0.000 mu 6.291e+01 6.291e+01 75: Last frame 0 time 0.000 75: Generated 331705 of the 331705 non-bonded parameter combinations 75: 75: Generated 331705 of the 331705 1-4 parameter combinations 75: 75: Excluding 2 bonded neighbours molecule type 'SOL' 75: 75: Excluding 3 bonded neighbours molecule type 'methane' 75: Analysing residue names: 75: There are: 216 Water residues 75: There are: 1 Other residues 75: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 75: 75: This run will generate roughly 0 Mb of data 75: [ OK ] Simple/TpiTest.ReproducesOutput/0 (606 ms) 75: [ RUN ] Simple/TpiTest.ReproducesOutput/1 75: Generating 1-4 interactions: fudge = 0.5 75: Number of degrees of freedom in T-Coupling group System is 1308.00 75: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 75: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 75: TPI is not implemented for GPUs. 75: 75: Using 1 MPI process 75: Using 1 OpenMP thread 75: 75: 75: NOTE: Thread affinity was not set. 75: Reading frames from gro file '216 water molecules', 648 atoms. 75: Reading frame 0 time 0.000 mu 4.535e+01 4.535e+01 75: Last frame 0 time 0.000 75: Generated 331705 of the 331705 non-bonded parameter combinations 75: 75: Generated 331705 of the 331705 1-4 parameter combinations 75: 75: Excluding 2 bonded neighbours molecule type 'SOL' 75: 75: Excluding 3 bonded neighbours molecule type 'methane' 75: Analysing residue names: 75: There are: 216 Water residues 75: There are: 1 Other residues 75: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 75: 75: This run will generate roughly 0 Mb of data 75: [ OK ] Simple/TpiTest.ReproducesOutput/1 (591 ms) 75: [ RUN ] Simple/TpiTest.ReproducesOutput/2 75: Generating 1-4 interactions: fudge = 0.5 75: Number of degrees of freedom in T-Coupling group System is 1308.00 75: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 75: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 75: TPI is not implemented for GPUs. 75: 75: Using 1 MPI process 75: Using 1 OpenMP thread 75: 75: 75: NOTE: Thread affinity was not set. 75: Reading frames from gro file '216 water molecules', 648 atoms. 75: Reading frame 0 time 0.000 mu 6.203e+01 6.203e+01 75: Last frame 0 time 0.000 75: Generated 331705 of the 331705 non-bonded parameter combinations 75: 75: Generated 331705 of the 331705 1-4 parameter combinations 75: 75: Excluding 2 bonded neighbours molecule type 'SOL' 75: 75: Excluding 3 bonded neighbours molecule type 'methane' 75: Analysing residue names: 75: There are: 216 Water residues 75: There are: 1 Other residues 75: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 75: 75: This run will generate roughly 0 Mb of data 75: [ OK ] Simple/TpiTest.ReproducesOutput/2 (605 ms) 75: [----------] 3 tests from Simple/TpiTest (1803 ms total) 75: 75: [----------] Global test environment tear-down 75: [==========] 3 tests from 1 test suite ran. (1871 ms total) 75: [ PASSED ] 3 tests. 75/94 Test #75: MdrunTpiTests ................................ Passed 2.21 sec test 76 Start 76: MdrunMpiTests 76: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2025.0/build/mpi/bin/mdrun-mpi-test" "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/MdrunMpiTests.xml" 76: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests 76: Test timeout computed to be: 600 76: [==========] Running 16 tests from 2 test suites. 76: [----------] Global test environment set-up. 76: [----------] 4 tests from MimicTest 76: [ RUN ] MimicTest.OneQuantumMol 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 76: For a correct single-point energy evaluation with nsteps = 0, use 76: continuation = yes to avoid constraining the input coordinates. 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Setting the LD random seed to -45679617 76: 76: Generated 10 of the 10 non-bonded parameter combinations 76: 76: Generated 10 of the 10 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 76: 76: This run will generate roughly 0 Mb of data 76: Number of degrees of freedom in T-Coupling group rest is 21.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 76: NVE simulation with an initial temperature of zero: will use a Verlet 76: buffer of 10%. Check your energy drift! 76: 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 NOTEs 76: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 76: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI processes 76: Using 2 OpenMP threads per MPI process 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro' 76: 76: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 76: Reading frame 0 time 0.000 Last frame 0 time 0.000 76: 76: NOTE: 16 % of the run time was spent in domain decomposition, 76: 18 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: NOTE: 7 % of the run time was spent communicating energies, 76: you might want to increase some nst* mdp options 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.001 381.1 76: (ns/day) (hour/ns) 76: Performance: 139.434 0.172 76: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] MimicTest.OneQuantumMol (166 ms) 76: [ RUN ] MimicTest.AllQuantumMol 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 76: For a correct single-point energy evaluation with nsteps = 0, use 76: continuation = yes to avoid constraining the input coordinates. 76: 76: Setting the LD random seed to -614636649 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 10 of the 10 non-bonded parameter combinations 76: 76: Generated 10 of the 10 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 76: Number of degrees of freedom in T-Coupling group rest is 21.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 76: NVE simulation with an initial temperature of zero: will use a Verlet 76: buffer of 10%. Check your energy drift! 76: 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 NOTEs 76: 76: This run will generate roughly 0 Mb of data 76: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 76: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI processes 76: Using 2 OpenMP threads per MPI process 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro' 76: 76: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 76: Reading frame 0 time 0.000 Last frame 0 time 0.000 76: 76: NOTE: 20 % of the run time was spent in domain decomposition, 76: 14 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: NOTE: 8 % of the run time was spent communicating energies, 76: you might want to increase some nst* mdp options 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 100.1 76: (ns/day) (hour/ns) 76: Performance: 54.895 0.437 76: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] MimicTest.AllQuantumMol (12 ms) 76: [ RUN ] MimicTest.TwoQuantumMol 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 76: For a correct single-point energy evaluation with nsteps = 0, use 76: continuation = yes to avoid constraining the input coordinates. 76: 76: Setting the LD random seed to -878198850 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 10 of the 10 non-bonded parameter combinations 76: 76: Generated 10 of the 10 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro', all velocities are zero 76: Number of degrees of freedom in T-Coupling group rest is 21.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 76: NVE simulation with an initial temperature of zero: will use a Verlet 76: buffer of 10%. Check your energy drift! 76: 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 NOTEs 76: 76: This run will generate roughly 0 Mb of data 76: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 76: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI processes 76: Using 2 OpenMP threads per MPI process 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/4water.gro' 76: 76: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 76: Reading frame 0 time 0.000 Last frame 0 time 0.000 76: 76: NOTE: 24 % of the run time was spent in domain decomposition, 76: 15 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: NOTE: 6 % of the run time was spent communicating energies, 76: you might want to increase some nst* mdp options 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.001 0.000 380.0 76: (ns/day) (hour/ns) 76: Performance: 227.416 0.106 76: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] MimicTest.TwoQuantumMol (11 ms) 76: [ RUN ] MimicTest.BondCuts 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 76: For a correct single-point energy evaluation with nsteps = 0, use 76: continuation = yes to avoid constraining the input coordinates. 76: 76: Setting the LD random seed to -404103369 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 2211 of the 2211 non-bonded parameter combinations 76: 76: Generated 2211 of the 2211 1-4 parameter combinations 76: 76: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 76: Number of degrees of freedom in T-Coupling group rest is 66.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 76: NVE simulation: will use the initial temperature of 300.368 K for 76: determining the Verlet buffer size 76: 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 76: 76: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 NOTEs 76: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 76: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI processes 76: Using 2 OpenMP threads per MPI process 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/ala.gro' 76: 76: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 76: Reading frame 0 time 0.000 Last frame 0 time 0.000 76: 76: NOTE: 23 % of the run time was spent in domain decomposition, 76: 13 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.001 384.9 76: (ns/day) (hour/ns) 76: Performance: 145.333 0.165 76: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] MimicTest.BondCuts (23 ms) 76: [----------] 4 tests from MimicTest (212 ms total) 76: 76: [----------] 12 tests from DomainDecomposition/DomDecSpecialCasesTest 76: Setting the LD random seed to -536945449 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 3 of the 3 non-bonded parameter combinations 76: 76: Generated 3 of the 3 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 76: Number of degrees of freedom in T-Coupling group rest is 9.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 76: NVE simulation with an initial temperature of zero: will use a Verlet 76: buffer of 10%. Check your energy drift! 76: 76: 76: There was 1 NOTE 76: 76: This run will generate roughly 0 Mb of data 76: Setting the LD random seed to -27912965 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 3 of the 3 non-bonded parameter combinations 76: 76: Generated 3 of the 3 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 76: Number of degrees of freedom in T-Coupling group System is 9.00 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 1.017 nm, buffer size 0.017 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 1.005 nm, buffer size 0.005 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: Setting the LD random seed to -279642663 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 3 of the 3 non-bonded parameter combinations 76: 76: Generated 3 of the 3 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 76: Number of degrees of freedom in T-Coupling group rest is 9.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 76: NVE simulation with an initial temperature of zero: will use a Verlet 76: buffer of 10%. Check your energy drift! 76: 76: 76: The largest distance between excluded atoms is 0.164 nm between atom 2 and 3 76: Calculating fourier grid dimensions for X Y Z 76: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 76: 76: Estimate for the relative computational load of the PME mesh part: 1.00 76: 76: This run will generate roughly 0 Mb of data 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 76: The optimal PME mesh load for parallel simulations is below 0.5 76: and for highly parallel simulations between 0.25 and 0.33, 76: for higher performance, increase the cut-off and the PME grid spacing. 76: 76: 76: 76: There were 2 NOTEs 76: Setting the LD random seed to -553698321 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 3 of the 3 non-bonded parameter combinations 76: 76: Generated 3 of the 3 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 76: Number of degrees of freedom in T-Coupling group System is 9.00 76: 76: The largest distance between excluded atoms is 0.164 nm between atom 2 and 3 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: Calculating fourier grid dimensions for X Y Z 76: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 76: 76: Estimate for the relative computational load of the PME mesh part: 1.00 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 76: The optimal PME mesh load for parallel simulations is below 0.5 76: and for highly parallel simulations between 0.25 and 0.33, 76: for higher performance, increase the cut-off and the PME grid spacing. 76: 76: 76: 76: There was 1 NOTE 76: 76: This run will generate roughly 0 Mb of data 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme0 76: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 76: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_RF_No.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI processes 76: Using 2 OpenMP threads per MPI process 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc2' 76: 20 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: 76: Dynamic load balancing report: 76: DLB was off during the run due to low measured imbalance. 76: Average load imbalance: 2.0%. 76: The balanceable part of the MD step is 50%, load imbalance is computed from this. 76: Part of the total run time spent waiting due to load imbalance: 1.0%. 76: 76: 76: NOTE: 43 % of the run time was spent communicating energies, 76: you might want to increase some nst* mdp options 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.048 0.012 396.1 76: (ns/day) (hour/ns) 76: Performance: 149.948 0.160 76: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme0 (16 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 (0 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 76: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 76: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_RF_TemperatureAndPressure.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 76: Changing nstlist from 10 to 50, rlist from 1.005 to 1.136 76: 76: Using 2 MPI processes 76: Using 2 OpenMP threads per MPI process 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc2' 76: 20 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: NOTE: 42 % of the run time was spent communicating energies, 76: you might want to increase some nst* mdp options 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.042 0.011 394.0 76: (ns/day) (hour/ns) 76: Performance: 172.193 0.139 76: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 (16 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 (0 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme0 76: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 76: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_No.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI processes 76: Using 2 OpenMP threads per MPI process 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc2' 76: 20 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: 76: Dynamic load balancing report: 76: DLB was off during the run due to low measured imbalance. 76: Average load imbalance: 19.3%. 76: The balanceable part of the MD step is 7%, load imbalance is computed from this. 76: Part of the total run time spent waiting due to load imbalance: 1.3%. 76: 76: 76: NOTE: 18 % of the run time was spent communicating energies, 76: you might want to increase some nst* mdp options 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.103 0.026 397.7 76: (ns/day) (hour/ns) 76: Performance: 70.139 0.342 76: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme0 (172 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme1 76: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 76: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_No.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI processes 76: Using 2 OpenMP threads per MPI process 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc2' 76: 20 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.087 0.022 396.8 76: (ns/day) (hour/ns) 76: Performance: 82.759 0.290 76: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme1 (128 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 76: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 76: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_TemperatureAndPressure.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 76: Changing nstlist from 10 to 100, rlist from 1 to 1 76: 76: Using 2 MPI processes 76: Using 2 OpenMP threads per MPI process 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc2' 76: 20 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: NOTE: 16 % of the run time was spent communicating energies, 76: you might want to increase some nst* mdp options 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.103 0.026 397.5 76: (ns/day) (hour/ns) 76: Performance: 70.055 0.343 76: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 (51 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 76: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 76: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_TemperatureAndPressure.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 76: Changing nstlist from 10 to 100, rlist from 1 to 1 76: 76: Using 2 MPI processes 76: Using 2 OpenMP threads per MPI process 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc2' 76: 20 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.081 0.021 395.7 76: (ns/day) (hour/ns) 76: Performance: 88.146 0.272 76: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 (46 ms) 76: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 76: [----------] 12 tests from DomainDecomposition/DomDecSpecialCasesTest (432 ms total) 76: 76: [----------] Global test environment tear-down 76: [==========] 16 tests from 2 test suites ran. (831 ms total) 76: [ PASSED ] 10 tests. 76: [ SKIPPED ] 6 tests, listed below: 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 76: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 76/94 Test #76: MdrunMpiTests ................................ Passed 1.29 sec test 77 Start 77: MdrunMultiSimTests 77: Test command: /usr/bin/mpiexec "-n" "4" "/build/reproducible-path/gromacs-2025.0/build/mpi/bin/mdrun-multisim-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/MdrunMultiSimTests.xml" 77: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests 77: Test timeout computed to be: 600 77: [==========] Running 6 tests from 2 test suites. 77: [----------] Global test environment set-up. 77: [----------] 4 tests from InNvt/MultiSimTest 77: [ RUN ] InNvt/MultiSimTest.ExitsNormally/0 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormally_0_input.mdp]: 77: You have set rlist larger than the interaction cut-off, but you also have 77: verlet-buffer-tolerance > 0. Will set rlist using 77: verlet-buffer-tolerance. 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 9.00 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormally_0_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 2 NOTEs 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTest_ExitsNormally_0_input.mdp]: 77: You have set rlist larger than the interaction cut-off, but you also have 77: verlet-buffer-tolerance > 0. Will set rlist using 77: verlet-buffer-tolerance. 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 9.00 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTest_ExitsNormally_0_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 2 NOTEs 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormally_0_input.mdp]: 77: You have set rlist larger than the interaction cut-off, but you also have 77: verlet-buffer-tolerance > 0. Will set rlist using 77: verlet-buffer-tolerance. 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 9.00 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormally_0_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 2 NOTEs 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTest_ExitsNormally_0_input.mdp]: 77: You have set rlist larger than the interaction cut-off, but you also have 77: verlet-buffer-tolerance > 0. Will set rlist using 77: verlet-buffer-tolerance. 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 9.00 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTest_ExitsNormally_0_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 2 NOTEs 77: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 77: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormally_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 77: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 77: 77: This is simulation 0 out of 4 running as a composite GROMACS 77: multi-simulation job. Setup for this simulation: 77: 77: Using 1 MPI process 77: Using 1 OpenMP thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTest_ExitsNormally_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 77: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 77: 77: This is simulation 2 out of 4 running as a composite GROMACS 77: multi-simulation job. Setup for this simulation: 77: 77: Using 1 MPI process 77: Using 1 OpenMP thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormally_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 77: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 77: 77: This is simulation 1 out of 4 running as a composite GROMACS 77: multi-simulation job. Setup for this simulation: 77: 77: Using 1 MPI process 77: Using 1 OpenMP thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTest_ExitsNormally_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 77: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 77: 77: This is simulation 3 out of 4 running as a composite GROMACS 77: multi-simulation job. Setup for this simulation: 77: 77: Using 1 MPI process 77: Using 1 OpenMP thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 2 steps, 0.0 ps. 77: starting mdrun 'spc2' 77: 2 steps, 0.0 ps. 77: starting mdrun 'spc2' 77: 2 steps, 0.0 ps. 77: starting mdrun 'spc2' 77: 2 steps, 0.0 ps. 77: Setting the LD random seed to 233824190 77: 77: Generated 3 of the 3 non-bonded parameter combinations 77: 77: Generated 3 of the 3 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Setting gen_seed to -131108 77: 77: Velocities were taken from a Maxwell distribution at 298 K 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: Setting the LD random seed to 1047756543 77: 77: Generated 3 of the 3 non-bonded parameter combinations 77: 77: Generated 3 of the 3 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Setting gen_seed to -570557605 77: 77: Velocities were taken from a Maxwell distribution at 278 K 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: Setting the LD random seed to -218366082 77: 77: Generated 3 of the 3 non-bonded parameter combinations 77: 77: Generated 3 of the 3 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Setting gen_seed to -2164243 77: 77: Velocities were taken from a Maxwell distribution at 288 K 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: Setting the LD random seed to -1681409 77: 77: Generated 3 of the 3 non-bonded parameter combinations 77: 77: Generated 3 of the 3 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Setting gen_seed to -306255877 77: 77: Velocities were taken from a Maxwell distribution at 268 K 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Writing final coordinates. 77: 77: Writing final coordinates. 77: 77: Writing final coordinates. 77: [ OK ] InNvt/MultiSimTest.ExitsNormally/0 (23 ms) 77: [ RUN ] InNvt/MultiSimTest.ExitsNormally/1 77: Setting the LD random seed to 1809573749 77: 77: Generated 3 of the 3 non-bonded parameter combinations 77: 77: Generated 3 of the 3 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Setting gen_seed to -706478202 77: 77: Velocities were taken from a Maxwell distribution at 298 K 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormally_1_input.mdp]: 77: You have set rlist larger than the interaction cut-off, but you also have 77: verlet-buffer-tolerance > 0. Will set rlist using 77: verlet-buffer-tolerance. 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 9.00 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormally_1_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 2 NOTEs 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormally_1_input.mdp]: 77: You have set rlist larger than the interaction cut-off, but you also have 77: verlet-buffer-tolerance > 0. Will set rlist using 77: verlet-buffer-tolerance. 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 9.00 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormally_1_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 2 NOTEs 77: Setting the LD random seed to -275776114 77: 77: Generated 3 of the 3 non-bonded parameter combinations 77: 77: Generated 3 of the 3 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Setting gen_seed to -545783835 77: 77: Velocities were taken from a Maxwell distribution at 278 K 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 77: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormally_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 77: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 77: 77: This is simulation 0 out of 2 running as a composite GROMACS 77: multi-simulation job. Setup for this simulation: 77: 77: Using 2 MPI processes 77: Using 1 OpenMP thread per MPI process 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormally_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 77: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 77: 77: This is simulation 1 out of 2 running as a composite GROMACS 77: multi-simulation job. Setup for this simulation: 77: 77: Using 2 MPI processes 77: Using 1 OpenMP thread per MPI process 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 2 steps, 0.0 ps. 77: starting mdrun 'spc2' 77: 2 steps, 0.0 ps. 77: 77: Writing final coordinates. 77: 77: NOTE: 44 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Writing final coordinates. 77: 77: NOTE: 49 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: [ OK ] InNvt/MultiSimTest.ExitsNormally/1 (22 ms) 77: [ RUN ] InNvt/MultiSimTest.ExitsNormallyWithDifferentNumbersOfStepsPerSimulation/0 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: 77: You have set rlist larger than the interaction cut-off, but you also have 77: verlet-buffer-tolerance > 0. Will set rlist using 77: verlet-buffer-tolerance. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: 77: For a correct single-point energy evaluation with nsteps = 0, use 77: continuation = yes to avoid constraining the input coordinates. 77: 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: 77: You have set rlist larger than the interaction cut-off, but you also have 77: verlet-buffer-tolerance > 0. Will set rlist using 77: verlet-buffer-tolerance. 77: 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: 77: You have set rlist larger than the interaction cut-off, but you also have 77: verlet-buffer-tolerance > 0. Will set rlist using 77: verlet-buffer-tolerance. 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Generating 1-4 interactions: fudge = 0.5 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: 77: You have set rlist larger than the interaction cut-off, but you also have 77: verlet-buffer-tolerance > 0. Will set rlist using 77: verlet-buffer-tolerance. 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 9.00 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 9.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 NOTEs 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 2 NOTEs 77: Number of degrees of freedom in T-Coupling group System is 9.00 77: Number of degrees of freedom in T-Coupling group System is 9.00 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 2 NOTEs 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 2 NOTEs 77: Setting the LD random seed to -1921132769 77: Setting the LD random seed to -77693489 77: 77: Generated 3 of the 3 non-bonded parameter combinations 77: 77: Generated 3 of the 3 1-4 parameter combinations 77: Setting the LD random seed to -782500069 77: 77: Generated 3 of the 3 non-bonded parameter combinations 77: 77: Generated 3 of the 3 1-4 parameter combinations 77: 77: Generated 3 of the 3 non-bonded parameter combinations 77: 77: Generated 3 of the 3 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Setting gen_seed to -67207434 77: 77: Velocities were taken from a Maxwell distribution at 298 K 77: Setting the LD random seed to 1906376187 77: 77: Generated 3 of the 3 non-bonded parameter combinations 77: 77: Generated 3 of the 3 1-4 parameter combinations 77: 77: Setting gen_seed to -1140984327 77: 77: Velocities were taken from a Maxwell distribution at 278 K 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Setting gen_seed to -275842563 77: 77: Velocities were taken from a Maxwell distribution at 268 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Setting gen_seed to -71321603 77: 77: Velocities were taken from a Maxwell distribution at 288 K 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: This run will generate roughly 0 Mb of data 77: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 77: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 77: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 77: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 77: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 77: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 77: 77: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 77: 77: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 77: 77: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 77: 77: This is simulation 0 out of 4 running as a composite GROMACS 77: multi-simulation job. Setup for this simulation: 77: 77: Using 1 MPI process 77: This is simulation 2 out of 4 running as a composite GROMACS 77: multi-simulation job. Setup for this simulation: 77: 77: Using 1 MPI process 77: This is simulation 3 out of 4 running as a composite GROMACS 77: multi-simulation job. Setup for this simulation: 77: 77: Using 1 MPI process 77: This is simulation 1 out of 4 running as a composite GROMACS 77: multi-simulation job. Setup for this simulation: 77: 77: Using 1 MPI process 77: Using 1 OpenMP thread 77: Using 1 OpenMP thread 77: 77: Using 1 OpenMP thread 77: 77: Using 1 OpenMP thread 77: 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 0 steps, 0.0 ps. 77: starting mdrun 'spc2' 77: 1 steps, 0.0 ps. 77: starting mdrun 'spc2' 77: 2 steps, 0.0 ps. 77: starting mdrun 'spc2' 77: 3 steps, 0.0 ps. 77: 77: Note: The number of steps is not consistent across multi simulations, 77: but we are proceeding anyway! 77: 77: Note: The number of steps is not consistent across multi simulations, 77: but we are proceeding anyway! 77: 77: Note: The number of steps is not consistent across multi simulations, 77: but we are proceeding anyway! 77: 77: Note: The number of steps is not consistent across multi simulations, 77: but we are proceeding anyway! 77: 77: NOTE: 10 % of the run time was spent in pair search, 77: you might want to increase nstlist (this has no effect on accuracy) 77: 77: Writing final coordinates. 77: 77: Writing final coordinates. 77: 77: Writing final coordinates. 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_1_input.mdp]: 77: You have set rlist larger than the interaction cut-off, but you also have 77: verlet-buffer-tolerance > 0. Will set rlist using 77: verlet-buffer-tolerance. 77: 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_1_input.mdp]: 77: You have set rlist larger than the interaction cut-off, but you also have 77: verlet-buffer-tolerance > 0. Will set rlist using 77: verlet-buffer-tolerance. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_1_input.mdp]: 77: For a correct single-point energy evaluation with nsteps = 0, use 77: continuation = yes to avoid constraining the input coordinates. 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Generating 1-4 interactions: fudge = 0.5 77: [ OK ] InNvt/MultiSimTest.ExitsNormallyWithDifferentNumbersOfStepsPerSimulation/0 (12 ms) 77: [ RUN ] InNvt/MultiSimTest.ExitsNormallyWithDifferentNumbersOfStepsPerSimulation/1 77: Setting the LD random seed to 1979645370 77: Setting the LD random seed to -436388003 77: 77: Generated 3 of the 3 non-bonded parameter combinations 77: 77: Generated 3 of the 3 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Generated 3 of the 3 non-bonded parameter combinations 77: 77: Generated 3 of the 3 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Setting gen_seed to -16933033 77: 77: Velocities were taken from a Maxwell distribution at 298 K 77: Number of degrees of freedom in T-Coupling group System is 9.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_1_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 NOTEs 77: Number of degrees of freedom in T-Coupling group System is 9.00 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_1_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 2 NOTEs 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 77: 77: Setting gen_seed to 2040491503 77: 77: Velocities were taken from a Maxwell distribution at 278 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 77: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 77: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 77: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 77: 77: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 77: 77: This is simulation 0 out of 2 running as a composite GROMACS 77: multi-simulation job. Setup for this simulation: 77: 77: Using 2 MPI processes 77: Using 1 OpenMP thread per MPI process 77: 77: This is simulation 1 out of 2 running as a composite GROMACS 77: multi-simulation job. Setup for this simulation: 77: 77: Using 2 MPI processes 77: Using 1 OpenMP thread per MPI process 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 0 steps, 0.0 ps. 77: starting mdrun 'spc2' 77: 1 steps, 0.0 ps. 77: 77: Note: The number of steps is not consistent across multi simulations, 77: but we are proceeding anyway! 77: 77: Note: The number of steps is not consistent across multi simulations, 77: but we are proceeding anyway! 77: 77: NOTE: 29 % of the run time was spent in domain decomposition, 77: 11 % of the run time was spent in pair search, 77: you might want to increase nstlist (this has no effect on accuracy) 77: 77: Writing final coordinates. 77: 77: NOTE: 48 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: [ OK ] InNvt/MultiSimTest.ExitsNormallyWithDifferentNumbersOfStepsPerSimulation/1 (11 ms) 77: [----------] 4 tests from InNvt/MultiSimTest (100 ms total) 77: 77: [----------] 2 tests from InNvt/MultiSimTerminationTest 77: [ RUN ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 77: You have set rlist larger than the interaction cut-off, but you also have 77: verlet-buffer-tolerance > 0. Will set rlist using 77: verlet-buffer-tolerance. 77: 77: Setting the LD random seed to -536936538 77: Generating 1-4 interactions: fudge = 0.5 77: 77: Generated 3 of the 3 non-bonded parameter combinations 77: 77: Generated 3 of the 3 1-4 parameter combinations 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 77: You have set rlist larger than the interaction cut-off, but you also have 77: verlet-buffer-tolerance > 0. Will set rlist using 77: verlet-buffer-tolerance. 77: 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 77: You have set rlist larger than the interaction cut-off, but you also have 77: verlet-buffer-tolerance > 0. Will set rlist using 77: verlet-buffer-tolerance. 77: 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: Setting the LD random seed to -1145045001 77: Setting the LD random seed to -271123458 77: 77: Setting gen_seed to 1050312391 77: 77: Velocities were taken from a Maxwell distribution at 288 K 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 9.00 77: 77: Generated 3 of the 3 non-bonded parameter combinations 77: 77: Generated 3 of the 3 1-4 parameter combinations 77: Generating 1-4 interactions: fudge = 0.5 77: 77: Generated 3 of the 3 non-bonded parameter combinations 77: 77: Generated 3 of the 3 1-4 parameter combinations 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: This run will generate roughly 0 Mb of data 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 2 NOTEs 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 77: You have set rlist larger than the interaction cut-off, but you also have 77: verlet-buffer-tolerance > 0. Will set rlist using 77: verlet-buffer-tolerance. 77: 77: 77: Setting gen_seed to -286802690 77: 77: Velocities were taken from a Maxwell distribution at 298 K 77: Setting the LD random seed to -279054610 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: Number of degrees of freedom in T-Coupling group System is 9.00 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 2 NOTEs 77: 77: Setting gen_seed to -471863169 77: 77: 77: This run will generate roughly 0 Mb of data 77: Velocities were taken from a Maxwell distribution at 268 K 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 9.00 77: 77: Generated 3 of the 3 non-bonded parameter combinations 77: 77: Generated 3 of the 3 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Setting gen_seed to -4199681 77: 77: Velocities were taken from a Maxwell distribution at 278 K 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 2 NOTEs 77: Number of degrees of freedom in T-Coupling group System is 9.00 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 2 NOTEs 77: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 77: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 77: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 77: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 77: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 77: Changing nstlist from 10 to 1, rlist from 0.736 to 0.7 77: 77: Changing nstlist from 10 to 1, rlist from 0.736 to 0.7 77: 77: Changing nstlist from 10 to 1, rlist from 0.736 to 0.7 77: 77: Changing nstlist from 10 to 1, rlist from 0.736 to 0.7 77: 77: This is simulation 1 out of 4 running as a composite GROMACS 77: multi-simulation job. Setup for this simulation: 77: 77: Using 1 MPI process 77: This is simulation 0 out of 4 running as a composite GROMACS 77: multi-simulation job. Setup for this simulation: 77: 77: Using 1 MPI process 77: Using 1 OpenMP thread 77: 77: This is simulation 3 out of 4 running as a composite GROMACS 77: multi-simulation job. Setup for this simulation: 77: 77: Using 1 MPI process 77: Using 1 OpenMP thread 77: 77: This is simulation 2 out of 4 running as a composite GROMACS 77: multi-simulation job. Setup for this simulation: 77: 77: Using 1 MPI process 77: Using 1 OpenMP thread 77: 77: Using 1 OpenMP thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 100 steps, 0.1 ps. 77: starting mdrun 'spc2' 77: 100 steps, 0.1 ps. 77: starting mdrun 'spc2' 77: 100 steps, 0.1 ps. 77: starting mdrun 'spc2' 77: 100 steps, 0.1 ps. 77: 77: Step 1: Run time exceeded 0.000 hours, will terminate the run within 2 steps 77: 77: Step 1: Run time exceeded 0.000 hours, will terminate the run within 2 steps 77: 77: Step 1: Run time exceeded 0.000 hours, will terminate the run within 2 steps 77: 77: Step 1: Run time exceeded 0.000 hours, will terminate the run within 2 steps 77: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 77: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 77: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 77: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 77: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 77: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 77: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 77: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 77: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 77: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 77: 77: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 77: 77: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 77: 77: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 77: 77: 77: This is simulation 1 out of 4 running as a composite GROMACS 77: multi-simulation job. Setup for this simulation: 77: 77: Using 1 MPI process 77: 77: This is simulation 2 out of 4 running as a composite GROMACS 77: multi-simulation job. Setup for this simulation: 77: 77: Using 1 MPI process 77: 77: This is simulation 0 out of 4 running as a composite GROMACS 77: multi-simulation job. Setup for this simulation: 77: 77: Using 1 MPI process 77: Using 1 OpenMP thread 77: 77: 77: This is simulation 3 out of 4 running as a composite GROMACS 77: multi-simulation job. Setup for this simulation: 77: 77: Using 1 MPI process 77: Using 1 OpenMP thread 77: 77: Using 1 OpenMP thread 77: 77: Using 1 OpenMP thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 77: starting mdrun 'spc2' 77: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 77: 77: Writing final coordinates. 77: 77: Writing final coordinates. 77: 77: Writing final coordinates. 77: 77: Writing final coordinates. 77: [ OK ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 (46 ms) 77: [ RUN ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/1 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_1_input.mdp]: 77: You have set rlist larger than the interaction cut-off, but you also have 77: verlet-buffer-tolerance > 0. Will set rlist using 77: verlet-buffer-tolerance. 77: 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_1_input.mdp]: 77: You have set rlist larger than the interaction cut-off, but you also have 77: verlet-buffer-tolerance > 0. Will set rlist using 77: verlet-buffer-tolerance. 77: 77: Setting the LD random seed to -168118613 77: Setting the LD random seed to -1820329985 77: Generating 1-4 interactions: fudge = 0.5 77: 77: Generated 3 of the 3 non-bonded parameter combinations 77: 77: Generated 3 of the 3 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: Generating 1-4 interactions: fudge = 0.5 77: 77: Generated 3 of the 3 non-bonded parameter combinations 77: 77: Generated 3 of the 3 1-4 parameter combinations 77: 77: Setting gen_seed to -1208762691 77: 77: Velocities were taken from a Maxwell distribution at 298 K 77: Number of degrees of freedom in T-Coupling group System is 9.00 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_1_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 2 NOTEs 77: 77: Setting gen_seed to 1877977534 77: 77: Velocities were taken from a Maxwell distribution at 278 K 77: Number of degrees of freedom in T-Coupling group System is 9.00 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_1_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 2 NOTEs 77: 77: This run will generate roughly 0 Mb of data 77: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 77: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 77: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 77: Changing nstlist from 10 to 1, rlist from 0.736 to 0.7 77: 77: Changing nstlist from 10 to 1, rlist from 0.736 to 0.7 77: 77: This is simulation 0 out of 2 running as a composite GROMACS 77: multi-simulation job. Setup for this simulation: 77: 77: Using 2 MPI processes 77: Using 1 OpenMP thread per MPI process 77: 77: This is simulation 1 out of 2 running as a composite GROMACS 77: multi-simulation job. Setup for this simulation: 77: 77: Using 2 MPI processes 77: Using 1 OpenMP thread per MPI process 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 100 steps, 0.1 ps. 77: starting mdrun 'spc2' 77: 100 steps, 0.1 ps. 77: 77: Step 0: Run time exceeded 0.000 hours, will terminate the run within 2 steps 77: 77: Step 1: Run time exceeded 0.000 hours, will terminate the run within 2 steps 77: 77: 77: Dynamic load balancing report: 77: DLB was off during the run due to low measured imbalance. 77: Average load imbalance: 1.0%. 77: The balanceable part of the MD step is 5%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 0.0%. 77: 77: 77: NOTE: 41 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: 77: Dynamic load balancing report: 77: DLB was off during the run due to low measured imbalance. 77: Average load imbalance: 14.3%. 77: The balanceable part of the MD step is 5%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 0.7%. 77: 77: 77: NOTE: 45 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 77: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 77: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 77: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 77: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 77: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 77: 77: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 77: 77: 77: This is simulation 0 out of 2 running as a composite GROMACS 77: multi-simulation job. Setup for this simulation: 77: 77: Using 2 MPI processes 77: Using 1 OpenMP thread per MPI process 77: 77: 77: This is simulation 1 out of 2 running as a composite GROMACS 77: multi-simulation job. Setup for this simulation: 77: 77: Using 2 MPI processes 77: Using 1 OpenMP thread per MPI process 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 3 steps, 0.0 ps (continuing from step 1, 0.0 ps). 77: starting mdrun 'spc2' 77: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 77: 77: Note: The initial step is not consistent across multi simulations, 77: but we are proceeding anyway! 77: 77: Note: The initial step is not consistent across multi simulations, 77: but we are proceeding anyway! 77: 77: Writing final coordinates. 77: 77: Writing final coordinates. 77: 77: NOTE: 45 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: NOTE: 46 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: [ OK ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/1 (37 ms) 77: [----------] 2 tests from InNvt/MultiSimTerminationTest (83 ms total) 77: 77: [----------] Global test environment tear-down 77: [==========] 6 tests from 2 test suites ran. (395 ms total) 77: [ PASSED ] 6 tests. 77/94 Test #77: MdrunMultiSimTests ........................... Passed 0.88 sec test 78 Start 78: MdrunMultiSimReplexTests 78: Test command: /usr/bin/mpiexec "-n" "4" "/build/reproducible-path/gromacs-2025.0/build/mpi/bin/mdrun-multisim-replex-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/MdrunMultiSimReplexTests.xml" 78: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests 78: Test timeout computed to be: 600 78: [==========] Running 5 tests from 2 test suites. 78: [----------] Global test environment set-up. 78: [----------] 4 tests from WithDifferentControlVariables/ReplicaExchangeEnsembleTest 78: [ RUN ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/0 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0_input.mdp]: 78: You have set rlist larger than the interaction cut-off, but you also have 78: verlet-buffer-tolerance > 0. Will set rlist using 78: verlet-buffer-tolerance. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0_input.mdp]: 78: You have set rlist larger than the interaction cut-off, but you also have 78: verlet-buffer-tolerance > 0. Will set rlist using 78: verlet-buffer-tolerance. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0_input.mdp]: 78: You have set rlist larger than the interaction cut-off, but you also have 78: verlet-buffer-tolerance > 0. Will set rlist using 78: verlet-buffer-tolerance. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Setting the LD random seed to -1363454211 78: 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Setting gen_seed to -412747337 78: 78: Velocities were taken from a Maxwell distribution at 288 K 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Setting the LD random seed to -16782357 78: 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Setting gen_seed to 931381183 78: 78: Velocities were taken from a Maxwell distribution at 278 K 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Setting the LD random seed to -1210589454 78: 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Setting gen_seed to -1091184641 78: 78: Velocities were taken from a Maxwell distribution at 298 K 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Setting the LD random seed to -287316641 78: 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Setting gen_seed to -18882593 78: 78: Velocities were taken from a Maxwell distribution at 268 K 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0_input.mdp]: 78: You have set rlist larger than the interaction cut-off, but you also have 78: verlet-buffer-tolerance > 0. Will set rlist using 78: verlet-buffer-tolerance. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 78: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 78: 78: This is simulation 3 out of 4 running as a composite GROMACS 78: multi-simulation job. Setup for this simulation: 78: 78: Using 1 MPI process 78: Using 1 OpenMP thread 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 78: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 78: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 78: 78: This is simulation 0 out of 4 running as a composite GROMACS 78: multi-simulation job. Setup for this simulation: 78: 78: Using 1 MPI process 78: Using 1 OpenMP thread 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 78: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 78: 78: This is simulation 1 out of 4 running as a composite GROMACS 78: multi-simulation job. Setup for this simulation: 78: 78: Using 1 MPI process 78: Using 1 OpenMP thread 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 78: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 78: 78: This is simulation 2 out of 4 running as a composite GROMACS 78: multi-simulation job. Setup for this simulation: 78: 78: Using 1 MPI process 78: Using 1 OpenMP thread 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 2 steps, 0.0 ps. 78: starting mdrun 'spc2' 78: 2 steps, 0.0 ps. 78: starting mdrun 'spc2' 78: 2 steps, 0.0 ps. 78: starting mdrun 'spc2' 78: 2 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Writing final coordinates. 78: 78: Writing final coordinates. 78: 78: Writing final coordinates. 78: [ OK ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/0 (25 ms) 78: [ RUN ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/1 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 78: You have set rlist larger than the interaction cut-off, but you also have 78: verlet-buffer-tolerance > 0. Will set rlist using 78: verlet-buffer-tolerance. 78: 78: 78: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 78: The Berendsen barostat does not generate any strictly correct ensemble, 78: and should not be used for new production simulations (in our opinion). 78: We recommend using the C-rescale barostat instead. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: 78: There was 1 WARNING 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 78: You have set rlist larger than the interaction cut-off, but you also have 78: verlet-buffer-tolerance > 0. Will set rlist using 78: verlet-buffer-tolerance. 78: 78: 78: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 78: The Berendsen barostat does not generate any strictly correct ensemble, 78: and should not be used for new production simulations (in our opinion). 78: We recommend using the C-rescale barostat instead. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: 78: There was 1 WARNING 78: Setting the LD random seed to -536903687 78: 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Setting gen_seed to -4993 78: 78: Velocities were taken from a Maxwell distribution at 288 K 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Setting the LD random seed to -1141117790 78: 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Setting gen_seed to -1544325681 78: 78: Velocities were taken from a Maxwell distribution at 278 K 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Setting the LD random seed to -415236273 78: 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Setting gen_seed to -1212425 78: 78: Velocities were taken from a Maxwell distribution at 298 K 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Setting the LD random seed to -1078988052 78: 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Setting gen_seed to 2147446746 78: 78: Velocities were taken from a Maxwell distribution at 268 K 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 78: You have set rlist larger than the interaction cut-off, but you also have 78: verlet-buffer-tolerance > 0. Will set rlist using 78: verlet-buffer-tolerance. 78: 78: 78: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 78: The Berendsen barostat does not generate any strictly correct ensemble, 78: and should not be used for new production simulations (in our opinion). 78: We recommend using the C-rescale barostat instead. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: 78: There was 1 WARNING 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 78: You have set rlist larger than the interaction cut-off, but you also have 78: verlet-buffer-tolerance > 0. Will set rlist using 78: verlet-buffer-tolerance. 78: 78: 78: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 78: The Berendsen barostat does not generate any strictly correct ensemble, 78: and should not be used for new production simulations (in our opinion). 78: We recommend using the C-rescale barostat instead. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: 78: There was 1 WARNING 78: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 78: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 78: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 78: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 78: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 78: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 78: 78: This is simulation 1 out of 4 running as a composite GROMACS 78: multi-simulation job. Setup for this simulation: 78: 78: Using 1 MPI process 78: Using 1 OpenMP thread 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 2 steps, 0.0 ps. 78: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 78: 78: This is simulation 3 out of 4 running as a composite GROMACS 78: multi-simulation job. Setup for this simulation: 78: 78: Using 1 MPI process 78: Using 1 OpenMP thread 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 2 steps, 0.0 ps. 78: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 78: 78: This is simulation 2 out of 4 running as a composite GROMACS 78: multi-simulation job. Setup for this simulation: 78: 78: Using 1 MPI process 78: Using 1 OpenMP thread 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 2 steps, 0.0 ps. 78: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 78: 78: This is simulation 0 out of 4 running as a composite GROMACS 78: multi-simulation job. Setup for this simulation: 78: 78: Using 1 MPI process 78: Using 1 OpenMP thread 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 2 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Writing final coordinates. 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_2_input.mdp]: 78: You have set rlist larger than the interaction cut-off, but you also have 78: verlet-buffer-tolerance > 0. Will set rlist using 78: verlet-buffer-tolerance. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: 78: Writing final coordinates. 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_2_input.mdp]: 78: You have set rlist larger than the interaction cut-off, but you also have 78: verlet-buffer-tolerance > 0. Will set rlist using 78: verlet-buffer-tolerance. 78: 78: 78: Writing final coordinates. 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_2_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 78: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 78: 78: [ OK ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/1 (21 ms) 78: [ RUN ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/2 78: Setting the LD random seed to -1183199369 78: Setting the LD random seed to -1074021005 78: 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Setting gen_seed to -178790984 78: 78: Velocities were taken from a Maxwell distribution at 278 K 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_2_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 78: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 78: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 78: 78: This is simulation 1 out of 2 running as a composite GROMACS 78: multi-simulation job. Setup for this simulation: 78: 78: Using 2 MPI processes 78: Using 1 OpenMP thread per MPI process 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 2 steps, 0.0 ps. 78: This is simulation 0 out of 2 running as a composite GROMACS 78: multi-simulation job. Setup for this simulation: 78: 78: Using 2 MPI processes 78: Using 1 OpenMP thread per MPI process 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 2 steps, 0.0 ps. 78: 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Setting gen_seed to -9642505 78: 78: Velocities were taken from a Maxwell distribution at 298 K 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: 78: Dynamic load balancing report: 78: DLB was off during the run due to low measured imbalance. 78: Average load imbalance: 10.0%. 78: The balanceable part of the MD step is 12%, load imbalance is computed from this. 78: Part of the total run time spent waiting due to load imbalance: 1.1%. 78: 78: 78: NOTE: 47 % of the run time was spent communicating energies, 78: you might want to increase some nst* mdp options 78: 78: Writing final coordinates. 78: 78: 78: Dynamic load balancing report: 78: DLB was off during the run due to low measured imbalance. 78: Average load imbalance: 9.2%. 78: The balanceable part of the MD step is 10%, load imbalance is computed from this. 78: Part of the total run time spent waiting due to load imbalance: 1.0%. 78: 78: 78: NOTE: 47 % of the run time was spent communicating energies, 78: you might want to increase some nst* mdp options 78: [ OK ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/2 (20 ms) 78: [ RUN ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/3 78: Setting the LD random seed to 1034413439 78: 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Setting gen_seed to 1605884886 78: 78: Velocities were taken from a Maxwell distribution at 278 K 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Setting the LD random seed to -1141006477 78: 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_3_input.mdp]: 78: You have set rlist larger than the interaction cut-off, but you also have 78: verlet-buffer-tolerance > 0. Will set rlist using 78: verlet-buffer-tolerance. 78: 78: 78: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_3_input.mdp]: 78: The Berendsen barostat does not generate any strictly correct ensemble, 78: and should not be used for new production simulations (in our opinion). 78: We recommend using the C-rescale barostat instead. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_3_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: 78: There was 1 WARNING 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_3_input.mdp]: 78: You have set rlist larger than the interaction cut-off, but you also have 78: verlet-buffer-tolerance > 0. Will set rlist using 78: verlet-buffer-tolerance. 78: 78: 78: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_3_input.mdp]: 78: The Berendsen barostat does not generate any strictly correct ensemble, 78: and should not be used for new production simulations (in our opinion). 78: We recommend using the C-rescale barostat instead. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Setting gen_seed to -1082279945 78: 78: Velocities were taken from a Maxwell distribution at 298 K 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_3_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: 78: There was 1 WARNING 78: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 78: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 78: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 78: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 78: 78: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 78: 78: This is simulation 1 out of 2 running as a composite GROMACS 78: multi-simulation job. Setup for this simulation: 78: 78: Using 2 MPI processes 78: This is simulation 0 out of 2 running as a composite GROMACS 78: multi-simulation job. Setup for this simulation: 78: 78: Using 2 MPI processes 78: Using 1 OpenMP thread per MPI process 78: 78: Using 1 OpenMP thread per MPI process 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 2 steps, 0.0 ps. 78: starting mdrun 'spc2' 78: 2 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Writing final coordinates. 78: 78: 78: Dynamic load balancing report: 78: DLB was off during the run due to low measured imbalance. 78: Average load imbalance: 12.5%. 78: The balanceable part of the MD step is 10%, load imbalance is computed from this. 78: Part of the total run time spent waiting due to load imbalance: 1.3%. 78: 78: 78: 78: Dynamic load balancing report: 78: DLB was off during the run due to low measured imbalance. 78: Average load imbalance: 12.9%. 78: The balanceable part of the MD step is 9%, load imbalance is computed from this. 78: Part of the total run time spent waiting due to load imbalance: 1.2%. 78: 78: 78: NOTE: 47 % of the run time was spent communicating energies, 78: you might want to increase some nst* mdp options 78: 78: NOTE: 47 % of the run time was spent communicating energies, 78: you might want to increase some nst* mdp options 78: [ OK ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/3 (19 ms) 78: [----------] 4 tests from WithDifferentControlVariables/ReplicaExchangeEnsembleTest (87 ms total) 78: 78: [----------] 1 test from InNvt/ReplicaExchangeTerminationTest 78: [ RUN ] InNvt/ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 78: You have set rlist larger than the interaction cut-off, but you also have 78: verlet-buffer-tolerance > 0. Will set rlist using 78: verlet-buffer-tolerance. 78: 78: Setting the LD random seed to -33593473 78: Generating 1-4 interactions: fudge = 0.5 78: 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 78: You have set rlist larger than the interaction cut-off, but you also have 78: verlet-buffer-tolerance > 0. Will set rlist using 78: verlet-buffer-tolerance. 78: 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: Setting the LD random seed to -555827845 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 78: You have set rlist larger than the interaction cut-off, but you also have 78: verlet-buffer-tolerance > 0. Will set rlist using 78: verlet-buffer-tolerance. 78: 78: Setting the LD random seed to -595657489 78: 78: Setting gen_seed to -340271121 78: 78: Velocities were taken from a Maxwell distribution at 288 K 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: Generating 1-4 interactions: fudge = 0.5 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Setting gen_seed to -35695873 78: 78: Velocities were taken from a Maxwell distribution at 278 K 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 78: You have set rlist larger than the interaction cut-off, but you also have 78: verlet-buffer-tolerance > 0. Will set rlist using 78: verlet-buffer-tolerance. 78: 78: Setting the LD random seed to -136318997 78: 78: Setting gen_seed to -285802603 78: 78: Velocities were taken from a Maxwell distribution at 268 K 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: This run will generate roughly 0 Mb of data 78: 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: There were 2 NOTEs 78: Generating 1-4 interactions: fudge = 0.5 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Setting gen_seed to -4458690 78: 78: Velocities were taken from a Maxwell distribution at 298 K 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: 78: This run will generate roughly 0 Mb of data 78: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 78: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 78: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 78: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 78: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 78: Changing nstlist from 10 to 1, rlist from 0.736 to 0.7 78: 78: Changing nstlist from 10 to 1, rlist from 0.736 to 0.7 78: 78: Changing nstlist from 10 to 1, rlist from 0.736 to 0.7 78: 78: Changing nstlist from 10 to 1, rlist from 0.736 to 0.7 78: 78: This is simulation 0 out of 4 running as a composite GROMACS 78: multi-simulation job. Setup for this simulation: 78: 78: Using 1 MPI process 78: This is simulation 1 out of 4 running as a composite GROMACS 78: multi-simulation job. Setup for this simulation: 78: 78: Using 1 MPI process 78: This is simulation 2 out of 4 running as a composite GROMACS 78: multi-simulation job. Setup for this simulation: 78: 78: Using 1 MPI process 78: This is simulation 3 out of 4 running as a composite GROMACS 78: multi-simulation job. Setup for this simulation: 78: 78: Using 1 MPI process 78: Using 1 OpenMP thread 78: 78: Using 1 OpenMP thread 78: 78: Using 1 OpenMP thread 78: 78: Using 1 OpenMP thread 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 100 steps, 0.1 ps. 78: starting mdrun 'spc2' 78: 100 steps, 0.1 ps. 78: starting mdrun 'spc2' 78: 100 steps, 0.1 ps. 78: starting mdrun 'spc2' 78: 100 steps, 0.1 ps. 78: 78: Step 2: Run time exceeded 0.000 hours, will terminate the run within 400 steps 78: 78: Step 2: Run time exceeded 0.000 hours, will terminate the run within 400 steps 78: 78: Step 2: Run time exceeded 0.000 hours, will terminate the run within 400 steps 78: 78: Step 2: Run time exceeded 0.000 hours, will terminate the run within 400 steps 78: 78: Writing final coordinates. 78: 78: Writing final coordinates. 78: 78: Writing final coordinates. 78: 78: Writing final coordinates. 78: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 78: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 78: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 78: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 78: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 78: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 78: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 78: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 78: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 78: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 78: 78: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 78: 78: Changing nstlist from 10 to 25, rlist from 0.737 to 0.812 78: 78: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 78: 78: 78: This is simulation 0 out of 4 running as a composite GROMACS 78: multi-simulation job. Setup for this simulation: 78: 78: Using 1 MPI process 78: 78: This is simulation 3 out of 4 running as a composite GROMACS 78: multi-simulation job. Setup for this simulation: 78: 78: Using 1 MPI process 78: Using 1 OpenMP thread 78: 78: 78: This is simulation 2 out of 4 running as a composite GROMACS 78: multi-simulation job. Setup for this simulation: 78: 78: Using 1 MPI process 78: Using 1 OpenMP thread 78: 78: 78: This is simulation 1 out of 4 running as a composite GROMACS 78: multi-simulation job. Setup for this simulation: 78: 78: Using 1 MPI process 78: Using 1 OpenMP thread 78: 78: Using 1 OpenMP thread 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 102 steps, 0.1 ps (continuing from step 100, 0.1 ps). 78: starting mdrun 'spc2' 78: 102 steps, 0.1 ps (continuing from step 100, 0.1 ps). 78: starting mdrun 'spc2' 78: 102 steps, 0.1 ps (continuing from step 100, 0.1 ps). 78: starting mdrun 'spc2' 78: 102 steps, 0.1 ps (continuing from step 100, 0.1 ps). 78: 78: Writing final coordinates. 78: 78: Writing final coordinates. 78: 78: Writing final coordinates. 78: 78: Writing final coordinates. 78: [ OK ] InNvt/ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 (50 ms) 78: [----------] 1 test from InNvt/ReplicaExchangeTerminationTest (50 ms total) 78: 78: [----------] Global test environment tear-down 78: [==========] 5 tests from 2 test suites ran. (386 ms total) 78: [ PASSED ] 5 tests. 78/94 Test #78: MdrunMultiSimReplexTests ..................... Passed 0.87 sec test 79 Start 79: MdrunMultiSimReplexEquivalenceTests 79: Test command: /usr/bin/mpiexec "-n" "4" "/build/reproducible-path/gromacs-2025.0/build/mpi/bin/mdrun-multisim-replex-equivalence-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/MdrunMultiSimReplexEquivalenceTests.xml" 79: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests 79: Test timeout computed to be: 600 79: [==========] Running 10 tests from 2 test suites. 79: [----------] Global test environment set-up. 79: [----------] 8 tests from LF/ReplicaExchangeTest 79: [ RUN ] LF/ReplicaExchangeTest.Works/md_Vrescale_Crescale_4Ranks_1RanksPerSim_s 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: Generating 1-4 interactions: fudge = 0.5 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: Generating 1-4 interactions: fudge = 0.5 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: Generating 1-4 interactions: fudge = 0.5 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: Generating 1-4 interactions: fudge = 0.5 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Velocities were taken from a Maxwell distribution at 278 K 79: Number of degrees of freedom in T-Coupling group System is 27.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Velocities were taken from a Maxwell distribution at 288 K 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Velocities were taken from a Maxwell distribution at 268 K 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Velocities were taken from a Maxwell distribution at 298 K 79: Number of degrees of freedom in T-Coupling group System is 27.00 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: Number of degrees of freedom in T-Coupling group System is 27.00 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: This run will generate roughly 0 Mb of data 79: 79: There were 2 NOTEs 79: Number of degrees of freedom in T-Coupling group System is 27.00 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: This run will generate roughly 0 Mb of data 79: 79: There were 2 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 79: 79: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 79: 79: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 79: 79: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 79: 79: This is simulation 2 out of 4 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 1 MPI process 79: This is simulation 0 out of 4 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 1 MPI process 79: This is simulation 3 out of 4 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 1 MPI process 79: This is simulation 1 out of 4 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 1 MPI process 79: Using 1 OpenMP thread 79: 79: Using 1 OpenMP thread 79: 79: Using 1 OpenMP thread 79: 79: Using 1 OpenMP thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Writing final coordinates. 79: 79: Writing final coordinates. 79: 79: Writing final coordinates. 79: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 trr version: GMX_trn_file (single precision) 79: 79: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: [ OK ] LF/ReplicaExchangeTest.Works/md_Vrescale_Crescale_4Ranks_1RanksPerSim_s (915 ms) 79: [ RUN ] LF/ReplicaExchangeTest.Works/md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 79: You are generating velocities so I am assuming you are equilibrating a 79: system. You are using Parrinello-Rahman pressure coupling, but this can 79: be unstable for equilibration. If your system crashes, try equilibrating 79: first with Berendsen pressure coupling. If you are not equilibrating the 79: system, you can probably ignore this warning. 79: 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 79: You are generating velocities so I am assuming you are equilibrating a 79: system. You are using Parrinello-Rahman pressure coupling, but this can 79: be unstable for equilibration. If your system crashes, try equilibrating 79: first with Berendsen pressure coupling. If you are not equilibrating the 79: system, you can probably ignore this warning. 79: 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 79: You are generating velocities so I am assuming you are equilibrating a 79: system. You are using Parrinello-Rahman pressure coupling, but this can 79: be unstable for equilibration. If your system crashes, try equilibrating 79: first with Berendsen pressure coupling. If you are not equilibrating the 79: system, you can probably ignore this warning. 79: 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 79: You are generating velocities so I am assuming you are equilibrating a 79: system. You are using Parrinello-Rahman pressure coupling, but this can 79: be unstable for equilibration. If your system crashes, try equilibrating 79: first with Berendsen pressure coupling. If you are not equilibrating the 79: system, you can probably ignore this warning. 79: 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: Generating 1-4 interactions: fudge = 0.5 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: Generating 1-4 interactions: fudge = 0.5 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: Generating 1-4 interactions: fudge = 0.5 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: Generating 1-4 interactions: fudge = 0.5 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Velocities were taken from a Maxwell distribution at 278 K 79: Number of degrees of freedom in T-Coupling group System is 27.00 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: 79: This run will generate roughly 0 Mb of data 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Velocities were taken from a Maxwell distribution at 288 K 79: Number of degrees of freedom in T-Coupling group System is 27.00 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: 79: This run will generate roughly 0 Mb of data 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Velocities were taken from a Maxwell distribution at 298 K 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Velocities were taken from a Maxwell distribution at 268 K 79: Number of degrees of freedom in T-Coupling group System is 27.00 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: 79: This run will generate roughly 0 Mb of data 79: Number of degrees of freedom in T-Coupling group System is 27.00 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: 79: This run will generate roughly 0 Mb of data 79: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 79: 79: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 79: 79: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 79: 79: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 79: 79: This is simulation 2 out of 4 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 1 MPI process 79: This is simulation 0 out of 4 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 1 MPI process 79: This is simulation 1 out of 4 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 1 MPI process 79: Using 1 OpenMP thread 79: 79: This is simulation 3 out of 4 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 1 MPI process 79: Using 1 OpenMP thread 79: 79: Using 1 OpenMP thread 79: 79: Using 1 OpenMP thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Writing final coordinates. 79: 79: Writing final coordinates. 79: 79: Writing final coordinates. 79: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: [ OK ] LF/ReplicaExchangeTest.Works/md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s (887 ms) 79: [ RUN ] LF/ReplicaExchangeTest.Works/md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: Generating 1-4 interactions: fudge = 0.5 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: Generating 1-4 interactions: fudge = 0.5 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: Generating 1-4 interactions: fudge = 0.5 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: Generating 1-4 interactions: fudge = 0.5 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Velocities were taken from a Maxwell distribution at 278 K 79: Number of degrees of freedom in T-Coupling group System is 27.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Velocities were taken from a Maxwell distribution at 288 K 79: Number of degrees of freedom in T-Coupling group System is 27.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Velocities were taken from a Maxwell distribution at 298 K 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Velocities were taken from a Maxwell distribution at 268 K 79: Number of degrees of freedom in T-Coupling group System is 27.00 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: Number of degrees of freedom in T-Coupling group System is 27.00 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 79: 79: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 79: 79: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 79: 79: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 79: 79: This is simulation 1 out of 4 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 1 MPI process 79: This is simulation 2 out of 4 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 1 MPI process 79: This is simulation 0 out of 4 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 1 MPI process 79: This is simulation 3 out of 4 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 1 MPI process 79: Using 1 OpenMP thread 79: 79: Using 1 OpenMP thread 79: 79: Using 1 OpenMP thread 79: 79: Using 1 OpenMP thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Writing final coordinates. 79: 79: Writing final coordinates. 79: 79: Writing final coordinates. 79: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: [ OK ] LF/ReplicaExchangeTest.Works/md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s (940 ms) 79: [ RUN ] LF/ReplicaExchangeTest.Works/md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 79: You are generating velocities so I am assuming you are equilibrating a 79: system. You are using Parrinello-Rahman pressure coupling, but this can 79: be unstable for equilibration. If your system crashes, try equilibrating 79: first with Berendsen pressure coupling. If you are not equilibrating the 79: system, you can probably ignore this warning. 79: 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 79: You are generating velocities so I am assuming you are equilibrating a 79: system. You are using Parrinello-Rahman pressure coupling, but this can 79: be unstable for equilibration. If your system crashes, try equilibrating 79: first with Berendsen pressure coupling. If you are not equilibrating the 79: system, you can probably ignore this warning. 79: 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 79: You are generating velocities so I am assuming you are equilibrating a 79: system. You are using Parrinello-Rahman pressure coupling, but this can 79: be unstable for equilibration. If your system crashes, try equilibrating 79: first with Berendsen pressure coupling. If you are not equilibrating the 79: system, you can probably ignore this warning. 79: 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 79: You are generating velocities so I am assuming you are equilibrating a 79: system. You are using Parrinello-Rahman pressure coupling, but this can 79: be unstable for equilibration. If your system crashes, try equilibrating 79: first with Berendsen pressure coupling. If you are not equilibrating the 79: system, you can probably ignore this warning. 79: 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: Generating 1-4 interactions: fudge = 0.5 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: Generating 1-4 interactions: fudge = 0.5 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: Generating 1-4 interactions: fudge = 0.5 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: Generating 1-4 interactions: fudge = 0.5 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Velocities were taken from a Maxwell distribution at 278 K 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Velocities were taken from a Maxwell distribution at 288 K 79: Number of degrees of freedom in T-Coupling group System is 27.00 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: 79: This run will generate roughly 0 Mb of data 79: Number of degrees of freedom in T-Coupling group System is 27.00 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Velocities were taken from a Maxwell distribution at 268 K 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Velocities were taken from a Maxwell distribution at 298 K 79: Number of degrees of freedom in T-Coupling group System is 27.00 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: 79: This run will generate roughly 0 Mb of data 79: Number of degrees of freedom in T-Coupling group System is 27.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 79: 79: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 79: 79: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 79: 79: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 79: 79: This is simulation 2 out of 4 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 1 MPI process 79: This is simulation 1 out of 4 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 1 MPI process 79: This is simulation 0 out of 4 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 1 MPI process 79: Using 1 OpenMP thread 79: 79: This is simulation 3 out of 4 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 1 MPI process 79: Using 1 OpenMP thread 79: 79: Using 1 OpenMP thread 79: 79: Using 1 OpenMP thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Writing final coordinates. 79: 79: Writing final coordinates. 79: 79: Writing final coordinates. 79: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: [ OK ] LF/ReplicaExchangeTest.Works/md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s (1127 ms) 79: [ RUN ] LF/ReplicaExchangeTest.Works/md_Vrescale_Crescale_4Ranks_2RanksPerSim_s 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: Generating 1-4 interactions: fudge = 0.5 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: Generating 1-4 interactions: fudge = 0.5 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Velocities were taken from a Maxwell distribution at 278 K 79: Number of degrees of freedom in T-Coupling group System is 27.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Velocities were taken from a Maxwell distribution at 298 K 79: Number of degrees of freedom in T-Coupling group System is 27.00 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: This run will generate roughly 0 Mb of data 79: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_2RanksPerSim_s.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_2RanksPerSim_s.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 79: 79: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 79: 79: This is simulation 0 out of 2 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 2 MPI processes 79: This is simulation 1 out of 2 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 2 MPI processes 79: Using 1 OpenMP thread per MPI process 79: 79: Using 1 OpenMP thread per MPI process 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Writing final coordinates. 79: 79: 79: Dynamic load balancing report: 79: DLB was turned on during the run due to measured imbalance. 79: Average load imbalance: 4.7%. 79: The balanceable part of the MD step is 44%, load imbalance is computed from this. 79: Part of the total run time spent waiting due to load imbalance: 2.1%. 79: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 79: 79: 79: 79: Dynamic load balancing report: 79: DLB was off during the run due to low measured imbalance. 79: Average load imbalance: 1.0%. 79: The balanceable part of the MD step is 41%, load imbalance is computed from this. 79: Part of the total run time spent waiting due to load imbalance: 0.4%. 79: 79: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_2RanksPerSim_s.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_2RanksPerSim_s.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: [ OK ] LF/ReplicaExchangeTest.Works/md_Vrescale_Crescale_4Ranks_2RanksPerSim_s (628 ms) 79: [ RUN ] LF/ReplicaExchangeTest.Works/md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 79: You are generating velocities so I am assuming you are equilibrating a 79: system. You are using Parrinello-Rahman pressure coupling, but this can 79: be unstable for equilibration. If your system crashes, try equilibrating 79: first with Berendsen pressure coupling. If you are not equilibrating the 79: system, you can probably ignore this warning. 79: 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 79: You are generating velocities so I am assuming you are equilibrating a 79: system. You are using Parrinello-Rahman pressure coupling, but this can 79: be unstable for equilibration. If your system crashes, try equilibrating 79: first with Berendsen pressure coupling. If you are not equilibrating the 79: system, you can probably ignore this warning. 79: 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: Generating 1-4 interactions: fudge = 0.5 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: Generating 1-4 interactions: fudge = 0.5 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Velocities were taken from a Maxwell distribution at 278 K 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Velocities were taken from a Maxwell distribution at 298 K 79: Number of degrees of freedom in T-Coupling group System is 27.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Number of degrees of freedom in T-Coupling group System is 27.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 79: 79: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 79: 79: This is simulation 0 out of 2 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 2 MPI processes 79: Using 1 OpenMP thread per MPI process 79: 79: This is simulation 1 out of 2 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 2 MPI processes 79: Using 1 OpenMP thread per MPI process 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Writing final coordinates. 79: 79: 79: Dynamic load balancing report: 79: DLB was off during the run due to low measured imbalance. 79: Average load imbalance: 3.5%. 79: The balanceable part of the MD step is 26%, load imbalance is computed from this. 79: Part of the total run time spent waiting due to load imbalance: 0.9%. 79: 79: 79: 79: Dynamic load balancing report: 79: DLB was off during the run due to low measured imbalance. 79: Average load imbalance: 0.5%. 79: The balanceable part of the MD step is 27%, load imbalance is computed from this. 79: Part of the total run time spent waiting due to load imbalance: 0.1%. 79: 79: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: [ OK ] LF/ReplicaExchangeTest.Works/md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s (683 ms) 79: [ RUN ] LF/ReplicaExchangeTest.Works/md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: Generating 1-4 interactions: fudge = 0.5 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: Generating 1-4 interactions: fudge = 0.5 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Velocities were taken from a Maxwell distribution at 278 K 79: Number of degrees of freedom in T-Coupling group System is 27.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Velocities were taken from a Maxwell distribution at 298 K 79: Number of degrees of freedom in T-Coupling group System is 27.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 79: 79: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 79: 79: This is simulation 0 out of 2 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 2 MPI processes 79: This is simulation 1 out of 2 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 2 MPI processes 79: Using 1 OpenMP thread per MPI process 79: 79: Using 1 OpenMP thread per MPI process 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Writing final coordinates. 79: 79: 79: Dynamic load balancing report: 79: DLB was turned on during the run due to measured imbalance. 79: Average load imbalance: 5.2%. 79: The balanceable part of the MD step is 45%, load imbalance is computed from this. 79: Part of the total run time spent waiting due to load imbalance: 2.3%. 79: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 79: 79: 79: 79: Dynamic load balancing report: 79: DLB was off during the run due to low measured imbalance. 79: Average load imbalance: 1.5%. 79: The balanceable part of the MD step is 42%, load imbalance is computed from this. 79: Part of the total run time spent waiting due to load imbalance: 0.6%. 79: 79: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: [ OK ] LF/ReplicaExchangeTest.Works/md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s (791 ms) 79: [ RUN ] LF/ReplicaExchangeTest.Works/md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 79: You are generating velocities so I am assuming you are equilibrating a 79: system. You are using Parrinello-Rahman pressure coupling, but this can 79: be unstable for equilibration. If your system crashes, try equilibrating 79: first with Berendsen pressure coupling. If you are not equilibrating the 79: system, you can probably ignore this warning. 79: 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 79: You are generating velocities so I am assuming you are equilibrating a 79: system. You are using Parrinello-Rahman pressure coupling, but this can 79: be unstable for equilibration. If your system crashes, try equilibrating 79: first with Berendsen pressure coupling. If you are not equilibrating the 79: system, you can probably ignore this warning. 79: 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: Generating 1-4 interactions: fudge = 0.5 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: Generating 1-4 interactions: fudge = 0.5 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Velocities were taken from a Maxwell distribution at 278 K 79: Number of degrees of freedom in T-Coupling group System is 27.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Velocities were taken from a Maxwell distribution at 298 K 79: Number of degrees of freedom in T-Coupling group System is 27.00 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 79: 79: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 79: 79: This is simulation 0 out of 2 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 2 MPI processes 79: This is simulation 1 out of 2 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 2 MPI processes 79: Using 1 OpenMP thread per MPI process 79: 79: Using 1 OpenMP thread per MPI process 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Writing final coordinates. 79: 79: 79: Dynamic load balancing report: 79: DLB was off during the run due to low measured imbalance. 79: Average load imbalance: 1.3%. 79: The balanceable part of the MD step is 38%, load imbalance is computed from this. 79: Part of the total run time spent waiting due to load imbalance: 0.5%. 79: 79: 79: 79: Dynamic load balancing report: 79: DLB was off during the run due to low measured imbalance. 79: Average load imbalance: 1.0%. 79: The balanceable part of the MD step is 49%, load imbalance is computed from this. 79: Part of the total run time spent waiting due to load imbalance: 0.5%. 79: 79: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: [ OK ] LF/ReplicaExchangeTest.Works/md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s (661 ms) 79: [----------] 8 tests from LF/ReplicaExchangeTest (6640 ms total) 79: 79: [----------] 2 tests from VV/ReplicaExchangeTest 79: [ RUN ] VV/ReplicaExchangeTest.Works/mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: Generating 1-4 interactions: fudge = 0.5 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: Generating 1-4 interactions: fudge = 0.5 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: Generating 1-4 interactions: fudge = 0.5 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: Generating 1-4 interactions: fudge = 0.5 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Velocities were taken from a Maxwell distribution at 288 K 79: Number of degrees of freedom in T-Coupling group System is 27.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Velocities were taken from a Maxwell distribution at 298 K 79: Number of degrees of freedom in T-Coupling group System is 27.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Velocities were taken from a Maxwell distribution at 278 K 79: Number of degrees of freedom in T-Coupling group System is 27.00 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Velocities were taken from a Maxwell distribution at 268 K 79: Number of degrees of freedom in T-Coupling group System is 27.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 79: 79: This is simulation 0 out of 4 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 1 MPI process 79: Using 1 OpenMP thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 79: 79: This is simulation 2 out of 4 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 1 MPI process 79: Using 1 OpenMP thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 79: 79: This is simulation 1 out of 4 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 1 MPI process 79: Using 1 OpenMP thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 79: 79: This is simulation 3 out of 4 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 1 MPI process 79: Using 1 OpenMP thread 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Writing final coordinates. 79: 79: Writing final coordinates. 79: 79: Writing final coordinates. 79: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: [ OK ] VV/ReplicaExchangeTest.Works/mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s (776 ms) 79: [ RUN ] VV/ReplicaExchangeTest.Works/mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: Generating 1-4 interactions: fudge = 0.5 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: Generating 1-4 interactions: fudge = 0.5 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Velocities were taken from a Maxwell distribution at 278 K 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Velocities were taken from a Maxwell distribution at 298 K 79: Number of degrees of freedom in T-Coupling group System is 27.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Number of degrees of freedom in T-Coupling group System is 27.00 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 79: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 79: 79: This is simulation 0 out of 2 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 2 MPI processes 79: Using 1 OpenMP thread per MPI process 79: 79: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 79: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 79: 79: This is simulation 1 out of 2 running as a composite GROMACS 79: multi-simulation job. Setup for this simulation: 79: 79: Using 2 MPI processes 79: Using 1 OpenMP thread per MPI process 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 16 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Writing final coordinates. 79: 79: 79: Dynamic load balancing report: 79: DLB was off during the run due to low measured imbalance. 79: Average load imbalance: 1.8%. 79: The balanceable part of the MD step is 35%, load imbalance is computed from this. 79: Part of the total run time spent waiting due to load imbalance: 0.6%. 79: 79: 79: 79: Dynamic load balancing report: 79: DLB was off during the run due to low measured imbalance. 79: Average load imbalance: 1.7%. 79: The balanceable part of the MD step is 27%, load imbalance is computed from this. 79: Part of the total run time spent waiting due to load imbalance: 0.4%. 79: 79: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: [ OK ] VV/ReplicaExchangeTest.Works/mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s (700 ms) 79: [----------] 2 tests from VV/ReplicaExchangeTest (1477 ms total) 79: 79: [----------] Global test environment tear-down 79: [==========] 10 tests from 2 test suites ran. (8367 ms total) 79: [ PASSED ] 10 tests. 79/94 Test #79: MdrunMultiSimReplexEquivalenceTests .......... Passed 8.86 sec test 80 Start 80: MdrunMpi1RankPmeTests 80: Test command: /usr/bin/mpiexec "-n" "1" "/build/reproducible-path/gromacs-2025.0/build/mpi/bin/mdrun-mpi-pme-test" "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/MdrunMpi1RankPmeTests.xml" 80: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests 80: Test timeout computed to be: 600 80: [==========] Running 19 tests from 1 test suite. 80: [----------] Global test environment set-up. 80: [----------] 19 tests from ReproducesEnergies/PmeTest 80: Setting the LD random seed to -134645890 80: 80: Generated 8 of the 10 non-bonded parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'Methanol' 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 80: 80: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 80: 80: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 80: 80: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: Calculating fourier grid dimensions for X Y Z 80: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 80: 80: Estimate for the relative computational load of the PME mesh part: 1.00 80: 80: This run will generate roughly 0 Mb of data 80: Number of degrees of freedom in T-Coupling group rest is 12.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 80: NVE simulation: will use the initial temperature of 1046.791 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 80: The optimal PME mesh load for parallel simulations is below 0.5 80: and for highly parallel simulations between 0.25 and 0.33, 80: for higher performance, increase the cut-off and the PME grid spacing. 80: 80: 80: 80: There were 2 NOTEs 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 80: For a correct single-point energy evaluation with nsteps = 0, use 80: continuation = yes to avoid constraining the input coordinates. 80: 80: Number of degrees of freedom in T-Coupling group rest is 13.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 80: NVE simulation: will use the initial temperature of 966.268 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 80: The optimal PME mesh load for parallel simulations is below 0.5 80: and for highly parallel simulations between 0.25 and 0.33, 80: for higher performance, increase the cut-off and the PME grid spacing. 80: 80: 80: 80: There were 3 NOTEs 80: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 80: Setting the LD random seed to -1619532036 80: 80: Generated 8 of the 10 non-bonded parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'Methanol' 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 80: 80: Searching the wall atom type(s) 80: 80: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 80: 80: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 80: 80: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: Calculating fourier grid dimensions for X Y Z 80: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118 80: 80: Estimate for the relative computational load of the PME mesh part: 1.00 80: 80: This run will generate roughly 0 Mb of data 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI process 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc-and-methanol' 80: 20 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.055 0.028 199.3 80: (ns/day) (hour/ns) 80: Performance: 65.905 0.364 80: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_cpu.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu (179 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto 80: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI process 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc-and-methanol' 80: 20 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.049 0.025 199.2 80: (ns/day) (hour/ns) 80: Performance: 73.371 0.327 80: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_auto.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto (33 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu 80: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI process 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc-and-methanol' 80: 0 steps, 0.0 ps. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.006 0.003 194.9 80: (ns/day) (hour/ns) 80: Performance: 26.500 0.906 80: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_0__pme_cpu.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu (550 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets using PME rank(s) but the simulation is using only one rank 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets using PME rank(s) but the simulation is using only one rank 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets using PME rank(s) but the simulation is using only one rank 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets using PME rank(s) but the simulation is using only one rank 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets using PME rank(s) but the simulation is using only one rank 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets using PME rank(s) but the simulation is using only one rank 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets using PME rank(s) but the simulation is using only one rank 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets using PME rank(s) but the simulation is using only one rank 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu 80: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 80: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI process 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc-and-methanol' 80: 20 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.054 0.027 199.3 80: (ns/day) (hour/ns) 80: Performance: 67.391 0.356 80: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__tunepme__npme_0__pme_cpu.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu (35 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 80: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 80: ./src/programs/mdrun/tests/pmetest.cpp:309: Skipped 80: Test is being skipped because: 80: it targets GPU execution, but no compatible devices were detected 80: PME GPU does not support: 80: Non-GPU build of GROMACS. 80: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 80: [----------] 19 tests from ReproducesEnergies/PmeTest (800 ms total) 80: 80: [----------] Global test environment tear-down 80: [==========] 19 tests from 1 test suite ran. (896 ms total) 80: [ PASSED ] 4 tests. 80: [ SKIPPED ] 15 tests, listed below: 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 80: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 80/94 Test #80: MdrunMpi1RankPmeTests ........................ Passed 1.34 sec test 81 Start 81: MdrunMpi2RankPmeTests 81: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2025.0/build/mpi/bin/mdrun-mpi-pme-test" "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/MdrunMpi2RankPmeTests.xml" 81: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests 81: Test timeout computed to be: 600 81: [==========] Running 19 tests from 1 test suite. 81: [----------] Global test environment set-up. 81: [----------] 19 tests from ReproducesEnergies/PmeTest 81: Setting the LD random seed to -1077936321 81: 81: Generated 8 of the 10 non-bonded parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'Methanol' 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 81: 81: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 81: 81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 81: 81: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: Calculating fourier grid dimensions for X Y Z 81: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 81: 81: Estimate for the relative computational load of the PME mesh part: 1.00 81: 81: This run will generate roughly 0 Mb of data 81: Number of degrees of freedom in T-Coupling group rest is 12.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 81: NVE simulation: will use the initial temperature of 1046.791 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 81: The optimal PME mesh load for parallel simulations is below 0.5 81: and for highly parallel simulations between 0.25 and 0.33, 81: for higher performance, increase the cut-off and the PME grid spacing. 81: 81: 81: 81: There were 2 NOTEs 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 81: For a correct single-point energy evaluation with nsteps = 0, use 81: continuation = yes to avoid constraining the input coordinates. 81: 81: Number of degrees of freedom in T-Coupling group rest is 13.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 81: NVE simulation: will use the initial temperature of 966.268 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 81: The optimal PME mesh load for parallel simulations is below 0.5 81: and for highly parallel simulations between 0.25 and 0.33, 81: for higher performance, increase the cut-off and the PME grid spacing. 81: 81: 81: 81: There were 3 NOTEs 81: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Setting the LD random seed to -71344161 81: 81: Generated 8 of the 10 non-bonded parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'Methanol' 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc-and-methanol.gro' 81: 81: Searching the wall atom type(s) 81: 81: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 81: 81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 81: 81: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: Calculating fourier grid dimensions for X Y Z 81: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118 81: 81: Estimate for the relative computational load of the PME mesh part: 1.00 81: 81: This run will generate roughly 0 Mb of data 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu 81: Using 2 MPI processes 81: Using 2 OpenMP threads per MPI process 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc-and-methanol' 81: 20 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 4.0%. 81: The balanceable part of the MD step is 7%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 0.3%. 81: 81: 81: NOTE: 17 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.085 0.021 398.0 81: (ns/day) (hour/ns) 81: Performance: 84.902 0.283 81: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_cpu.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 81: [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu (175 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI processes 81: Using 2 OpenMP threads per MPI process 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc-and-methanol' 81: 20 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 5.3%. 81: The balanceable part of the MD step is 7%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 0.4%. 81: 81: 81: NOTE: 20 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.093 0.023 397.6 81: (ns/day) (hour/ns) 81: Performance: 77.469 0.310 81: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_auto.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto (32 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto (0 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu 81: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI processes 81: Using 2 OpenMP threads per MPI process 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc-and-methanol' 81: 0 steps, 0.0 ps. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.013 0.003 366.7 81: (ns/day) (hour/ns) 81: Performance: 24.768 0.969 81: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_0__pme_cpu.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu (602 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu 81: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI processes 81: Using 2 OpenMP threads per MPI process 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc-and-methanol' 81: 20 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.083 0.021 395.1 81: (ns/day) (hour/ns) 81: Performance: 86.058 0.279 81: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_1__pme_cpu.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu (116 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto 81: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI processes 81: Using 2 OpenMP threads per MPI process 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc-and-methanol' 81: 20 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.083 0.021 395.7 81: (ns/day) (hour/ns) 81: Performance: 86.102 0.279 81: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_1__pme_auto.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto (30 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto (0 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu 81: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI processes 81: Using 2 OpenMP threads per MPI process 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc-and-methanol' 81: 0 steps, 0.0 ps. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.013 0.004 361.0 81: (ns/day) (hour/ns) 81: Performance: 23.789 1.009 81: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_1__pme_cpu.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu (425 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu 81: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 81: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI processes 81: Using 2 OpenMP threads per MPI process 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'spc-and-methanol' 81: 20 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 11.8%. 81: The balanceable part of the MD step is 8%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 0.9%. 81: 81: 81: NOTE: 16 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.089 0.022 397.2 81: (ns/day) (hour/ns) 81: Performance: 80.657 0.298 81: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__tunepme__npme_0__pme_cpu.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu (32 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 81: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 81: [----------] 19 tests from ReproducesEnergies/PmeTest (1419 ms total) 81: 81: [----------] Global test environment tear-down 81: [==========] 19 tests from 1 test suite ran. (1538 ms total) 81: [ PASSED ] 7 tests. 81: [ SKIPPED ] 12 tests, listed below: 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 81: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 81/94 Test #81: MdrunMpi2RankPmeTests ........................ Passed 2.00 sec test 82 Start 82: MdrunCoordinationBasicTests1Rank 82: Test command: /usr/bin/mpiexec "-n" "1" "/build/reproducible-path/gromacs-2025.0/build/mpi/bin/mdrun-coordination-basic-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/MdrunCoordinationBasicTests1Rank.xml" 82: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests 82: Test timeout computed to be: 1920 82: [==========] Running 1 test from 1 test suite. 82: [----------] Global test environment set-up. 82: [----------] 1 test from BasicPropagators/PeriodicActionsTest 82: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI process 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.013 0.013 99.5 82: (ns/day) (hour/ns) 82: Performance: 110.611 0.217 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI process 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.008 0.008 99.4 82: (ns/day) (hour/ns) 82: Performance: 178.931 0.134 82: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: COM removal frequency is set to (1). 82: Other settings require a global communication frequency of 4. 82: Note that this will require additional global communication steps, 82: rmance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 4. 82: 82: 82: There were 5 NOTEs 82: which will reduce perfoGenerated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI process 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.007 0.008 99.4 82: (ns/day) (hour/ns) 82: Performance: 195.141 0.123 82: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: COM removal frequency is set to (1). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI process 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.009 0.009 99.4 82: (ns/day) (hour/ns) 82: Performance: 157.992 0.152 82: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: COM removal frequency is set to (1). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI process 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.007 0.008 99.3 82: (ns/day) (hour/ns) 82: Performance: 195.543 0.123 82: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: COM removal frequency is set to (1). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 82: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 1 MPI process 82: Using 1 OpenMP thread 82: 82: 82: NOTE: Thread affinity was not set. 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.011 0.011 99.5 82: (ns/day) (hour/ns) 82: Performance: 128.260 0.187 82: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 82: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (94 ms) 82: [----------] 1 test from BasicPropagators/PeriodicActionsTest (94 ms total) 82: 82: [----------] Global test environment tear-down 82: [==========] 1 test from 1 test suite ran. (174 ms total) 82: [ PASSED ] 1 test. 82/94 Test #82: MdrunCoordinationBasicTests1Rank ............. Passed 0.62 sec test 83 Start 83: MdrunCoordinationBasicTests2Ranks 83: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2025.0/build/mpi/bin/mdrun-coordination-basic-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/MdrunCoordinationBasicTests2Ranks.xml" 83: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests 83: Test timeout computed to be: 1920 83: [==========] Running 1 test from 1 test suite. 83: [----------] Global test environment set-up. 83: [----------] 1 test from BasicPropagators/PeriodicActionsTest 83: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI processes 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: Using 1 OpenMP thread per MPI process 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.4%. 83: The balanceable part of the MD step is 56%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.3%. 83: 83: 83: NOTE: 46 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.026 0.013 198.1 83: (ns/day) (hour/ns) 83: Performance: 112.799 0.213 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: There were 3 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI processes 83: Using 1 OpenMP thread per MPI process 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 0.9%. 83: The balanceable part of the MD step is 51%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.5%. 83: 83: 83: NOTE: 46 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.016 0.008 197.5 83: (ns/day) (hour/ns) 83: Performance: 178.260 0.135 83: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: COM removal frequency is set to (1). 83: Other settings require a global communication frequency of 4. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 4. 83: 83: 83: There were 5 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI processes 83: Using 1 OpenMP thread per MPI process 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.0%. 83: The balanceable part of the MD step is 48%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.0%. 83: 83: 83: NOTE: 47 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.016 0.008 197.7 83: (ns/day) (hour/ns) 83: Performance: 181.755 0.132 83: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 83: Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: COM removal frequency is set to (1). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 4 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI processes 83: Using 1 OpenMP thread per MPI process 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 2.2%. 83: The balanceable part of the MD step is 46%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 1.0%. 83: 83: 83: NOTE: 48 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.024 0.012 198.1 83: (ns/day) (hour/ns) 83: Performance: 120.954 0.198 83: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: COM removal frequency is set to (1). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 4 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI processes 83: Using 1 OpenMP thread per MPI process 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.3%. 83: The balanceable part of the MD step is 47%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.6%. 83: 83: 83: NOTE: 47 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.018 0.009 197.0 83: (ns/day) (hour/ns) 83: Performance: 163.290 0.147 83: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 68.810 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: COM removal frequency is set to (1). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 4 NOTEs 83: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 83: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 2 MPI processes 83: Using 1 OpenMP thread per MPI process 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'Argon' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: 83: Dynamic load balancing report: 83: DLB was off during the run due to low measured imbalance. 83: Average load imbalance: 1.4%. 83: The balanceable part of the MD step is 48%, load imbalance is computed from this. 83: Part of the total run time spent waiting due to load imbalance: 0.7%. 83: 83: 83: NOTE: 48 % of the run time was spent communicating energies, 83: you might want to increase some nst* mdp options 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.022 0.011 197.9 83: (ns/day) (hour/ns) 83: Performance: 132.163 0.182 83: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 83: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (110 ms) 83: [----------] 1 test from BasicPropagators/PeriodicActionsTest (110 ms total) 83: 83: [----------] Global test environment tear-down 83: [==========] 1 test from 1 test suite ran. (218 ms total) 83: [ PASSED ] 1 test. 83/94 Test #83: MdrunCoordinationBasicTests2Ranks ............ Passed 0.70 sec test 84 Start 84: MdrunCoordinationCouplingTests1Rank 84: Test command: /usr/bin/mpiexec "-n" "1" "/build/reproducible-path/gromacs-2025.0/build/mpi/bin/mdrun-coordination-coupling-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/MdrunCoordinationCouplingTests1Rank.xml" 84: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests 84: Test timeout computed to be: 1920 84: [==========] Running 25 tests from 1 test suite. 84: [----------] Global test environment set-up. 84: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.015 0.015 99.6 84: (ns/day) (hour/ns) 84: Performance: 97.941 0.245 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.009 0.009 99.4 84: (ns/day) (hour/ns) 84: Performance: 171.104 0.140 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 4. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 4. 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.007 0.007 99.1 84: (ns/day) (hour/ns) 84: Performance: 200.410 0.120 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.009 0.009 99.4 84: (ns/day) (hour/ns) 84: Performance: 159.295 0.151 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.009 0.009 99.3 84: (ns/day) (hour/ns) 84: Performance: 162.240 0.148 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.010 0.010 99.2 84: (ns/day) (hour/ns) 84: Performance: 141.890 0.169 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (99 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.012 0.012 99.3 84: (ns/day) (hour/ns) 84: Performance: 123.086 0.195 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.007 0.007 99.1 84: (ns/day) (hour/ns) 84: Performance: 208.135 0.115 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.006 0.006 99.1 84: (ns/day) (hour/ns) 84: Performance: 227.337 0.106 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.009 0.009 99.1 84: (ns/day) (hour/ns) 84: Performance: 169.695 0.141 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.011 0.011 99.2 84: (ns/day) (hour/ns) 84: Performance: 134.776 0.178 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.010 0.010 99.3 84: (ns/day) (hour/ns) 84: Performance: 153.493 0.156 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (95 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.010 0.010 99.4 84: (ns/day) (hour/ns) 84: Performance: 146.625 0.164 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.007 0.007 98.9 84: (ns/day) (hour/ns) 84: Performance: 196.937 0.122 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.007 0.007 99.1 84: (ns/day) (hour/ns) 84: Performance: 206.766 0.116 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.009 0.009 99.1 84: (ns/day) (hour/ns) 84: Performance: 163.052 0.147 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.015 0.016 99.6 84: (ns/day) (hour/ns) 84: Performance: 94.691 0.253 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.010 0.010 99.0 84: (ns/day) (hour/ns) 84: Performance: 145.455 0.165 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (98 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.011 0.012 99.4 84: (ns/day) (hour/ns) 84: Performance: 127.285 0.189 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.007 0.008 99.0 84: (ns/day) (hour/ns) 84: Performance: 194.955 0.123 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.007 0.007 99.1 84: (ns/day) (hour/ns) 84: Performance: 199.831 0.120 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.026 0.026 99.7 84: (ns/day) (hour/ns) 84: Performance: 55.818 0.430 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.011 0.011 99.0 84: (ns/day) (hour/ns) 84: Performance: 130.626 0.184 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.011 0.011 99.4 84: (ns/day) (hour/ns) 84: Performance: 129.768 0.185 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (113 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.010 0.010 99.2 84: (ns/day) (hour/ns) 84: Performance: 150.574 0.159 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.009 0.009 99.3 84: (ns/day) (hour/ns) 84: Performance: 165.906 0.145 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.006 0.006 99.0 84: (ns/day) (hour/ns) 84: Performance: 233.276 0.103 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.010 0.010 99.4 84: (ns/day) (hour/ns) 84: Performance: 141.295 0.170 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.010 0.010 99.3 84: (ns/day) (hour/ns) 84: Performance: 152.392 0.157 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.017 0.017 99.6 84: (ns/day) (hour/ns) 84: Performance: 87.076 0.276 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (102 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.010 0.010 99.2 84: (ns/day) (hour/ns) 84: Performance: 146.392 0.164 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.007 0.007 99.0 84: (ns/day) (hour/ns) 84: Performance: 212.339 0.113 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.008 0.008 99.1 84: (ns/day) (hour/ns) 84: Performance: 187.709 0.128 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.011 0.011 99.3 84: (ns/day) (hour/ns) 84: Performance: 135.042 0.178 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.013 0.013 99.4 84: (ns/day) (hour/ns) 84: Performance: 111.542 0.215 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.010 0.010 99.2 84: (ns/day) (hour/ns) 84: Performance: 146.912 0.163 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (100 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.009 0.010 99.3 84: (ns/day) (hour/ns) 84: Performance: 154.130 0.156 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.007 0.007 99.0 84: (ns/day) (hour/ns) 84: Performance: 200.834 0.120 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.006 0.006 99.0 84: (ns/day) (hour/ns) 84: Performance: 233.586 0.103 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.009 0.009 99.2 84: (ns/day) (hour/ns) 84: Performance: 155.728 0.154 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.010 0.010 99.2 84: (ns/day) (hour/ns) 84: Performance: 150.688 0.159 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.011 0.011 99.2 84: (ns/day) (hour/ns) 84: Performance: 137.645 0.174 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (93 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.009 0.010 99.3 84: (ns/day) (hour/ns) 84: Performance: 154.598 0.155 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.006 0.006 99.0 84: (ns/day) (hour/ns) 84: Performance: 234.261 0.102 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.008 0.008 99.1 84: (ns/day) (hour/ns) 84: Performance: 193.529 0.124 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.009 0.009 99.3 84: (ns/day) (hour/ns) 84: Performance: 158.537 0.151 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.009 0.010 99.1 84: (ns/day) (hour/ns) 84: Performance: 154.509 0.155 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.008 0.008 98.9 84: (ns/day) (hour/ns) 84: Performance: 181.986 0.132 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (91 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.009 0.009 99.3 84: (ns/day) (hour/ns) 84: Performance: 155.308 0.155 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.006 0.007 99.0 84: (ns/day) (hour/ns) 84: Performance: 224.128 0.107 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.007 0.007 98.9 84: (ns/day) (hour/ns) 84: Performance: 208.191 0.115 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.010 0.010 99.2 84: (ns/day) (hour/ns) 84: Performance: 152.668 0.157 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.010 0.010 99.3 84: (ns/day) (hour/ns) 84: Performance: 144.829 0.166 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.244 0.244 100.0 84: (ns/day) (hour/ns) 84: Performance: 6.018 3.988 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (407 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.776 0.776 100.0 84: (ns/day) (hour/ns) 84: Performance: 1.893 12.681 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.574 0.574 100.0 84: (ns/day) (hour/ns) 84: Performance: 2.560 9.375 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.009 0.009 99.0 84: (ns/day) (hour/ns) 84: Performance: 170.427 0.141 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.012 0.012 99.0 84: (ns/day) (hour/ns) 84: Performance: 123.674 0.194 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.019 0.019 99.6 84: (ns/day) (hour/ns) 84: Performance: 77.592 0.309 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.025 0.025 99.7 84: (ns/day) (hour/ns) 84: Performance: 59.771 0.402 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (1620 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.010 0.010 99.3 84: (ns/day) (hour/ns) 84: Performance: 151.915 0.158 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.008 0.008 98.9 84: (ns/day) (hour/ns) 84: Performance: 177.749 0.135 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.007 0.008 99.0 84: (ns/day) (hour/ns) 84: Performance: 194.408 0.123 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.010 0.010 98.9 84: (ns/day) (hour/ns) 84: Performance: 149.189 0.161 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.008 0.009 99.2 84: (ns/day) (hour/ns) 84: Performance: 171.428 0.140 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.009 0.010 99.3 84: (ns/day) (hour/ns) 84: Performance: 153.876 0.156 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (94 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.010 0.010 99.0 84: (ns/day) (hour/ns) 84: Performance: 146.402 0.164 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.008 0.008 99.2 84: (ns/day) (hour/ns) 84: Performance: 177.339 0.135 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.007 0.007 99.1 84: (ns/day) (hour/ns) 84: Performance: 214.543 0.112 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.009 0.009 99.2 84: (ns/day) (hour/ns) 84: Performance: 167.149 0.144 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.009 0.009 99.2 84: (ns/day) (hour/ns) 84: Performance: 168.217 0.143 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 84: 1 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 3 NOTEs 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.010 0.010 99.1 84: (ns/day) (hour/ns) 84: Performance: 145.242 0.165 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (92 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.010 0.010 99.4 84: (ns/day) (hour/ns) 84: Performance: 143.070 0.168 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.007 0.007 99.2 84: (ns/day) (hour/ns) 84: Performance: 209.366 0.115 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 4. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 4. 84: 84: 84: There were 3 NOTEs 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.007 0.007 99.3 84: (ns/day) (hour/ns) 84: Performance: 199.708 0.120 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 3 NOTEs 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.021 0.021 99.7 84: (ns/day) (hour/ns) 84: Performance: 70.965 0.338 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.011 0.011 99.5 84: (ns/day) (hour/ns) 84: Performance: 137.695 0.174 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.009 0.009 99.4 84: (ns/day) (hour/ns) 84: Performance: 154.641 0.155 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (108 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.009 0.009 99.3 84: (ns/day) (hour/ns) 84: Performance: 157.222 0.153 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.007 0.007 99.2 84: (ns/day) (hour/ns) 84: Performance: 220.533 0.109 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.018 0.018 99.6 84: (ns/day) (hour/ns) 84: Performance: 81.384 0.295 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.019 0.020 99.6 84: (ns/day) (hour/ns) 84: Performance: 75.174 0.319 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.011 0.011 99.4 84: (ns/day) (hour/ns) 84: Performance: 134.276 0.179 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.010 0.010 99.3 84: (ns/day) (hour/ns) 84: Performance: 149.991 0.160 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (119 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.010 0.010 99.2 84: (ns/day) (hour/ns) 84: Performance: 145.999 0.164 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 2 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.008 0.008 99.1 84: (ns/day) (hour/ns) 84: Performance: 193.760 0.124 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 2 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.007 0.007 98.9 84: (ns/day) (hour/ns) 84: Performance: 198.160 0.121 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 2 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.010 0.010 99.3 84: (ns/day) (hour/ns) 84: Performance: 144.456 0.166 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.011 0.011 99.4 84: (ns/day) (hour/ns) 84: Performance: 132.978 0.180 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 2 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.015 0.015 99.5 84: (ns/day) (hour/ns) 84: Performance: 100.396 0.239 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (120 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 2 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.012 0.012 99.4 84: (ns/day) (hour/ns) 84: Performance: 119.172 0.201 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.007 0.007 99.0 84: (ns/day) (hour/ns) 84: Performance: 198.109 0.121 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.008 0.008 99.0 84: (ns/day) (hour/ns) 84: Performance: 182.352 0.132 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: There were 2 NOTEs 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.012 0.012 99.1 84: (ns/day) (hour/ns) 84: Performance: 118.341 0.203 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.012 0.012 99.3 84: (ns/day) (hour/ns) 84: Performance: 119.667 0.201 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 2 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.010 0.010 98.7 84: (ns/day) (hour/ns) 84: Performance: 144.884 0.166 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (126 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.010 0.011 97.0 84: (ns/day) (hour/ns) 84: Performance: 137.308 0.175 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.008 0.008 99.3 84: (ns/day) (hour/ns) 84: Performance: 187.076 0.128 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 4. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 4. 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.007 0.007 96.7 84: (ns/day) (hour/ns) 84: Performance: 214.632 0.112 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.011 0.011 99.6 84: (ns/day) (hour/ns) 84: Performance: 134.054 0.179 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.012 0.012 99.5 84: (ns/day) (hour/ns) 84: Performance: 117.789 0.204 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.012 0.012 99.5 84: (ns/day) (hour/ns) 84: Performance: 123.595 0.194 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (122 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.012 0.013 97.6 84: (ns/day) (hour/ns) 84: Performance: 116.764 0.206 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.009 0.009 99.4 84: (ns/day) (hour/ns) 84: Performance: 159.180 0.151 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.009 0.009 97.0 84: (ns/day) (hour/ns) 84: Performance: 161.666 0.148 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.011 0.011 97.2 84: (ns/day) (hour/ns) 84: Performance: 131.738 0.182 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.011 0.011 99.5 84: (ns/day) (hour/ns) 84: Performance: 133.170 0.180 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: 84: There was 1 WARNING 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.014 0.014 98.0 84: (ns/day) (hour/ns) 84: Performance: 104.300 0.230 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (122 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.013 0.013 99.6 84: (ns/day) (hour/ns) 84: Performance: 115.495 0.208 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.010 0.010 99.5 84: (ns/day) (hour/ns) 84: Performance: 147.538 0.163 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.009 0.009 99.3 84: (ns/day) (hour/ns) 84: Performance: 159.870 0.150 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 3 NOTEs 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.012 0.012 99.5 84: (ns/day) (hour/ns) 84: Performance: 124.105 0.193 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.012 0.012 99.6 84: (ns/day) (hour/ns) 84: Performance: 119.403 0.201 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.013 0.013 99.6 84: (ns/day) (hour/ns) 84: Performance: 109.248 0.220 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (124 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 2 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.012 0.012 99.5 84: (ns/day) (hour/ns) 84: Performance: 125.101 0.192 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: 84: There were 2 NOTEs 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.006 0.006 99.1 84: (ns/day) (hour/ns) 84: Performance: 228.593 0.105 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.007 0.007 99.2 84: (ns/day) (hour/ns) 84: Performance: 199.482 0.120 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.025 0.026 98.8 84: (ns/day) (hour/ns) 84: Performance: 57.593 0.417 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.021 0.021 99.7 84: (ns/day) (hour/ns) 84: Performance: 70.412 0.341 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.012 0.012 97.7 84: (ns/day) (hour/ns) 84: Performance: 122.878 0.195 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (140 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.013 0.013 97.1 84: (ns/day) (hour/ns) 84: Performance: 109.393 0.219 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.012 0.013 99.2 84: (ns/day) (hour/ns) 84: Performance: 117.302 0.205 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.012 0.012 99.2 84: (ns/day) (hour/ns) 84: Performance: 121.319 0.198 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.015 0.015 99.3 84: (ns/day) (hour/ns) 84: Performance: 96.226 0.249 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.016 0.016 97.4 84: (ns/day) (hour/ns) 84: Performance: 92.208 0.260 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: 84: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 84: The Berendsen barostat does not generate any strictly correct ensemble, 84: and should not be used for new production simulations (in our opinion). 84: We recommend using the C-rescale barostat instead. 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 2 NOTEs 84: 84: There was 1 WARNING 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.031 0.031 99.7 84: (ns/day) (hour/ns) 84: Performance: 46.710 0.514 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (168 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 2 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.051 0.051 99.2 84: (ns/day) (hour/ns) 84: Performance: 28.775 0.834 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.016 0.017 97.1 84: (ns/day) (hour/ns) 84: Performance: 88.690 0.271 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 2 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.011 0.011 96.5 84: (ns/day) (hour/ns) 84: Performance: 128.474 0.187 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.014 0.014 99.5 84: (ns/day) (hour/ns) 84: Performance: 103.046 0.233 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.016 0.016 97.4 84: (ns/day) (hour/ns) 84: Performance: 90.371 0.266 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 2 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.022 0.023 99.6 84: (ns/day) (hour/ns) 84: Performance: 65.225 0.368 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (200 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.014 0.014 97.6 84: (ns/day) (hour/ns) 84: Performance: 104.228 0.230 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 2 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.011 0.011 97.2 84: (ns/day) (hour/ns) 84: Performance: 134.244 0.179 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.010 0.010 99.3 84: (ns/day) (hour/ns) 84: Performance: 143.313 0.167 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.010 0.010 97.0 84: (ns/day) (hour/ns) 84: Performance: 140.141 0.171 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.012 0.013 97.8 84: (ns/day) (hour/ns) 84: Performance: 115.962 0.207 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 3 NOTEs 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.012 0.013 97.4 84: (ns/day) (hour/ns) 84: Performance: 115.456 0.208 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 (124 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: MTTK coupling is deprecated and will soon be removed 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: for current Trotter decomposition methods with vv, nsttcouple and 84: nstpcouple must be equal. Both have been reset to 84: min(nsttcouple,nstpcouple) = 2 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 4 NOTEs 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.012 0.012 97.2 84: (ns/day) (hour/ns) 84: Performance: 119.426 0.201 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: MTTK coupling is deprecated and will soon be removed 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: for current Trotter decomposition methods with vv, nsttcouple and 84: nstpcouple must be equal. Both have been reset to 84: min(nsttcouple,nstpcouple) = 2 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 4 NOTEs 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.010 0.010 96.8 84: (ns/day) (hour/ns) 84: Performance: 145.034 0.165 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: MTTK coupling is deprecated and will soon be removed 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: for current Trotter decomposition methods with vv, nsttcouple and 84: nstpcouple must be equal. Both have been reset to 84: min(nsttcouple,nstpcouple) = 2 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 5 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.011 0.011 96.6 84: (ns/day) (hour/ns) 84: Performance: 135.003 0.178 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: MTTK coupling is deprecated and will soon be removed 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: for current Trotter decomposition methods with vv, nsttcouple and 84: nstpcouple must be equal. Both have been reset to 84: min(nsttcouple,nstpcouple) = 2 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 5 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.012 0.012 99.1 84: (ns/day) (hour/ns) 84: Performance: 121.597 0.197 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: MTTK coupling is deprecated and will soon be removed 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: for current Trotter decomposition methods with vv, nsttcouple and 84: nstpcouple must be equal. Both have been reset to 84: min(nsttcouple,nstpcouple) = 2 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 5 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.016 0.017 97.6 84: (ns/day) (hour/ns) 84: Performance: 87.221 0.275 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: MTTK coupling is deprecated and will soon be removed 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: for current Trotter decomposition methods with vv, nsttcouple and 84: nstpcouple must be equal. Both have been reset to 84: min(nsttcouple,nstpcouple) = 2 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 5 NOTEs 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.054 0.055 99.4 84: (ns/day) (hour/ns) 84: Performance: 26.889 0.893 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 (173 ms) 84: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There were 2 NOTEs 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.018 0.018 99.6 84: (ns/day) (hour/ns) 84: Performance: 83.511 0.287 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 2 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.009 0.010 96.9 84: (ns/day) (hour/ns) 84: Performance: 153.658 0.156 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 2 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.014 0.014 99.5 84: (ns/day) (hour/ns) 84: Performance: 107.241 0.224 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 2 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.013 0.013 97.5 84: (ns/day) (hour/ns) 84: Performance: 109.279 0.220 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 2 NOTEs 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.011 0.011 97.1 84: (ns/day) (hour/ns) 84: Performance: 128.646 0.187 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: There were 2 NOTEs 84: 84: This run will generate roughly 0 Mb of data 84: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 84: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI process 84: Using 1 OpenMP thread 84: 84: 84: NOTE: Thread affinity was not set. 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.012 0.012 99.3 84: (ns/day) (hour/ns) 84: Performance: 120.515 0.199 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 84: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 (129 ms) 84: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest (4790 ms total) 84: 84: [----------] Global test environment tear-down 84: [==========] 25 tests from 1 test suite ran. (4877 ms total) 84: [ PASSED ] 25 tests. 84/94 Test #84: MdrunCoordinationCouplingTests1Rank .......... Passed 5.36 sec test 85 Start 85: MdrunCoordinationCouplingTests2Ranks 85: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2025.0/build/mpi/bin/mdrun-coordination-coupling-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/MdrunCoordinationCouplingTests2Ranks.xml" 85: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests 85: Test timeout computed to be: 1920 85: [==========] Running 25 tests from 1 test suite. 85: [----------] Global test environment set-up. 85: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 6.3%. 85: The balanceable part of the MD step is 55%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 3.4%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: 85: NOTE: 48 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.052 0.026 199.3 85: (ns/day) (hour/ns) 85: Performance: 56.073 0.428 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 7.5%. 85: The balanceable part of the MD step is 47%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 3.5%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: 85: NOTE: 49 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.054 0.027 199.1 85: (ns/day) (hour/ns) 85: Performance: 54.519 0.440 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 4. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 4. 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 26.6%. 85: The balanceable part of the MD step is 34%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 9.1%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: NOTE: 9.1 % of the available CPU time was lost due to load imbalance 85: in the domain decomposition. 85: You can consider manually changing the decomposition (option -dd); 85: e.g. by using fewer domains along the box dimension in which there is 85: considerable inhomogeneity in the simulated system. 85: 85: NOTE: 46 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.022 0.011 198.5 85: (ns/day) (hour/ns) 85: Performance: 132.506 0.181 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple rOpened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 anks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 13.1%. 85: The balanceable part of the MD step is 36%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 4.7%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: 85: NOTE: 47 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.026 0.013 198.7 85: (ns/day) (hour/ns) 85: Performance: 113.503 0.211 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 11.4%. 85: The balanceable part of the MD step is 38%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 4.4%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: 85: NOTE: 46 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.017 0.009 197.6 85: (ns/day) (hour/ns) 85: Performance: 167.617 0.143 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 14.6%. 85: The balanceable part of the MD step is 34%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 4.9%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: 85: NOTE: 46 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.018 0.009 198.0 85: (ns/day) (hour/ns) 85: Performance: 159.628 0.150 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (145 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 5.6%. 85: The balanceable part of the MD step is 49%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 2.8%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: 85: NOTE: 45 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.021 0.010 198.0 85: (ns/day) (hour/ns) 85: Performance: 141.817 0.169 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 5.8%. 85: The balanceable part of the MD step is 49%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 2.8%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: 85: NOTE: 43 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.015 0.008 191.9 85: (ns/day) (hour/ns) 85: Performance: 189.755 0.126 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 85: Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 3 time 0.003 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 7 time 0.007 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 7 time 0.007 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 8 time 0.008 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 8 time 0.008 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 9 time 0.009 Last energy frame read 16 time 0.016 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 9.4%. 85: The balanceable part of the MD step is 43%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 4.0%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: 85: NOTE: 46 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.015 0.008 197.6 85: (ns/day) (hour/ns) 85: Performance: 192.305 0.125 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_Peri Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 odicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 85: Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 85: Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 11.3%. 85: The balanceable part of the MD step is 43%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 4.9%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: 85: NOTE: 47 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.019 0.009 197.7 85: (ns/day) (hour/ns) 85: Performance: 155.009 0.155 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: This run will generate roughly 0 Mb of data 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 16.1%. 85: The balanceable part of the MD step is 41%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 6.6%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: NOTE: 6.6 % of the available CPU time was lost due to load imbalance 85: in the domain decomposition. 85: You can consider manually changing the decomposition (option -dd); 85: e.g. by using fewer domains along the box dimension in which there is 85: considerable inhomogeneity in the simulated system. 85: 85: NOTE: 46 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.021 0.011 196.5 85: (ns/day) (hour/ns) 85: Performance: 136.349 0.176 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 12.5%. 85: The balanceable part of the MD step is 41%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 5.1%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: NOTE: 5.1 % of the available CPU time was lost due to load imbalance 85: in the domain decomposition. 85: You can consider manually changing the decomposition (option -dd); 85: e.g. by using fewer domains along the box dimension in which there is 85: considerable inhomogeneity in the simulated system. 85: 85: NOTE: 46 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.019 0.010 193.5 85: (ns/day) (hour/ns) 85: Performance: 151.621 0.158 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (108 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 13.1%. 85: The balanceable part of the MD step is 47%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 6.2%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: NOTE: 6.2 % of the available CPU time was lost due to load imbalance 85: in the domain decomposition. 85: You can consider manually changing the decomposition (option -dd); 85: e.g. by using fewer domains along the box dimension in which there is 85: considerable inhomogeneity in the simulated system. 85: 85: NOTE: 44 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.024 0.012 196.9 85: (ns/day) (hour/ns) 85: Performance: 121.885 0.197 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 6.5%. 85: The balanceable part of the MD step is 31%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 2.0%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: 85: NOTE: 42 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.021 0.011 196.8 85: (ns/day) (hour/ns) 85: Performance: 139.020 0.173 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 85: Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 85: Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 0 time 0.000 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 0 time 0.000 Last energy frame read 16 time 0.016 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 16.6%. 85: The balanceable part of the MD step is 42%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 6.9%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: NOTE: 6.9 % of the available CPU time was lost due to load imbalance 85: in the domain decomposition. 85: You can consider manually changing the decomposition (option -dd); 85: e.g. by using fewer domains along the box dimension in which there is 85: considerable inhomogeneity in the simulated system. 85: 85: NOTE: 46 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.017 0.008 197.7 85: (ns/day) (hour/ns) 85: Performance: 172.931 0.139 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 3 time 0.003 Reading energy frame 2 time 0.008 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 2 time 0.008 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: There were 3 NOTEs 85: 85: This run will generate roughly 0 Mb of data 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 15.6%. 85: The balanceable part of the MD step is 12%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.8%. 85: 85: 85: NOTE: 46 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.039 0.020 195.4 85: (ns/day) (hour/ns) 85: Performance: 74.534 0.322 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 20.0%. 85: The balanceable part of the MD step is 38%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 7.6%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: NOTE: 7.6 % of the available CPU time was lost due to load imbalance 85: in the domain decomposition. 85: You can consider manually changing the decomposition (option -dd); 85: e.g. by using fewer domains along the box dimension in which there is 85: considerable inhomogeneity in the simulated system. 85: 85: NOTE: 45 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.020 0.010 196.6 85: (ns/day) (hour/ns) 85: Performance: 144.156 0.166 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 23.6%. 85: The balanceable part of the MD step is 40%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 9.4%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: NOTE: 9.4 % of the available CPU time was lost due to load imbalance 85: in the domain decomposition. 85: You can consider manually changing the decomposition (option -dd); 85: e.g. by using fewer domains along the box dimension in which there is 85: considerable inhomogeneity in the simulated system. 85: 85: NOTE: 45 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.023 0.011 197.8 85: (ns/day) (hour/ns) 85: Performance: 128.810 0.186 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (143 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: There were 3 NOTEs 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 8.0%. 85: The balanceable part of the MD step is 49%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 3.9%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: 85: NOTE: 44 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.025 0.013 196.3 85: (ns/day) (hour/ns) 85: Performance: 117.412 0.204 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 13.6%. 85: The balanceable part of the MD step is 41%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 5.6%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: NOTE: 5.6 % of the available CPU time was lost due to load imbalance 85: in the domain decomposition. 85: You can consider manually changing the decomposition (option -dd); 85: e.g. by using fewer domains along the box dimension in which there is 85: considerable inhomogeneity in the simulated system. 85: 85: NOTE: 44 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.022 0.011 196.4 85: (ns/day) (hour/ns) 85: Performance: 132.284 0.181 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_Peri Reading energy frame 1 time 0.001 odicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 85: Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 85: Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: There were 3 NOTEs 85: 85: This run will generate roughly 0 Mb of data 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 15.8%. 85: The balanceable part of the MD step is 43%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 6.8%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: NOTE: 6.8 % of the available CPU time was lost due to load imbalance 85: in the domain decomposition. 85: You can consider manually changing the decomposition (option -dd); 85: e.g. by using fewer domains along the box dimension in which there is 85: considerable inhomogeneity in the simulated system. 85: 85: NOTE: 46 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.023 0.012 198.3 85: (ns/day) (hour/ns) 85: Performance: 127.041 0.189 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 85: Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 85: Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 0 time 0.000 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 11.0%. 85: The balanceable part of the MD step is 44%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 4.8%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: 85: NOTE: 48 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.023 0.012 196.2 85: (ns/day) (hour/ns) 85: Performance: 125.696 0.191 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 10.6%. 85: The balanceable part of the MD step is 44%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 4.7%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: 85: NOTE: 49 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.033 0.017 197.5 85: (ns/day) (hour/ns) 85: Performance: 87.278 0.275 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 10.4%. 85: The balanceable part of the MD step is 45%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 4.6%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: 85: NOTE: 49 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.047 0.024 199.1 85: (ns/day) (hour/ns) 85: Performance: 62.277 0.385 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (147 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 46 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.026 0.013 196.6 85: (ns/day) (hour/ns) 85: Performance: 110.287 0.218 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 48 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.021 0.011 195.4 85: (ns/day) (hour/ns) 85: Performance: 134.821 0.178 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 85: Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 85: Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Last energy frame read 16 time 0.016 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: 85: This run will generate roughly 0 Mb of data 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 48 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.022 0.011 196.9 85: (ns/day) (hour/ns) 85: Performance: 133.531 0.180 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 49 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.029 0.015 198.6 85: (ns/day) (hour/ns) 85: Performance: 100.045 0.240 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 48 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.032 0.016 197.8 85: (ns/day) (hour/ns) 85: Performance: 89.480 0.268 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 49 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.031 0.015 198.5 85: (ns/day) (hour/ns) 85: Performance: 94.900 0.253 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (143 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 48 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.033 0.017 197.8 85: (ns/day) (hour/ns) 85: Performance: 86.894 0.276 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 47 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.016 0.008 196.7 85: (ns/day) (hour/ns) 85: Performance: 185.460 0.129 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 85: Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 0 time 0.000 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 0 time 0.000 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Last energy frame read 16 time 0.016 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 47 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.019 0.010 197.1 85: (ns/day) (hour/ns) 85: Performance: 152.849 0.157 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 85: Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 85: Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 48 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.020 0.010 197.4 85: (ns/day) (hour/ns) 85: Performance: 143.497 0.167 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 48 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.032 0.016 197.2 85: (ns/day) (hour/ns) 85: Performance: 91.080 0.264 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 48 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.024 0.012 197.7 85: (ns/day) (hour/ns) 85: Performance: 119.049 0.202 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (126 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 46 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.025 0.013 197.1 85: (ns/day) (hour/ns) 85: Performance: 113.939 0.211 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 46 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.020 0.010 195.9 85: (ns/day) (hour/ns) 85: Performance: 142.013 0.169 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 85: Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 85: Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 15 time 0.015 Reading energy frame 5 time 0.005 Reading energy frame 15 time 0.015 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Last energy frame read 16 time 0.016 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 48 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.020 0.010 197.8 85: (ns/day) (hour/ns) 85: Performance: 142.696 0.168 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_Peri Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 odicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 85: Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 0 time 0.000 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 16 time 0.016 Reading energy frame 3 time 0.012 Last energy frame read 4 time 0.016 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 49 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.032 0.016 198.5 85: (ns/day) (hour/ns) 85: Performance: 91.560 0.262 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 48 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.025 0.013 196.7 85: (ns/day) (hour/ns) 85: Performance: 116.252 0.206 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 48 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.025 0.013 198.2 85: (ns/day) (hour/ns) 85: Performance: 117.113 0.205 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (136 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 50 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.245 0.123 199.8 85: (ns/day) (hour/ns) 85: Performance: 11.962 2.006 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 49 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.076 0.038 198.7 85: (ns/day) (hour/ns) 85: Performance: 38.288 0.627 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 2 time 0.002 Reading energy frame 4 time 0.004 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 6 time 0.006 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 6 time 0.006 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 7 time 0.007 Reading energy frame 14 time 0.014 Reading energy frame 7 time 0.007 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Last energy frame read 16 time 0.016 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 48 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.019 0.010 197.8 85: (ns/day) (hour/ns) 85: Performance: 150.506 0.159 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 85: Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 85: Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 48 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.028 0.014 198.3 85: (ns/day) (hour/ns) 85: Performance: 104.503 0.230 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 48 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.028 0.014 198.4 85: (ns/day) (hour/ns) 85: Performance: 105.864 0.227 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: There were 2 NOTEs 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 48 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.024 0.012 195.1 85: (ns/day) (hour/ns) 85: Performance: 119.645 0.201 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (264 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 48 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.048 0.024 198.5 85: (ns/day) (hour/ns) 85: Performance: 60.209 0.399 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 48 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.028 0.014 198.7 85: (ns/day) (hour/ns) 85: Performance: 103.954 0.231 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 0 time 0.000 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 0 time 0.000 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 2 time 0.002 Reading energy frame 7 time 0.007 Reading energy frame 2 time 0.002 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 6 time 0.006 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 8 time 0.008 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 9 time 0.009 Last energy frame read 16 time 0.016 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 49 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.026 0.013 197.0 85: (ns/day) (hour/ns) 85: Performance: 111.138 0.216 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 85: Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 12 time 0.012 Last energy frame read 4 time 0.016 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 48 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.038 0.019 197.1 85: (ns/day) (hour/ns) 85: Performance: 76.335 0.314 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 49 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.024 0.012 198.4 85: (ns/day) (hour/ns) 85: Performance: 119.810 0.200 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 48 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.030 0.016 196.0 85: (ns/day) (hour/ns) 85: Performance: 94.657 0.254 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (154 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: This run will generate roughly 0 Mb of data 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 43 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.029 0.014 197.2 85: (ns/day) (hour/ns) 85: Performance: 101.605 0.236 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 46 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.018 0.009 195.8 85: (ns/day) (hour/ns) 85: Performance: 163.216 0.147 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 85: Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 85: Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Last energy frame read 16 time 0.016 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: 85: This run will generate roughly 0 Mb of data 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 47 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.019 0.010 195.8 85: (ns/day) (hour/ns) 85: Performance: 153.508 0.156 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 85: Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 0 time 0.000 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: This run will generate roughly 0 Mb of data 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 48 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.025 0.013 195.4 85: (ns/day) (hour/ns) 85: Performance: 115.854 0.207 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 48 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.026 0.013 196.8 85: (ns/day) (hour/ns) 85: Performance: 113.103 0.212 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 48 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.029 0.015 197.4 85: (ns/day) (hour/ns) 85: Performance: 98.655 0.243 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (130 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 48 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.038 0.019 198.7 85: (ns/day) (hour/ns) 85: Performance: 77.512 0.310 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 46 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.021 0.011 195.9 85: (ns/day) (hour/ns) 85: Performance: 139.315 0.172 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 85: Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 1 time 0.001 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 48 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.024 0.012 196.3 85: (ns/day) (hour/ns) 85: Performance: 122.126 0.197 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 85: Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 85: Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 0 time 0.000 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 0 time 0.000 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 10 time 0.010 Reading energy frame 4 time 0.004 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 48 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.023 0.012 198.2 85: (ns/day) (hour/ns) 85: Performance: 125.954 0.191 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 48 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.023 0.012 195.6 85: (ns/day) (hour/ns) 85: Performance: 123.164 0.195 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: There were 3 NOTEs 85: 85: This run will generate roughly 0 Mb of data 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 48 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.028 0.014 196.6 85: (ns/day) (hour/ns) 85: Performance: 101.336 0.237 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (136 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 47 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.029 0.015 198.3 85: (ns/day) (hour/ns) 85: Performance: 99.211 0.242 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: There were 3 NOTEs 85: 85: This run will generate roughly 0 Mb of data 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 43 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.031 0.016 192.8 85: (ns/day) (hour/ns) 85: Performance: 89.961 0.267 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 85: Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 1 time 0.001 Reading energy frame 4 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 5 time 0.005 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 15 time 0.015 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Last energy frame read 16 time 0.016 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 49 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.048 0.024 197.5 85: (ns/day) (hour/ns) 85: Performance: 60.521 0.397 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 85: Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 85: Last energy frame read 4 time 0.016 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 48 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.031 0.016 198.3 85: (ns/day) (hour/ns) 85: Performance: 92.769 0.259 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 3 NOTEs 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 49 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.024 0.012 197.5 85: (ns/day) (hour/ns) 85: Performance: 123.081 0.195 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 85: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 85: 1 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 49 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.024 0.012 197.7 85: (ns/day) (hour/ns) 85: Performance: 122.124 0.197 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (152 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 46 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.021 0.011 196.3 85: (ns/day) (hour/ns) 85: Performance: 136.860 0.175 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 46 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.019 0.009 197.5 85: (ns/day) (hour/ns) 85: Performance: 155.331 0.155 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 85: Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 0 time 0.000 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 9 time 0.009 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 12 time 0.012 Last energy frame read 16 time 0.016 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 4. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 4. 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 47 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.022 0.011 196.7 85: (ns/day) (hour/ns) 85: Performance: 131.992 0.182 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 16 time 0.016 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 48 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.025 0.013 198.3 85: (ns/day) (hour/ns) 85: Performance: 115.274 0.208 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 3 NOTEs 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 48 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.025 0.012 198.6 85: (ns/day) (hour/ns) 85: Performance: 118.537 0.202 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 47 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.025 0.013 197.4 85: (ns/day) (hour/ns) 85: Performance: 114.224 0.210 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (121 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 46 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.024 0.012 197.1 85: (ns/day) (hour/ns) 85: Performance: 119.769 0.200 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 46 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.023 0.011 196.6 85: (ns/day) (hour/ns) 85: Performance: 128.205 0.187 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 85: Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_Peri Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 odicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 85: Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 9 time 0.009 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 10 time 0.010 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 10 time 0.010 Reading energy frame 5 time 0.005 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 47 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.021 0.011 195.3 85: (ns/day) (hour/ns) 85: Performance: 136.053 0.176 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 85: Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 85: Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 0 time 0.000 Last energy frame read 4 time 0.016 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 48 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.027 0.014 196.4 85: (ns/day) (hour/ns) 85: Performance: 106.298 0.226 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 48 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.027 0.014 195.7 85: (ns/day) (hour/ns) 85: Performance: 105.370 0.228 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 48 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.023 0.011 196.6 85: (ns/day) (hour/ns) 85: Performance: 127.901 0.188 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (136 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 49 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.115 0.058 198.8 85: (ns/day) (hour/ns) 85: Performance: 25.404 0.945 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 47 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.020 0.010 197.6 85: (ns/day) (hour/ns) 85: Performance: 147.487 0.163 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 85: Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 85: Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: There were 2 NOTEs 85: 85: This run will generate roughly 0 Mb of data 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 48 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.020 0.010 195.6 85: (ns/day) (hour/ns) 85: Performance: 146.599 0.164 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 85: Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: There were 2 NOTEs 85: 85: This run will generate roughly 0 Mb of data 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 48 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.026 0.013 196.6 85: (ns/day) (hour/ns) 85: Performance: 112.628 0.213 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 48 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.025 0.012 198.5 85: (ns/day) (hour/ns) 85: Performance: 117.728 0.204 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 49 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.026 0.013 198.0 85: (ns/day) (hour/ns) 85: Performance: 111.863 0.215 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (172 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 47 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.032 0.016 198.6 85: (ns/day) (hour/ns) 85: Performance: 92.411 0.260 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 47 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.021 0.011 197.7 85: (ns/day) (hour/ns) 85: Performance: 137.212 0.175 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 8 time 0.008 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 10 time 0.010 Reading energy frame 12 time 0.012 Reading energy frame 10 time 0.010 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 11 time 0.011 Reading energy frame 13 time 0.013 Reading energy frame 11 time 0.011 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 12 time 0.012 Reading energy frame 15 time 0.015 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 15 time 0.015 Reading energy frame 13 time 0.013 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 14 time 0.014 Last energy frame read 16 time 0.016 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 48 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.021 0.010 198.0 85: (ns/day) (hour/ns) 85: Performance: 140.836 0.170 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 85: Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 85: Last energy frame read 4 time 0.016 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: There were 2 NOTEs 85: 85: This run will generate roughly 0 Mb of data 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 48 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.032 0.016 197.3 85: (ns/day) (hour/ns) 85: Performance: 90.336 0.266 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: There were 2 NOTEs 85: 85: This run will generate roughly 0 Mb of data 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 48 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.035 0.018 197.6 85: (ns/day) (hour/ns) 85: Performance: 83.370 0.288 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: There were 2 NOTEs 85: 85: This run will generate roughly 0 Mb of data 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: NOTE: 48 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.026 0.013 194.8 85: (ns/day) (hour/ns) 85: Performance: 111.383 0.215 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (140 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: There were 3 NOTEs 85: 85: This run will generate roughly 0 Mb of data 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.3%. 85: The balanceable part of the MD step is 59%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.4%. 85: 85: 85: NOTE: 45 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.029 0.015 196.7 85: (ns/day) (hour/ns) 85: Performance: 99.769 0.241 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.3%. 85: The balanceable part of the MD step is 57%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.3%. 85: 85: 85: NOTE: 44 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.021 0.011 192.8 85: (ns/day) (hour/ns) 85: Performance: 134.437 0.179 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 85: Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 85: Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 9 time 0.009 Reading energy frame 2 time 0.002 Reading energy frame 10 time 0.010 Reading energy frame 2 time 0.002 Reading energy frame 10 time 0.010 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 6 time 0.006 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Last energy frame read 16 time 0.016 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 4. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 4. 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 14.3%. 85: The balanceable part of the MD step is 45%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 6.4%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: NOTE: 6.4 % of the available CPU time was lost due to load imbalance 85: in the domain decomposition. 85: You can consider manually changing the decomposition (option -dd); 85: e.g. by using fewer domains along the box dimension in which there is 85: considerable inhomogeneity in the simulated system. 85: 85: NOTE: 44 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.022 0.011 195.9 85: (ns/day) (hour/ns) 85: Performance: 133.248 0.180 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 85: Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 0 time 0.000 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 0 time 0.000 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 1 time 0.004 Reading energy frame 16 time 0.016 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Last energy frame read 4 time 0.016 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 11.7%. 85: The balanceable part of the MD step is 41%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 4.8%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: 85: NOTE: 47 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.038 0.019 197.8 85: (ns/day) (hour/ns) 85: Performance: 75.612 0.317 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 4 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 14.9%. 85: The balanceable part of the MD step is 36%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 5.4%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: NOTE: 5.4 % of the available CPU time was lost due to load imbalance 85: in the domain decomposition. 85: You can consider manually changing the decomposition (option -dd); 85: e.g. by using fewer domains along the box dimension in which there is 85: considerable inhomogeneity in the simulated system. 85: 85: NOTE: 46 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.034 0.017 197.4 85: (ns/day) (hour/ns) 85: Performance: 86.071 0.279 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 100. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 100. 85: 85: 85: There were 4 NOTEs 85: 85: This run will generate roughly 0 Mb of data 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 9.6%. 85: The balanceable part of the MD step is 39%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 3.8%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: 85: NOTE: 46 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.027 0.014 197.0 85: (ns/day) (hour/ns) 85: Performance: 106.729 0.225 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (139 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 4.2%. 85: The balanceable part of the MD step is 57%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 2.4%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: 85: NOTE: 44 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.031 0.016 197.0 85: (ns/day) (hour/ns) 85: Performance: 94.521 0.254 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 3.3%. 85: The balanceable part of the MD step is 55%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.8%. 85: 85: 85: NOTE: 45 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.027 0.014 196.9 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 85: (ns/day) (hour/ns) 85: Performance: 107.137 0.224 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 85: Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_Peri Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 odicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 85: Reading energy frame 13 time 0.013 Reading energy frame 0 time 0.000 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 5.3%. 85: The balanceable part of the MD step is 52%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 2.8%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: 85: NOTE: 46 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.027 0.014 194.2 85: (ns/day) (hour/ns) 85: Performance: 105.887 0.227 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 85: Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 3.2%. 85: The balanceable part of the MD step is 53%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.7%. 85: 85: 85: NOTE: 46 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.034 0.018 195.0 85: (ns/day) (hour/ns) 85: Performance: 83.517 0.287 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 10.8%. 85: The balanceable part of the MD step is 46%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 4.9%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 85: 85: NOTE: 47 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.050 0.025 198.2 85: (ns/day) (hour/ns) 85: Performance: 58.762 0.408 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 6.8%. 85: The balanceable part of the MD step is 51%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 3.5%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: 85: NOTE: 47 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.042 0.021 196.4 85: (ns/day) (hour/ns) 85: Performance: 68.855 0.349 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (165 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 2.5%. 85: The balanceable part of the MD step is 59%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.5%. 85: 85: 85: NOTE: 45 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.031 0.016 195.1 85: (ns/day) (hour/ns) 85: Performance: 92.122 0.261 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was off during the run due to low measured imbalance. 85: Average load imbalance: 3.4%. 85: The balanceable part of the MD step is 54%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 1.8%. 85: 85: 85: NOTE: 44 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.024 0.013 193.4 85: (ns/day) (hour/ns) 85: Performance: 117.112 0.205 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 85: Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 85: Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 7.9%. 85: The balanceable part of the MD step is 51%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 4.0%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: 85: NOTE: 46 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.033 0.017 197.6 85: (ns/day) (hour/ns) 85: Performance: 89.010 0.270 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_Peri Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 odicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 85: Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 85: Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 0 time 0.000 Reading energy frame 15 time 0.015 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: There were 3 NOTEs 85: 85: This run will generate roughly 0 Mb of data 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 3.9%. 85: The balanceable part of the MD step is 52%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 2.0%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: 85: NOTE: 48 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.061 0.030 198.5 85: (ns/day) (hour/ns) 85: Performance: 48.176 0.498 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 6.0%. 85: The balanceable part of the MD step is 49%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 2.9%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: 85: NOTE: 46 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.033 0.017 195.2 85: (ns/day) (hour/ns) 85: Performance: 87.858 0.273 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 85: NVE simulation: will use the initial temperature of 68.810 K for 85: determining the Verlet buffer size 85: 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: 85: Dynamic load balancing report: 85: DLB was turned on during the run due to measured imbalance. 85: Average load imbalance: 7.4%. 85: The balanceable part of the MD step is 51%, load imbalance is computed from this. 85: Part of the total run time spent waiting due to load imbalance: 3.8%. 85: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 85: 85: 85: NOTE: 46 % of the run time was spent communicating energies, 85: you might want to increase some nst* mdp options 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.031 0.016 195.0 85: (ns/day) (hour/ns) 85: Performance: 91.583 0.262 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (161 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.036 0.018 195.1 85: (ns/day) (hour/ns) 85: Performance: 79.476 0.302 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: There were 2 NOTEs 85: 85: This run will generate roughly 0 Mb of data 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.024 0.012 193.2 85: (ns/day) (hour/ns) 85: Performance: 119.300 0.201 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 6 time 0.006 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 4 time 0.004 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 4 time 0.004 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 6 time 0.006 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.023 0.012 192.4 85: (ns/day) (hour/ns) 85: Performance: 123.136 0.195 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 85: Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_Peri Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 odicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: This run will generate roughly 0 Mb of data 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.030 0.015 196.7 85: (ns/day) (hour/ns) 85: Performance: 97.234 0.247 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.045 0.023 197.8 85: (ns/day) (hour/ns) 85: Performance: 64.270 0.373 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.038 0.019 195.5 85: (ns/day) (hour/ns) 85: Performance: 75.999 0.316 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (157 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.038 0.019 197.1 85: (ns/day) (hour/ns) 85: Performance: 76.803 0.312 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.030 0.015 194.4 85: (ns/day) (hour/ns) 85: Performance: 96.150 0.250 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.002 Reading energy frame 5 time 0.005 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 5 time 0.005 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: 85: This run will generate roughly 0 Mb of data 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.027 0.014 193.6 85: (ns/day) (hour/ns) 85: Performance: 104.384 0.230 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 1 time 0.004 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 10 time 0.010 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Last energy frame read 4 time 0.016 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.038 0.019 197.5 85: (ns/day) (hour/ns) 85: Performance: 76.402 0.314 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.041 0.021 195.4 85: (ns/day) (hour/ns) 85: Performance: 70.031 0.343 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 85: The Berendsen barostat does not generate any strictly correct ensemble, 85: and should not be used for new production simulations (in our opinion). 85: We recommend using the C-rescale barostat instead. 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.026 0.013 193.7 85: (ns/day) (hour/ns) 85: Performance: 110.606 0.217 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (153 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: There were 2 NOTEs 85: 85: This run will generate roughly 0 Mb of data 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.032 0.016 194.3 85: (ns/day) (hour/ns) 85: Performance: 90.187 0.266 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.028 0.014 196.5 85: (ns/day) (hour/ns) 85: Performance: 103.532 0.232 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 9 time 0.009 Reading energy frame 6 time 0.006 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: There were 2 NOTEs 85: 85: This run will generate roughly 0 Mb of data 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.032 0.016 197.0 85: (ns/day) (hour/ns) 85: Performance: 89.579 0.268 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_Peri Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 odicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 85: Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 10 time 0.010 Reading energy frame 1 time 0.004 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Last energy frame read 4 time 0.016 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: There were 2 NOTEs 85: 85: This run will generate roughly 0 Mb of data 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.035 0.018 196.9 85: (ns/day) (hour/ns) 85: Performance: 82.574 0.291 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.051 0.026 197.5 85: (ns/day) (hour/ns) 85: Performance: 56.704 0.423 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.036 0.018 197.0 85: (ns/day) (hour/ns) 85: Performance: 81.378 0.295 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (168 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.034 0.017 196.7 85: (ns/day) (hour/ns) 85: Performance: 84.831 0.283 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: There were 2 NOTEs 85: 85: This run will generate roughly 0 Mb of data 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.030 0.015 195.7 85: (ns/day) (hour/ns) 85: Performance: 96.900 0.248 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 0 time 0.000 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 0 time 0.000 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 2 time 0.002 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 10 time 0.010 Reading energy frame 3 time 0.003 Reading energy frame 11 time 0.011 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 5 time 0.005 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 5 time 0.005 Reading energy frame 13 time 0.013 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 8 time 0.008 Last energy frame read 16 time 0.016 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.033 0.017 196.9 85: (ns/day) (hour/ns) 85: Performance: 86.444 0.278 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 85: Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 0 time 0.000 Last energy frame read 4 time 0.016 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.033 0.017 196.7 85: (ns/day) (hour/ns) 85: Performance: 88.223 0.272 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: 85: This run will generate roughly 0 Mb of data 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.033 0.017 196.7 85: (ns/day) (hour/ns) 85: Performance: 88.059 0.273 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 3 NOTEs 85: 85: This run will generate roughly 0 Mb of data 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.031 0.016 196.0 85: (ns/day) (hour/ns) 85: Performance: 92.729 0.259 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 (157 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: MTTK coupling is deprecated and will soon be removed 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: for current Trotter decomposition methods with vv, nsttcouple and 85: nstpcouple must be equal. Both have been reset to 85: min(nsttcouple,nstpcouple) = 2 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 4 NOTEs 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.031 0.016 195.9 85: (ns/day) (hour/ns) 85: Performance: 94.143 0.255 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: MTTK coupling is deprecated and will soon be removed 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: for current Trotter decomposition methods with vv, nsttcouple and 85: nstpcouple must be equal. Both have been reset to 85: min(nsttcouple,nstpcouple) = 2 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: There were 4 NOTEs 85: 85: This run will generate roughly 0 Mb of data 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.030 0.016 196.5 85: (ns/day) (hour/ns) 85: Performance: 94.632 0.254 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 2 time 0.002 Reading energy frame 4 time 0.004 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 8 time 0.008 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 11 time 0.011 Last energy frame read 16 time 0.016 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: MTTK coupling is deprecated and will soon be removed 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: for current Trotter decomposition methods with vv, nsttcouple and 85: nstpcouple must be equal. Both have been reset to 85: min(nsttcouple,nstpcouple) = 2 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 5 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.028 0.014 195.5 85: (ns/day) (hour/ns) 85: Performance: 102.380 0.234 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Last energy frame read 4 time 0.016 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: MTTK coupling is deprecated and will soon be removed 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: for current Trotter decomposition methods with vv, nsttcouple and 85: nstpcouple must be equal. Both have been reset to 85: min(nsttcouple,nstpcouple) = 2 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 5 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.031 0.016 196.5 85: (ns/day) (hour/ns) 85: Performance: 93.625 0.256 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: MTTK coupling is deprecated and will soon be removed 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: for current Trotter decomposition methods with vv, nsttcouple and 85: nstpcouple must be equal. Both have been reset to 85: min(nsttcouple,nstpcouple) = 2 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 5 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.031 0.016 196.8 85: (ns/day) (hour/ns) 85: Performance: 92.152 0.260 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: MTTK coupling is deprecated and will soon be removed 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: for current Trotter decomposition methods with vv, nsttcouple and 85: nstpcouple must be equal. Both have been reset to 85: min(nsttcouple,nstpcouple) = 2 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 85: COM removal frequency is set to (5). 85: Other settings require a global communication frequency of 2. 85: Note that this will require additional global communication steps, 85: which will reduce performance when using multiple ranks. 85: Consider setting nstcomm to a multiple of 2. 85: 85: 85: There were 5 NOTEs 85: 85: This run will generate roughly 0 Mb of data 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.034 0.017 196.7 85: (ns/day) (hour/ns) 85: Performance: 84.285 0.285 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 (156 ms) 85: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.030 0.015 196.6 85: (ns/day) (hour/ns) 85: Performance: 95.450 0.251 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (1) 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.027 0.014 196.3 85: (ns/day) (hour/ns) 85: Performance: 104.938 0.229 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 0 time 0.000 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 3 time 0.003 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 2 time 0.002 Reading energy frame 4 time 0.004 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 9 time 0.009 Reading energy frame 11 time 0.011 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 11 time 0.011 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 11 time 0.011 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Last energy frame read 16 time 0.016 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: Setting nstcalcenergy (100) equal to nstenergy (4) 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.029 0.015 196.5 85: (ns/day) (hour/ns) 85: Performance: 99.682 0.241 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: There were 2 NOTEs 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.036 0.018 196.8 85: (ns/day) (hour/ns) 85: Performance: 81.264 0.295 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: This run will generate roughly 0 Mb of data 85: 85: There were 2 NOTEs 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.044 0.022 197.6 85: (ns/day) (hour/ns) 85: Performance: 65.399 0.367 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 85: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 85: setting nstcomm equal to nstcalcenergy for less overhead 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'Argon' 85: 85: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon12.gro' 85: Number of degrees of freedom in T-Coupling group System is 33.00 85: 85: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 85: 85: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: 85: There were 2 NOTEs 85: 85: This run will generate roughly 0 Mb of data 85: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 85: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 85: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 85: 85: Using 2 MPI processes 85: Using 1 OpenMP thread per MPI process 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Argon' 85: 16 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.032 0.016 196.8 85: (ns/day) (hour/ns) 85: Performance: 89.882 0.267 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 85: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 85: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 (154 ms) 85: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest (3776 ms total) 85: 85: [----------] Global test environment tear-down 85: [==========] 25 tests from 1 test suite ran. (3896 ms total) 85: [ PASSED ] 25 tests. 85/94 Test #85: MdrunCoordinationCouplingTests2Ranks ......... Passed 4.42 sec test 86 Start 86: MdrunCoordinationConstraintsTests1Rank 86: Test command: /usr/bin/mpiexec "-n" "1" "/build/reproducible-path/gromacs-2025.0/build/mpi/bin/mdrun-coordination-constraints-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/MdrunCoordinationConstraintsTests1Rank.xml" 86: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests 86: Test timeout computed to be: 1920 86: [==========] Running 13 tests from 1 test suite. 86: [----------] Global test environment set-up. 86: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.043 0.043 99.8 86: (ns/day) (hour/ns) 86: Performance: 34.408 0.698 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: 86: This run will generate roughly 0 Mb of data 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.009 0.009 99.1 86: (ns/day) (hour/ns) 86: Performance: 171.085 0.140 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 4. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 4. 86: 86: 86: There were 5 NOTEs 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.010 0.010 99.1 86: (ns/day) (hour/ns) 86: Performance: 150.167 0.160 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 100. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 100. 86: 86: 86: There were 5 NOTEs 86: 86: This run will generate roughly 0 Mb of data 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.024 0.024 99.6 86: (ns/day) (hour/ns) 86: Performance: 60.559 0.396 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 100. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 100. 86: 86: 86: There were 5 NOTEs 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.014 0.014 99.4 86: (ns/day) (hour/ns) 86: Performance: 103.029 0.233 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 100. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 100. 86: 86: 86: There were 5 NOTEs 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.051 0.051 99.7 86: (ns/day) (hour/ns) 86: Performance: 28.668 0.837 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (4089 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.014 0.014 99.2 86: (ns/day) (hour/ns) 86: Performance: 105.218 0.228 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.043 0.043 99.7 86: (ns/day) (hour/ns) 86: Performance: 34.068 0.704 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.184 0.184 100.0 86: (ns/day) (hour/ns) 86: Performance: 7.998 3.001 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.017 0.018 99.4 86: (ns/day) (hour/ns) 86: Performance: 83.579 0.287 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.566 0.566 100.0 86: (ns/day) (hour/ns) 86: Performance: 2.595 9.249 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.024 0.024 99.6 86: (ns/day) (hour/ns) 86: Performance: 60.126 0.399 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (4916 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.013 0.013 99.3 86: (ns/day) (hour/ns) 86: Performance: 111.990 0.214 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.011 0.011 99.0 86: (ns/day) (hour/ns) 86: Performance: 137.271 0.175 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.008 0.008 98.2 86: (ns/day) (hour/ns) 86: Performance: 190.142 0.126 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.010 0.011 99.1 86: (ns/day) (hour/ns) 86: Performance: 138.624 0.173 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.032 0.032 99.7 86: (ns/day) (hour/ns) 86: Performance: 45.266 0.530 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.012 0.012 99.1 86: (ns/day) (hour/ns) 86: Performance: 122.838 0.195 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (4179 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.359 0.360 100.0 86: (ns/day) (hour/ns) 86: Performance: 4.085 5.876 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.413 0.413 100.0 86: (ns/day) (hour/ns) 86: Performance: 3.554 6.753 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 4 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.213 0.213 100.0 86: (ns/day) (hour/ns) 86: Performance: 6.905 3.476 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 4 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 1.001 1.001 100.0 86: (ns/day) (hour/ns) 86: Performance: 1.467 16.364 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 4 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.551 0.551 100.0 86: (ns/day) (hour/ns) 86: Performance: 2.668 8.997 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 4 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.704 0.705 100.0 86: (ns/day) (hour/ns) 86: Performance: 2.085 11.512 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (8169 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.751 0.751 100.0 86: (ns/day) (hour/ns) 86: Performance: 1.956 12.267 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.019 0.019 99.5 86: (ns/day) (hour/ns) 86: Performance: 76.428 0.314 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: 86: This run will generate roughly 0 Mb of data 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.009 0.009 99.0 86: (ns/day) (hour/ns) 86: Performance: 162.441 0.148 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: 86: This run will generate roughly 0 Mb of data 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.011 0.011 99.1 86: (ns/day) (hour/ns) 86: Performance: 138.596 0.173 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.587 0.587 100.0 86: (ns/day) (hour/ns) 86: Performance: 2.503 9.588 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: 86: This run will generate roughly 0 Mb of data 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.009 0.009 99.2 86: (ns/day) (hour/ns) 86: Performance: 164.889 0.146 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (5771 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.011 0.011 99.2 86: (ns/day) (hour/ns) 86: Performance: 131.606 0.182 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.061 0.061 99.8 86: (ns/day) (hour/ns) 86: Performance: 23.948 1.002 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.041 0.041 99.8 86: (ns/day) (hour/ns) 86: Performance: 35.817 0.670 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.025 0.025 99.6 86: (ns/day) (hour/ns) 86: Performance: 59.348 0.404 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.015 0.016 99.5 86: (ns/day) (hour/ns) 86: Performance: 94.414 0.254 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.014 0.014 99.3 86: (ns/day) (hour/ns) 86: Performance: 102.764 0.234 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (3617 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.016 0.016 99.5 86: (ns/day) (hour/ns) 86: Performance: 91.390 0.263 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.008 0.008 99.0 86: (ns/day) (hour/ns) 86: Performance: 182.872 0.131 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 4. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 4. 86: 86: 86: There were 4 NOTEs 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.008 0.008 99.3 86: (ns/day) (hour/ns) 86: Performance: 184.025 0.130 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 100. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 100. 86: 86: 86: There were 4 NOTEs 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.008 0.008 99.3 86: (ns/day) (hour/ns) 86: Performance: 177.769 0.135 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 100. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 100. 86: 86: 86: There were 4 NOTEs 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.010 0.010 98.9 86: (ns/day) (hour/ns) 86: Performance: 151.851 0.158 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 100. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 100. 86: 86: 86: There were 4 NOTEs 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.023 0.023 99.6 86: (ns/day) (hour/ns) 86: Performance: 62.622 0.383 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (3440 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.013 0.013 99.4 86: (ns/day) (hour/ns) 86: Performance: 114.686 0.209 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.008 0.008 99.3 86: (ns/day) (hour/ns) 86: Performance: 183.816 0.131 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.007 0.007 99.0 86: (ns/day) (hour/ns) 86: Performance: 200.136 0.120 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.016 0.016 99.6 86: (ns/day) (hour/ns) 86: Performance: 89.440 0.268 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.010 0.010 99.1 86: (ns/day) (hour/ns) 86: Performance: 139.940 0.172 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.010 0.010 99.4 86: (ns/day) (hour/ns) 86: Performance: 143.366 0.167 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (3356 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.014 0.014 99.4 86: (ns/day) (hour/ns) 86: Performance: 106.598 0.225 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.009 0.009 99.3 86: (ns/day) (hour/ns) 86: Performance: 166.395 0.144 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.009 0.009 99.3 86: (ns/day) (hour/ns) 86: Performance: 163.645 0.147 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.010 0.010 99.3 86: (ns/day) (hour/ns) 86: Performance: 151.642 0.158 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.010 0.010 99.3 86: (ns/day) (hour/ns) 86: Performance: 148.063 0.162 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.010 0.010 99.3 86: (ns/day) (hour/ns) 86: Performance: 147.789 0.162 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (3346 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.011 0.011 99.2 86: (ns/day) (hour/ns) 86: Performance: 129.479 0.185 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.012 0.012 99.5 86: (ns/day) (hour/ns) 86: Performance: 125.747 0.191 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 4. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 4. 86: 86: 86: There were 5 NOTEs 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.014 0.014 99.5 86: (ns/day) (hour/ns) 86: Performance: 103.766 0.231 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 100. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 100. 86: 86: 86: There were 5 NOTEs 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.012 0.012 99.4 86: (ns/day) (hour/ns) 86: Performance: 118.935 0.202 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 100. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 100. 86: 86: 86: There were 5 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 1.014 1.014 100.0 86: (ns/day) (hour/ns) 86: Performance: 1.449 16.566 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 100. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 100. 86: 86: 86: There were 5 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.022 0.022 99.7 86: (ns/day) (hour/ns) 86: Performance: 67.624 0.355 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (4663 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: 86: This run will generate roughly 0 Mb of data 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.025 0.025 99.7 86: (ns/day) (hour/ns) 86: Performance: 58.354 0.411 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.013 0.013 99.5 86: (ns/day) (hour/ns) 86: Performance: 115.727 0.207 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.013 0.013 99.5 86: (ns/day) (hour/ns) 86: Performance: 111.595 0.215 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.017 0.017 99.6 86: (ns/day) (hour/ns) 86: Performance: 84.563 0.284 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.117 0.117 99.9 86: (ns/day) (hour/ns) 86: Performance: 12.568 1.910 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.016 0.016 99.5 86: (ns/day) (hour/ns) 86: Performance: 89.289 0.269 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (3693 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.013 0.013 99.4 86: (ns/day) (hour/ns) 86: Performance: 115.696 0.207 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.014 0.014 98.9 86: (ns/day) (hour/ns) 86: Performance: 107.165 0.224 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 4 NOTEs 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.013 0.013 98.9 86: (ns/day) (hour/ns) 86: Performance: 114.891 0.209 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 4 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.017 0.017 99.5 86: (ns/day) (hour/ns) 86: Performance: 85.238 0.282 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 4 NOTEs 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.019 0.019 99.6 86: (ns/day) (hour/ns) 86: Performance: 77.531 0.310 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 86: COM removal frequency is set to (5). 86: Other settings require a global communication frequency of 2. 86: Note that this will require additional global communication steps, 86: which will reduce performance when using multiple ranks. 86: Consider setting nstcomm to a multiple of 2. 86: 86: 86: There were 4 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.012 0.012 99.4 86: (ns/day) (hour/ns) 86: Performance: 125.412 0.191 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (3497 ms) 86: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.014 0.014 99.4 86: (ns/day) (hour/ns) 86: Performance: 102.853 0.233 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (1) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.009 0.009 99.1 86: (ns/day) (hour/ns) 86: Performance: 159.659 0.150 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.012 0.012 99.3 86: (ns/day) (hour/ns) 86: Performance: 122.640 0.196 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.033 0.033 99.7 86: (ns/day) (hour/ns) 86: Performance: 43.881 0.547 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.400 0.400 100.0 86: (ns/day) (hour/ns) 86: Performance: 3.674 6.532 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 86: setting nstcomm equal to nstcalcenergy for less overhead 86: 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: Generating 1-4 interactions: fudge = 0.5 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 86: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 86: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 86: 86: Using 1 MPI process 86: Using 1 OpenMP thread 86: 86: 86: NOTE: Thread affinity was not set. 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.013 0.013 99.4 86: (ns/day) (hour/ns) 86: Performance: 110.778 0.217 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 86: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 86: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (3822 ms) 86: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest (56564 ms total) 86: 86: [----------] Global test environment tear-down 86: [==========] 13 tests from 1 test suite ran. (56644 ms total) 86: [ PASSED ] 13 tests. 86/94 Test #86: MdrunCoordinationConstraintsTests1Rank ....... Passed 57.13 sec test 87 Start 87: MdrunCoordinationConstraintsTests2Ranks 87: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2025.0/build/mpi/bin/mdrun-coordination-constraints-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/MdrunCoordinationConstraintsTests2Ranks.xml" 87: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests 87: Test timeout computed to be: 1920 87: [==========] Running 13 tests from 1 test suite. 87: [----------] Global test environment set-up. 87: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 0.8%. 87: The balanceable part of the MD step is 54%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.4%. 87: 87: 87: NOTE: 45 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.020 0.010 197.7 87: (ns/day) (hour/ns) 87: Performance: 146.665 0.164 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: 87: This run will generate roughly 0 Mb of data 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.2%. 87: The balanceable part of the MD step is 50%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.6%. 87: 87: 87: NOTE: 46 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.019 0.010 197.1 87: (ns/day) (hour/ns) 87: Performance: 148.663 0.161 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Last energy frame read 16 time 0.016 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: aints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 4. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 4. 87: 87: 87: There were 5 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstr 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 3.4%. 87: The balanceable part of the MD step is 42%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 1.4%. 87: 87: 87: NOTE: 49 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.051 0.025 199.2 87: (ns/day) (hour/ns) 87: Performance: 57.810 0.415 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 100. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 100. 87: 87: 87: There were 5 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 2.3%. 87: The balanceable part of the MD step is 39%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.9%. 87: 87: 87: NOTE: 48 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.033 0.016 198.3 87: (ns/day) (hour/ns) 87: Performance: 89.513 0.268 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 100. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 100. 87: 87: 87: There were 5 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.3%. 87: The balanceable part of the MD step is 38%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.5%. 87: 87: 87: NOTE: 48 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.026 0.013 197.5 87: (ns/day) (hour/ns) 87: Performance: 112.849 0.213 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 100. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 100. 87: 87: 87: There were 5 NOTEs 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 2.4%. 87: The balanceable part of the MD step is 32%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.8%. 87: 87: 87: NOTE: 47 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.038 0.019 198.7 87: (ns/day) (hour/ns) 87: Performance: 77.201 0.311 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (3675 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 0.6%. 87: The balanceable part of the MD step is 54%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.3%. 87: 87: 87: NOTE: 46 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.032 0.016 198.4 87: (ns/day) (hour/ns) 87: Performance: 92.411 0.260 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.6%. 87: The balanceable part of the MD step is 50%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.8%. 87: 87: 87: NOTE: 50 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.459 0.230 199.8 87: (ns/day) (hour/ns) 87: Performance: 6.397 3.752 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.9%. 87: The balanceable part of the MD step is 42%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.8%. 87: 87: 87: NOTE: 50 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.262 0.131 199.8 87: (ns/day) (hour/ns) 87: Performance: 11.196 2.144 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 87: Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Last energy frame read 4 time 0.016 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.2%. 87: The balanceable part of the MD step is 41%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.5%. 87: 87: 87: NOTE: 48 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.042 0.021 198.5 87: (ns/day) (hour/ns) 87: Performance: 68.623 0.350 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 0.9%. 87: The balanceable part of the MD step is 25%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.2%. 87: 87: 87: NOTE: 48 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.035 0.018 198.4 87: (ns/day) (hour/ns) 87: Performance: 82.788 0.290 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 0.7%. 87: The balanceable part of the MD step is 12%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.1%. 87: 87: 87: NOTE: 49 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.050 0.025 199.0 87: (ns/day) (hour/ns) 87: Performance: 58.092 0.413 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (4051 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 0.5%. 87: The balanceable part of the MD step is 56%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.3%. 87: 87: 87: NOTE: 50 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.547 0.274 199.9 87: (ns/day) (hour/ns) 87: Performance: 5.365 4.474 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 0.5%. 87: The balanceable part of the MD step is 48%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.2%. 87: 87: 87: NOTE: 48 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.045 0.023 198.8 87: (ns/day) (hour/ns) 87: Performance: 64.782 0.370 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 0.7%. 87: The balanceable part of the MD step is 46%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.3%. 87: 87: 87: NOTE: 48 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.035 0.018 198.4 87: (ns/day) (hour/ns) 87: Performance: 83.370 0.288 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.3%. 87: The balanceable part of the MD step is 30%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.4%. 87: 87: 87: NOTE: 48 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.031 0.016 198.1 87: (ns/day) (hour/ns) 87: Performance: 94.427 0.254 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 0.9%. 87: The balanceable part of the MD step is 44%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.4%. 87: 87: 87: NOTE: 48 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.031 0.016 198.1 87: (ns/day) (hour/ns) 87: Performance: 94.211 0.255 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 0.2%. 87: The balanceable part of the MD step is 21%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.1%. 87: 87: 87: NOTE: 48 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.037 0.018 198.3 87: (ns/day) (hour/ns) 87: Performance: 79.778 0.301 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (3861 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: 87: This run will generate roughly 0 Mb of data 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.024 0.012 197.2 87: (ns/day) (hour/ns) 87: Performance: 121.092 0.198 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 1.415 0.708 199.9 87: (ns/day) (hour/ns) 87: Performance: 2.075 11.564 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 87: Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 87: Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 11 time 0.011 Reading energy frame 5 time 0.005 Reading energy frame 11 time 0.011 Reading energy frame 5 time 0.005 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 13 time 0.013 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 13 time 0.013 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 14 time 0.014 Reading energy frame 9 time 0.009 Reading energy frame 14 time 0.014 Reading energy frame 9 time 0.009 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: which wi 87: This run will generate roughly 0 Mb of data 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: ll reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 4 NOTEs 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 1.359 0.679 200.0 87: (ns/day) (hour/ns) 87: Performance: 2.162 11.101 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 4 NOTEs 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.021 0.011 197.3 87: (ns/day) (hour/ns) 87: Performance: 139.292 0.172 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 4 NOTEs 87: 87: This run will generate roughly 0 Mb of data 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.024 0.012 197.5 87: (ns/day) (hour/ns) 87: Performance: 120.163 0.200 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 4 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.481 0.347 138.7 87: (ns/day) (hour/ns) 87: Performance: 4.233 5.669 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (5787 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.718 0.359 199.9 87: (ns/day) (hour/ns) 87: Performance: 4.089 5.870 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 1.180 0.590 199.9 87: (ns/day) (hour/ns) 87: Performance: 2.490 9.640 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 87: Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 87: Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 0 time 0.000 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: There were 3 NOTEs 87: 87: This run will generate roughly 0 Mb of data 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.035 0.018 198.1 87: (ns/day) (hour/ns) 87: Performance: 82.504 0.291 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 87: Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 87: Last energy frame read 4 time 0.016 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.029 0.015 197.9 87: (ns/day) (hour/ns) 87: Performance: 98.680 0.243 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: 87: This run will generate roughly 0 Mb of data 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.026 0.013 197.2 87: (ns/day) (hour/ns) 87: Performance: 111.674 0.215 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.038 0.019 198.7 87: (ns/day) (hour/ns) 87: Performance: 76.580 0.313 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (4976 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.023 0.012 194.2 87: (ns/day) (hour/ns) 87: Performance: 122.432 0.196 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.018 0.009 195.4 87: (ns/day) (hour/ns) 87: Performance: 161.704 0.148 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 87: Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 5 time 0.005 Reading energy frame 13 time 0.013 Reading energy frame 5 time 0.005 Reading energy frame 13 time 0.013 Reading energy frame 6 time 0.006 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 15 time 0.015 Reading energy frame 7 time 0.007 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.676 0.338 199.9 87: (ns/day) (hour/ns) 87: Performance: 4.344 5.525 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Last energy frame read 4 time 0.016 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.469 0.235 199.9 87: (ns/day) (hour/ns) 87: Performance: 6.253 3.838 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.574 0.287 199.9 87: (ns/day) (hour/ns) 87: Performance: 5.110 4.696 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.303 0.152 199.8 87: (ns/day) (hour/ns) 87: Performance: 9.679 2.480 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (5241 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.470 0.235 199.9 87: (ns/day) (hour/ns) 87: Performance: 6.243 3.844 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.016 0.008 196.6 87: (ns/day) (hour/ns) 87: Performance: 185.638 0.129 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 87: Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 4. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 4. 87: 87: 87: There were 4 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.679 0.340 199.9 87: (ns/day) (hour/ns) 87: Performance: 4.323 5.552 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 100. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 100. 87: 87: 87: There were 4 NOTEs 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.472 0.236 199.9 87: (ns/day) (hour/ns) 87: Performance: 6.219 3.859 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 100. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 100. 87: 87: 87: There were 4 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.841 0.421 199.9 87: (ns/day) (hour/ns) 87: Performance: 3.493 6.871 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 100. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 100. 87: 87: 87: There were 4 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.874 0.437 199.9 87: (ns/day) (hour/ns) 87: Performance: 3.362 7.140 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (5489 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.155 0.078 199.7 87: (ns/day) (hour/ns) 87: Performance: 18.928 1.268 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.017 0.009 197.3 87: (ns/day) (hour/ns) 87: Performance: 170.137 0.141 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 0 time 0.000 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 1 time 0.001 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 1 time 0.001 Reading energy frame 12 time 0.012 Reading energy frame 2 time 0.002 Reading energy frame 13 time 0.013 Reading energy frame 2 time 0.002 Reading energy frame 13 time 0.013 Reading energy frame 3 time 0.003 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.016 0.008 197.3 87: (ns/day) (hour/ns) 87: Performance: 179.173 0.134 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.032 0.016 198.3 87: (ns/day) (hour/ns) 87: Performance: 91.048 0.264 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.019 0.009 197.6 87: (ns/day) (hour/ns) 87: Performance: 154.682 0.155 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.017 0.009 196.7 87: (ns/day) (hour/ns) 87: Performance: 165.699 0.145 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (3566 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.022 0.011 197.6 87: (ns/day) (hour/ns) 87: Performance: 131.917 0.182 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.017 0.009 196.8 87: (ns/day) (hour/ns) 87: Performance: 171.327 0.140 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 9 time 0.009 Reading energy frame 5 time 0.005 Reading energy frame 9 time 0.009 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 12 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 16 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: 87: This run will generate roughly 0 Mb of data 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.015 0.007 196.9 87: (ns/day) (hour/ns) 87: Performance: 196.626 0.122 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.019 0.010 197.2 87: (ns/day) (hour/ns) 87: Performance: 153.859 0.156 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.023 0.012 196.6 87: (ns/day) (hour/ns) 87: Performance: 125.999 0.190 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 1.287 0.644 200.0 87: (ns/day) (hour/ns) 87: Performance: 2.282 10.515 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (4089 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.5%. 87: The balanceable part of the MD step is 55%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.8%. 87: 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.029 0.015 195.5 87: (ns/day) (hour/ns) 87: Performance: 98.983 0.242 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 0.6%. 87: The balanceable part of the MD step is 57%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.3%. 87: 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.250 0.125 199.6 87: (ns/day) (hour/ns) 87: Performance: 11.740 2.044 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 0 time 0.000 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 0 time 0.000 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 4 time 0.004 Reading energy frame 7 time 0.007 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 4. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 4. 87: 87: 87: There were 5 NOTEs 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB got disabled because it was unsuitable to use. 87: Average load imbalance: 4.4%. 87: The balanceable part of the MD step is 48%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 2.1%. 87: 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.140 0.070 199.2 87: (ns/day) (hour/ns) 87: Performance: 20.851 1.151 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 4 time 0.004 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 8 time 0.008 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 100. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 100. 87: 87: 87: There were 5 NOTEs 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB got disabled because it was unsuitable to use. 87: Average load imbalance: 4.7%. 87: The balanceable part of the MD step is 44%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 2.1%. 87: 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.956 0.478 199.9 87: (ns/day) (hour/ns) 87: Performance: 3.073 7.811 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 100. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 100. 87: 87: 87: There were 5 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 0.8%. 87: The balanceable part of the MD step is 46%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.4%. 87: 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.277 0.139 199.6 87: (ns/day) (hour/ns) 87: Performance: 10.588 2.267 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 100. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 100. 87: 87: 87: There were 5 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.8%. 87: The balanceable part of the MD step is 41%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.8%. 87: 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.054 0.027 198.2 87: (ns/day) (hour/ns) 87: Performance: 54.381 0.441 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (4299 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 0.6%. 87: The balanceable part of the MD step is 59%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.4%. 87: 87: 87: Core t (s) Wall t (s) (%) 87: Time: 2.992 1.496 200.0 87: (ns/day) (hour/ns) 87: Performance: 0.982 24.447 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 0.6%. 87: The balanceable part of the MD step is 56%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.3%. 87: 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.028 0.014 195.6 87: (ns/day) (hour/ns) 87: Performance: 104.301 0.230 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.0%. 87: The balanceable part of the MD step is 56%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.6%. 87: 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.266 0.145 183.3 87: (ns/day) (hour/ns) 87: Performance: 10.139 2.367 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.0%. 87: The balanceable part of the MD step is 56%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.6%. 87: 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.029 0.015 196.5 87: (ns/day) (hour/ns) 87: Performance: 100.766 0.238 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 3.2%. 87: The balanceable part of the MD step is 55%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 1.8%. 87: 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.042 0.021 197.7 87: (ns/day) (hour/ns) 87: Performance: 68.936 0.348 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: NVE simulation: will use the initial temperature of 398.997 K for 87: determining the Verlet buffer size 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 0.4%. 87: The balanceable part of the MD step is 56%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.2%. 87: 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.027 0.014 194.7 87: (ns/day) (hour/ns) 87: Performance: 107.010 0.224 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (5242 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.030 0.016 188.5 87: (ns/day) (hour/ns) 87: Performance: 91.278 0.263 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.020 0.010 195.2 87: (ns/day) (hour/ns) 87: Performance: 143.983 0.167 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 87: Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 0 time 0.000 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 14 time 0.014 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 4 NOTEs 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.027 0.014 196.7 87: (ns/day) (hour/ns) 87: Performance: 105.995 0.226 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 87: Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 4 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.027 0.014 196.1 87: (ns/day) (hour/ns) 87: Performance: 108.126 0.222 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 4 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.041 0.022 188.4 87: (ns/day) (hour/ns) 87: Performance: 66.874 0.359 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 87: COM removal frequency is set to (5). 87: Other settings require a global communication frequency of 2. 87: Note that this will require additional global communication steps, 87: which will reduce performance when using multiple ranks. 87: Consider setting nstcomm to a multiple of 2. 87: 87: 87: There were 4 NOTEs 87: 87: This run will generate roughly 0 Mb of data 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.037 0.019 195.8 87: (ns/day) (hour/ns) 87: Performance: 77.362 0.310 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (3429 ms) 87: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.447 0.224 199.8 87: (ns/day) (hour/ns) 87: Performance: 6.560 3.658 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (1) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.425 0.213 199.8 87: (ns/day) (hour/ns) 87: Performance: 6.900 3.478 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: 87: This run will generate roughly 0 Mb of data 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 1.395 0.698 199.9 87: (ns/day) (hour/ns) 87: Performance: 2.105 11.402 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 87: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.003 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 4 time 0.004 Reading energy frame 7 time 0.007 Reading energy frame 2 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 7 time 0.007 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 8 time 0.008 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 1.751 0.876 199.8 87: (ns/day) (hour/ns) 87: Performance: 1.676 14.321 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.027 0.014 196.2 87: (ns/day) (hour/ns) 87: Performance: 105.427 0.228 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 87: setting nstcomm equal to nstcalcenergy for less overhead 87: 87: Generated 330891 of the 330891 non-bonded parameter combinations 87: Generating 1-4 interactions: fudge = 0.5 87: 87: Generated 330891 of the 330891 1-4 parameter combinations 87: 87: Excluding 2 bonded neighbours molecule type 'SOL' 87: 87: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/tip3p5.gro' 87: Number of degrees of freedom in T-Coupling group System is 27.00 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 3 NOTEs 87: 87: This run will generate roughly 0 Mb of data 87: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 87: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 87: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 87: 87: Using 2 MPI processes 87: Using 1 OpenMP thread per MPI process 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'spc2' 87: 16 steps, 0.0 ps. 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.427 0.214 199.7 87: (ns/day) (hour/ns) 87: Performance: 6.865 3.496 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 87: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 87: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (5955 ms) 87: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest (59666 ms total) 87: 87: [----------] Global test environment tear-down 87: [==========] 13 tests from 1 test suite ran. (59749 ms total) 87: [ PASSED ] 13 tests. 87/94 Test #87: MdrunCoordinationConstraintsTests2Ranks ...... Passed 60.29 sec test 88 Start 88: MdrunFEPTests 88: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/mdrun-fep-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/MdrunFEPTests.xml" 88: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests 88: Test timeout computed to be: 600 88: [==========] Running 14 tests from 2 test suites. 88: [----------] Global test environment set-up. 88: [----------] 2 tests from ExpandedEnsembleTest 88: [ RUN ] ExpandedEnsembleTest.ContinuationPreservesExpandedEnsembleState 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: Number of degrees of freedom in T-Coupling group System is 79.00 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: There were 2 NOTEs 88: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 88: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 88: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 88: 88: Using 1 MPI process 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun '30 atom system in water' 88: 16 steps, 0.0 ps. 88: Generated 2485 of the 2485 non-bonded parameter combinations 88: 88: Generated 2485 of the 2485 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'nonanol' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.720 0.360 199.9 88: (ns/day) (hour/ns) 88: Performance: 4.077 5.887 88: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 88: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 88: Overriding nsteps with value passed on the command line: 8 steps, 0.008 ps 88: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 88: 88: 88: Using 1 MPI process 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun '30 atom system in water' 88: 24 steps, 0.0 ps (continuing from step 16, 0.0 ps). 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 1.259 0.630 200.0 88: (ns/day) (hour/ns) 88: Performance: 1.234 19.441 88: [ OK ] ExpandedEnsembleTest.ContinuationPreservesExpandedEnsembleState (1672 ms) 88: [ RUN ] ExpandedEnsembleTest.WeightEquilibrationReported 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_WeightEquilibrationReported_input.mdp]: 88: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 88: that with the Verlet scheme, nstlist has no effect on the accuracy of 88: your simulation. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: Number of degrees of freedom in T-Coupling group System is 79.00 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_WeightEquilibrationReported_input.mdp]: 88: You are using a plain Coulomb cut-off, which might produce artifacts. 88: You might want to consider using PME electrostatics. 88: 88: 88: 88: There were 2 NOTEs 88: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 88: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_WeightEquilibrationReported.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 88: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 88: 88: Using 1 MPI process 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun '30 atom system in water' 88: 1 steps, 0.0 ps. 88: Generated 2485 of the 2485 non-bonded parameter combinations 88: 88: Generated 2485 of the 2485 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'nonanol' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/nonanol_vacuo.gro' 88: 88: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 1.058 0.529 200.0 88: (ns/day) (hour/ns) 88: Performance: 0.327 73.449 88: [ OK ] ExpandedEnsembleTest.WeightEquilibrationReported (746 ms) 88: [----------] 2 tests from ExpandedEnsembleTest (2419 ms total) 88: 88: [----------] 12 tests from EquivalentToReference/FreeEnergyReferenceTest 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_s 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp, line 149]: 88: For proper sampling of the (nearly) decoupled state, stochastic dynamics 88: should be used 88: 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: Number of degrees of freedom in T-Coupling group System is 355.00 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 3 NOTEs 88: 88: There was 1 WARNING 88: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 88: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_s_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 88: Changing nstlist from 10 to 100, rlist from 1 to 1 88: 88: Using 1 MPI process 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: Setting the LD random seed to 536524713 88: 88: Generated 153 of the 153 non-bonded parameter combinations 88: 88: Generated 153 of the 153 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Coupling 1 copies of molecule type 'ASN' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 88: 88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 88: 88: Estimate for the relative computational load of the PME mesh part: 0.94 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.112 0.056 199.4 88: (ns/day) (hour/ns) 88: Performance: 32.404 0.741 88: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_s_energy.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 trr version: GMX_trn_file (single precision) 88: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_s (418 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_s 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp, line 148]: 88: For proper sampling of the (nearly) decoupled state, stochastic dynamics 88: should be used 88: 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: Number of degrees of freedom in T-Coupling group System is 355.00 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 3 NOTEs 88: 88: There was 1 WARNING 88: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 88: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_s_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 88: Changing nstlist from 10 to 100, rlist from 1 to 1 88: 88: Using 1 MPI process 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: Setting the LD random seed to -335949121 88: 88: Generated 153 of the 153 non-bonded parameter combinations 88: 88: Generated 153 of the 153 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Coupling 1 copies of molecule type 'ASN' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 88: 88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 88: 88: Estimate for the relative computational load of the PME mesh part: 0.94 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.113 0.057 199.6 88: (ns/day) (hour/ns) 88: Performance: 32.072 0.748 88: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_s_energy.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_s (228 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_s 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp, line 147]: 88: For proper sampling of the (nearly) decoupled state, stochastic dynamics 88: should be used 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 88: With PME there is a minor soft core effect present at the cut-off, 88: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 88: energy conservation, but usually other effects dominate. With a common 88: sigma value of 0.34 nm the fraction of the particle-particle potential at 88: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 88: 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: Number of degrees of freedom in T-Coupling group System is 355.00 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 4 NOTEs 88: 88: There was 1 WARNING 88: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 88: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_s_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 88: Changing nstlist from 10 to 100, rlist from 1 to 1 88: 88: Using 1 MPI process 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: Setting the LD random seed to -533060 88: 88: Generated 153 of the 153 non-bonded parameter combinations 88: 88: Generated 153 of the 153 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Coupling 1 copies of molecule type 'ASN' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 88: 88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 88: 88: Estimate for the relative computational load of the PME mesh part: 0.94 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.092 0.046 199.6 88: (ns/day) (hour/ns) 88: Performance: 39.335 0.610 88: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_s_energy.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_s (216 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_net_charge_s 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp, line 147]: 88: For proper sampling of the (nearly) decoupled state, stochastic dynamics 88: should be used 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 88: With PME there is a minor soft core effect present at the cut-off, 88: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 88: energy conservation, but usually other effects dominate. With a common 88: sigma value of 0.34 nm the fraction of the particle-particle potential at 88: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 88: 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: 88: NOTE 3 [file topol.top, line 155]: 88: System has non-zero total charge: 1.000000 88: Total charge should normally be an integer. See 88: https://manual.gromacs.org/current/user-guide/floating-point.html 88: for discussion on how close it should be to an integer. 88: 88: 88: 88: 88: WARNING 2 [file topol.top, line 155]: 88: You are using Ewald electrostatics in a system with net charge. This can 88: lead to severe artifacts, such as ions moving into regions with low 88: dielectric, due to the uniform background charge. We suggest to 88: neutralize your system with counter ions, possibly in combination with a 88: physiological salt concentration. 88: 88: Setting the LD random seed to -268519937 88: 88: Generated 171 of the 171 non-bonded parameter combinations 88: 88: Generated 171 of the 171 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Excluding 1 bonded neighbours molecule type 'NA' 88: 88: turning H bonds into constraints... 88: 88: Coupling 1 copies of molecule type 'ASN' 88: 88: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 88: J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof 88: Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net 88: Charge 88: J. Chem. Theory Comput. (2014) 88: DOI: 10.1021/ct400626b 88: -------- -------- --- Thank You --- -------- -------- 88: 88: Number of degrees of freedom in T-Coupling group System is 358.00 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 5 NOTEs 88: 88: There were 2 WARNINGs 88: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 88: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_net_charge_s_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 88: Changing nstlist from 10 to 50, rlist from 1.004 to 1.101 88: 88: Using 1 MPI process 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: There are: 1 Ion residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 88: 88: Determining Verlet buffer for a tolerance of 5e-05 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.004 nm, buffer size 0.004 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 32x32x32, spacing 0.095 0.095 0.095 88: 88: Estimate for the relative computational load of the PME mesh part: 0.96 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.108 0.054 199.6 88: (ns/day) (hour/ns) 88: Performance: 33.427 0.718 88: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_net_charge_s_energy.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_net_charge_s (259 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_decouple_counter_charge_s 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp, line 147]: 88: For proper sampling of the (nearly) decoupled state, stochastic dynamics 88: should be used 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 88: With PME there is a minor soft core effect present at the cut-off, 88: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 88: energy conservation, but usually other effects dominate. With a common 88: sigma value of 0.34 nm the fraction of the particle-particle potential at 88: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 88: 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: 88: NOTE 3 [file topol.top, line 165]: 88: System has non-zero total charge: 1.000000 88: Total charge should normally be an integer. See 88: https://manual.gromacs.org/current/user-guide/floating-point.html 88: for discussion on how close it should be to an integer. 88: 88: 88: 88: 88: WARNING 2 [file topol.top, line 165]: 88: You are using Ewald electrostatics in a system with net charge. This can 88: lead to severe artifacts, such as ions moving into regions with low 88: dielectric, due to the uniform background charge. We suggest to 88: neutralize your system with counter ions, possibly in combination with a 88: physiological salt concentration. 88: 88: Setting the LD random seed to 457145341 88: 88: Generated 190 of the 190 non-bonded parameter combinations 88: 88: Generated 190 of the 190 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Excluding 1 bonded neighbours molecule type 'NA' 88: 88: turning H bonds into constraints... 88: 88: Excluding 1 bonded neighbours molecule type 'CL' 88: 88: turning H bonds into constraints... 88: 88: Coupling 1 copies of molecule type 'CL' 88: 88: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 88: J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof 88: Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net 88: Charge 88: J. Chem. Theory Comput. (2014) 88: DOI: 10.1021/ct400626b 88: -------- -------- --- Thank You --- -------- -------- 88: 88: Number of degrees of freedom in T-Coupling group System is 361.00 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 5 NOTEs 88: 88: There were 2 WARNINGs 88: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 88: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_decouple_counter_charge_s_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 88: Changing nstlist from 10 to 50, rlist from 1.004 to 1.102 88: 88: Using 1 MPI process 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: There are: 2 Ion residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.331 nm between atom 1 and 9 88: 88: Determining Verlet buffer for a tolerance of 5e-05 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.004 nm, buffer size 0.004 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 32x32x32, spacing 0.095 0.095 0.095 88: 88: Estimate for the relative computational load of the PME mesh part: 0.96 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.103 0.052 199.6 88: (ns/day) (hour/ns) 88: Performance: 35.022 0.685 88: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_decouple_counter_charge_s_energy.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_decouple_counter_charge_s (81 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_s 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp, line 171]: 88: For proper sampling of the (nearly) decoupled state, stochastic dynamics 88: should be used 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 88: Replacing vdwtype=Shift by the equivalent combination of vdwtype=Cut-off 88: and vdw_modifier=Force-switch 88: 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: Number of degrees of freedom in T-Coupling group System is 355.00 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 4 NOTEs 88: 88: There was 1 WARNING 88: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 88: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_s_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 88: Changing nstlist from 10 to 100, rlist from 1 to 1 88: 88: Using 1 MPI process 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 100 steps, 0.1 ps. 88: Setting the LD random seed to 2130558782 88: 88: Generated 153 of the 153 non-bonded parameter combinations 88: 88: Generated 153 of the 153 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Coupling 1 copies of molecule type 'ASN' 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/expanded/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 88: 88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 88: 88: Estimate for the relative computational load of the PME mesh part: 0.94 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.447 0.224 199.9 88: (ns/day) (hour/ns) 88: Performance: 39.011 0.615 88: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_s_energy.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Reading energy frame 30 time 0.030 Reading energy frame 40 time 0.040 Reading energy frame 50 time 0.050 Reading energy frame 60 time 0.060 Reading energy frame 70 time 0.070 Reading energy frame 80 time 0.080 Reading energy frame 90 time 0.090 Reading energy frame 100 time 0.100 Last energy frame read 100 time 0.100 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_s (388 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_s 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: 88: WARNING 2 [file topol.top, line 72]: 88: No default Bond types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '7 8 1'. 88: 88: 88: WARNING 3 [file topol.top, line 73]: 88: No default Bond types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '7 9 1'. 88: 88: 88: WARNING 4 [file topol.top, line 98]: 88: No default Angle types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '6 5 7 1'. 88: 88: 88: WARNING 5 [file topol.top, line 99]: 88: No default Angle types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '5 7 8 1'. 88: 88: 88: WARNING 6 [file topol.top, line 100]: 88: No default Angle types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '5 7 9 1'. 88: 88: 88: WARNING 7 [file topol.top, line 101]: 88: No default Angle types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '8 7 9 1'. 88: 88: 88: WARNING 8 [file topol.top, line 111]: 88: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 88: normal values. The interaction was 88: '1 5 7 8 3'. 88: 88: 88: WARNING 9 [file topol.top, line 112]: 88: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 88: normal values. The interaction was 88: '1 5 7 9 3'. 88: 88: 88: WARNING 10 [file topol.top, line 113]: 88: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 88: normal values. The interaction was 88: '6 5 7 8 3'. 88: 88: 88: WARNING 11 [file topol.top, line 114]: 88: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 88: normal values. The interaction was 88: '6 5 7 9 3'. 88: 88: Number of degrees of freedom in T-Coupling group System is 355.00 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 2 NOTEs 88: 88: There were 11 WARNINGs 88: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 88: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_s_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 88: Changing nstlist from 10 to 100, rlist from 1 to 1 88: 88: Using 1 MPI process 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: Setting the LD random seed to -65817 88: 88: Generated 136 of the 136 non-bonded parameter combinations 88: 88: Generated 136 of the 136 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/relative/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 88: 88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 88: 88: Estimate for the relative computational load of the PME mesh part: 0.94 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.145 0.073 199.7 88: (ns/day) (hour/ns) 88: Performance: 24.962 0.961 88: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_s_energy.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_s (234 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_s 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: 88: WARNING 2 [file topol.top, line 72]: 88: No default Bond types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '7 8 1'. 88: 88: 88: WARNING 3 [file topol.top, line 73]: 88: No default Bond types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '7 9 1'. 88: 88: 88: WARNING 4 [file topol.top, line 98]: 88: No default Angle types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '6 5 7 1'. 88: 88: 88: WARNING 5 [file topol.top, line 99]: 88: No default Angle types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '5 7 8 1'. 88: 88: 88: WARNING 6 [file topol.top, line 100]: 88: No default Angle types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '5 7 9 1'. 88: 88: 88: WARNING 7 [file topol.top, line 101]: 88: No default Angle types for perturbed atoms in interaction, using normal 88: values. The interaction was 88: '8 7 9 1'. 88: 88: 88: WARNING 8 [file topol.top, line 111]: 88: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 88: normal values. The interaction was 88: '1 5 7 8 3'. 88: 88: 88: WARNING 9 [file topol.top, line 112]: 88: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 88: normal values. The interaction was 88: '1 5 7 9 3'. 88: 88: 88: WARNING 10 [file topol.top, line 113]: 88: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 88: normal values. The interaction was 88: '6 5 7 8 3'. 88: 88: 88: WARNING 11 [file topol.top, line 114]: 88: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 88: normal values. The interaction was 88: '6 5 7 9 3'. 88: 88: Number of degrees of freedom in T-Coupling group System is 355.00 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 88: Removing center of mass motion in the presence of position restraints 88: might cause artifacts. When you are using position restraints to 88: equilibrate a macro-molecule, the artifacts are usually negligible. 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 3 NOTEs 88: 88: There were 11 WARNINGs 88: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 88: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_s_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 88: Changing nstlist from 10 to 100, rlist from 1 to 1 88: 88: Using 1 MPI process 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: Setting the LD random seed to -9175169 88: 88: Generated 136 of the 136 non-bonded parameter combinations 88: 88: Generated 136 of the 136 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 88: 88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 88: 88: Estimate for the relative computational load of the PME mesh part: 0.94 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.200 0.100 199.8 88: (ns/day) (hour/ns) 88: Performance: 18.099 1.326 88: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_s_energy.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_s (263 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/restraints_s 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: Number of degrees of freedom in T-Coupling group System is 355.00 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 2 NOTEs 88: 88: There was 1 WARNING 88: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 88: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_s_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 88: Changing nstlist from 10 to 100, rlist from 1 to 1 88: 88: Using 1 MPI process 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: Setting the LD random seed to -673197258 88: 88: Generated 136 of the 136 non-bonded parameter combinations 88: 88: Generated 136 of the 136 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/restraints/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.331 nm between atom 1 and 9 88: 88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 88: 88: Estimate for the relative computational load of the PME mesh part: 0.88 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.080 0.040 199.3 88: (ns/day) (hour/ns) 88: Performance: 45.385 0.529 88: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_s_energy.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/restraints_s (198 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_s 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/simtemp/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: Number of degrees of freedom in T-Coupling group System is 355.00 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/simtemp/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: There was 1 NOTE 88: 88: There was 1 WARNING 88: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 88: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_s_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 88: Changing nstlist from 10 to 100, rlist from 1 to 1 88: 88: Using 1 MPI process 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.041 0.021 198.7 88: (ns/day) (hour/ns) 88: Performance: 88.221 0.272 88: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_s_energy.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Setting the LD random seed to 536181977 88: 88: Generated 136 of the 136 non-bonded parameter combinations 88: 88: Generated 136 of the 136 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/simtemp/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: Analysing Protein... 88: 88: The largest distance between excluded atoms is 0.331 nm between atom 1 and 9 88: 88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 88: 88: Estimate for the relative computational load of the PME mesh part: 0.88 88: 88: This run will generate roughly 0 Mb of data 88: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_s (178 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_s 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 88: With PME there is a minor soft core effect present at the cut-off, 88: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 88: energy conservation, but usually other effects dominate. With a common 88: sigma value of 0.34 nm the fraction of the particle-particle potential at 88: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 88: 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: Number of degrees of freedom in T-Coupling group System is 355.00 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 3 NOTEs 88: 88: There was 1 WARNING 88: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 88: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_s_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 88: Changing nstlist from 10 to 100, rlist from 1 to 1 88: 88: Using 1 MPI process 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: Setting the LD random seed to 1341386463 88: 88: Generated 136 of the 136 non-bonded parameter combinations 88: 88: Generated 136 of the 136 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/transformAtoB/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 88: 88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 88: 88: Estimate for the relative computational load of the PME mesh part: 0.94 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.697 0.349 199.9 88: (ns/day) (hour/ns) 88: Performance: 5.206 4.610 88: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_s_energy.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_s (514 ms) 88: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/vdwalone_s 88: 88: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 88: With PME there is a minor soft core effect present at the cut-off, 88: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 88: energy conservation, but usually other effects dominate. With a common 88: sigma value of 0.34 nm the fraction of the particle-particle potential at 88: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 88: 88: 88: WARNING 1 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 88: The Berendsen thermostat does not generate the correct kinetic energy 88: distribution, and should not be used for new production simulations (in 88: our opinion). We would recommend the V-rescale thermostat. 88: 88: Generating 1-4 interactions: fudge = 0.5 88: Number of degrees of freedom in T-Coupling group System is 355.00 88: 88: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 88: The optimal PME mesh load for parallel simulations is below 0.5 88: and for highly parallel simulations between 0.25 and 0.33, 88: for higher performance, increase the cut-off and the PME grid spacing. 88: 88: 88: 88: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 88: For free energy simulations, the optimal load limit increases from 0.5 to 88: 0.667 88: 88: 88: 88: There were 3 NOTEs 88: 88: There was 1 WARNING 88: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 88: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_s_sim.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 88: Changing nstlist from 10 to 100, rlist from 1 to 1 88: 88: Using 1 MPI process 88: Using 2 OpenMP threads 88: 88: 88: NOTE: The number of threads is not equal to the number of (logical) cpus 88: and the -pin option is set to auto: will not pin threads to cpus. 88: This can lead to significant performance degradation. 88: Consider using -pin on (and -pinoffset in case you run multiple jobs). 88: starting mdrun 'AA' 88: 20 steps, 0.0 ps. 88: Setting the LD random seed to 1939855100 88: 88: Generated 136 of the 136 non-bonded parameter combinations 88: 88: Generated 136 of the 136 1-4 parameter combinations 88: 88: Excluding 3 bonded neighbours molecule type 'ASN' 88: 88: turning H bonds into constraints... 88: 88: Excluding 2 bonded neighbours molecule type 'SOL' 88: 88: turning H bonds into constraints... 88: 88: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/freeenergy/vdwalone/conf.gro' 88: Analysing residue names: 88: There are: 1 Protein residues 88: There are: 56 Water residues 88: Analysing Protein... 88: 88: The largest distance between non-perturbed excluded atoms is 0.172 nm between atom 8 and 9 88: 88: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 88: 88: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 88: 88: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 88: 88: Note that mdrun will redetermine rlist based on the actual pair-list setup 88: Calculating fourier grid dimensions for X Y Z 88: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 88: 88: Estimate for the relative computational load of the PME mesh part: 0.88 88: 88: This run will generate roughly 0 Mb of data 88: 88: Writing final coordinates. 88: 88: Core t (s) Wall t (s) (%) 88: Time: 0.135 0.068 199.7 88: (ns/day) (hour/ns) 88: Performance: 26.832 0.894 88: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_s_energy.edr as single precision energy file 88: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/vdwalone_s (229 ms) 88: [----------] 12 tests from EquivalentToReference/FreeEnergyReferenceTest (3212 ms total) 88: 88: [----------] Global test environment tear-down 88: [==========] 14 tests from 2 test suites ran. (5739 ms total) 88: [ PASSED ] 14 tests. 88/94 Test #88: MdrunFEPTests ................................ Passed 6.06 sec test 89 Start 89: MdrunPullTests 89: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/mdrun-pull-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/MdrunPullTests.xml" 89: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests 89: Test timeout computed to be: 600 89: [==========] Running 4 tests from 1 test suite. 89: [----------] Global test environment set-up. 89: [----------] 4 tests from PullTest/PullIntegrationTest 89: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/0 89: Generating 1-4 interactions: fudge = 0.5 89: Pull group 1 'r_1' has 3 atoms 89: Pull group 2 'r_2' has 3 atoms 89: Number of degrees of freedom in T-Coupling group System is 1293.00 89: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0_input.mdp]: 89: NVE simulation: will use the initial temperature of 303.122 K for 89: determining the Verlet buffer size 89: 89: Pull group natoms pbc atom distance at start reference at t=0 89: 1 3 2 89: 2 3 5 0.575 nm 0.600 nm 89: 89: There was 1 NOTE 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI process 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 20 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc216.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: NOTE: 11 % of the run time was spent in pair search, 89: you might want to increase nstlist (this has no effect on accuracy) 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.047 0.024 199.4 89: (ns/day) (hour/ns) 89: Performance: 76.785 0.313 89: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0.edr as single precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/0 (654 ms) 89: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/1 89: Generating 1-4 interactions: fudge = 0.5 89: Pull group 1 'r_1' has 3 atoms 89: Pull group 2 'r_2' has 3 atoms 89: Number of degrees of freedom in T-Coupling group System is 1293.00 89: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1_input.mdp]: 89: NVE simulation: will use the initial temperature of 303.122 K for 89: determining the Verlet buffer size 89: 89: Pull group natoms pbc atom distance at start reference at t=0 89: 1 3 2 89: 2 3 5 0.301 nm 0.400 nm 89: 89: There was 1 NOTE 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI process 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 20 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc216.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.058 0.029 199.4 89: (ns/day) (hour/ns) 89: Performance: 62.691 0.383 89: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1.edr as single precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/1 (582 ms) 89: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/2 89: Generating 1-4 interactions: fudge = 0.5 89: Pull group 1 'r_1' has 3 atoms 89: Pull group 2 'r_2' has 3 atoms 89: Pull group 3 'r_3' has 3 atoms 89: Number of degrees of freedom in T-Coupling group System is 1292.00 89: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2_input.mdp]: 89: NVE simulation: will use the initial temperature of 303.357 K for 89: determining the Verlet buffer size 89: 89: Pull group natoms pbc atom distance at start reference at t=0 89: 1 3 2 89: 2 3 5 0.575 nm 0.500 nm 89: 1 3 2 89: 3 3 8 0.331 nm 0.400 nm 89: 89: There was 1 NOTE 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI process 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 20 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc216.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.357 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.619 0.309 199.9 89: (ns/day) (hour/ns) 89: Performance: 5.863 4.093 89: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2.edr as single precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/2 (845 ms) 89: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/3 89: Generating 1-4 interactions: fudge = 0.5 89: Pull group 1 'r_1' has 3 atoms 89: Pull group 2 'r_2' has 3 atoms 89: Number of degrees of freedom in T-Coupling group System is 1293.00 89: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3_input.mdp]: 89: NVE simulation: will use the initial temperature of 303.122 K for 89: determining the Verlet buffer size 89: 89: Pull group natoms pbc atom distance at start reference at t=0 89: 1 3 2 89: 2 3 5 0.575 nm 0.000 nm 89: 1 3 2 89: 2 3 5 0.050 nm 0.000 nm 89: 89: There was 1 NOTE 89: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 89: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Using 1 MPI process 89: Using 2 OpenMP threads 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'spc2' 89: 20 steps, 0.0 ps. 89: Generated 330891 of the 330891 non-bonded parameter combinations 89: 89: Generated 330891 of the 330891 1-4 parameter combinations 89: 89: Excluding 2 bonded neighbours molecule type 'SOL' 89: 89: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/spc216.gro' 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: Writing final coordinates. 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.055 0.028 199.2 89: (ns/day) (hour/ns) 89: Performance: 65.480 0.367 89: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3.edr as single precision energy file 89: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/3 (583 ms) 89: [----------] 4 tests from PullTest/PullIntegrationTest (2666 ms total) 89: 89: [----------] Global test environment tear-down 89: [==========] 4 tests from 1 test suite ran. (2724 ms total) 89: [ PASSED ] 4 tests. 89/94 Test #89: MdrunPullTests ............................... Passed 3.07 sec test 90 Start 90: MdrunRotationTests 90: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/mdrun-rotation-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/MdrunRotationTests.xml" 90: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests 90: Test timeout computed to be: 600 90: [==========] Running 12 tests from 1 test suite. 90: [----------] Global test environment set-up. 90: [----------] 12 tests from RotationWorks/RotationTest 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/0 90: Enforced rotation: Group 0 (iso) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 90: trr version: GMX_trn_file (single precision) 90: 90: There were 2 NOTEs 90: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 90: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI process 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to 1070985194 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.027 0.014 198.7 90: (ns/day) (hour/ns) 90: Performance: 325.641 0.074 90: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/0 (23 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/1 90: Enforced rotation: Group 0 (iso-pf) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 90: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI process 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to -10485939 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.023 0.012 198.9 90: (ns/day) (hour/ns) 90: Performance: 390.488 0.061 90: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/1 (19 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/2 90: Enforced rotation: Group 0 (pm) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 90: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI process 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to -167904329 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.026 0.013 198.9 90: (ns/day) (hour/ns) 90: Performance: 347.236 0.069 90: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/2 (20 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/3 90: Enforced rotation: Group 0 (pm-pf) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 90: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI process 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to 802553079 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.029 0.014 198.9 90: (ns/day) (hour/ns) 90: Performance: 311.618 0.077 90: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/3 (22 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/4 90: Enforced rotation: Group 0 (rm) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 90: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI process 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to -269488706 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.065 0.033 199.5 90: (ns/day) (hour/ns) 90: Performance: 136.895 0.175 90: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/4 (40 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/5 90: Enforced rotation: Group 0 (rm-pf) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 90: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI process 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to -1140885505 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.025 0.013 198.9 90: (ns/day) (hour/ns) 90: Performance: 353.888 0.068 90: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/5 (21 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/6 90: Enforced rotation: Group 0 (rm2) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 90: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI process 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to -1418331713 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.027 0.014 199.1 90: (ns/day) (hour/ns) 90: Performance: 330.252 0.073 90: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/6 (24 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/7 90: Enforced rotation: Group 0 (rm2-pf) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 90: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI process 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to -354559025 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.028 0.014 199.0 90: (ns/day) (hour/ns) 90: Performance: 319.425 0.075 90: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/7 (22 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/8 90: Enforced rotation: Group 0 (flex) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 90: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI process 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to -312803481 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.046 0.023 199.3 90: (ns/day) (hour/ns) 90: Performance: 193.117 0.124 90: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/8 (31 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/9 90: Enforced rotation: Group 0 (flex-t) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 90: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI process 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to 2140657139 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.026 0.013 198.7 90: (ns/day) (hour/ns) 90: Performance: 338.571 0.071 90: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/9 (21 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/10 90: Enforced rotation: Group 0 (flex2) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 90: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI process 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to 1039662847 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.031 0.016 199.0 90: (ns/day) (hour/ns) 90: Performance: 284.072 0.084 90: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/10 (26 ms) 90: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/11 90: Enforced rotation: Group 0 (flex2-t) normalized rot. vector: 0.267261 0.534522 0.801784 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11_input.mdp]: 90: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 90: that with the Verlet scheme, nstlist has no effect on the accuracy of 90: your simulation. 90: 90: Rotation group 0 'system' has 4 atoms 90: Number of degrees of freedom in T-Coupling group rest is 9.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11_input.mdp]: 90: NVE simulation with an initial temperature of zero: will use a Verlet 90: buffer of 10%. Check your energy drift! 90: 90: Enforced rotation: group 0 has 4 reference positions. 90: Reading them from /build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/rotref.0.trr. 90: 90: There were 2 NOTEs 90: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 90: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI process 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 90: 25 steps, 0.1 ps. 90: Setting the LD random seed to 457406462 90: 90: Generated 1 of the 1 non-bonded parameter combinations 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonA' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonB' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonC' 90: 90: Excluding 1 bonded neighbours molecule type 'ArgonD' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 90: 90: This run will generate roughly 0 Mb of data 90: 90: Writing final coordinates. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.028 0.014 198.9 90: (ns/day) (hour/ns) 90: Performance: 321.985 0.075 90: Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.edr as single precision energy file 90: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 90: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/11 (22 ms) 90: [----------] 12 tests from RotationWorks/RotationTest (298 ms total) 90: 90: [----------] Global test environment tear-down 90: [==========] 12 tests from 1 test suite ran. (367 ms total) 90: [ PASSED ] 12 tests. 90/94 Test #90: MdrunRotationTests ........................... Passed 0.70 sec test 91 Start 91: MdrunSimulatorComparison 91: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/mdrun-simulator-comparison-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/MdrunSimulatorComparison.xml" 91: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests 91: Test timeout computed to be: 600 91: [==========] Running 0 tests from 0 test suites. 91: [==========] 0 tests from 0 test suites ran. (0 ms total) 91: [ PASSED ] 0 tests. 91: 91: YOU HAVE 82 DISABLED TESTS 91: 91/94 Test #91: MdrunSimulatorComparison ..................... Passed 0.34 sec test 92 Start 92: MdrunVirtualSiteTests 92: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2025.0/build/mpi/bin/mdrun-vsites-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2025.0/build/mpi/Testing/Temporary/MdrunVirtualSiteTests.xml" 92: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests 92: Test timeout computed to be: 600 92: [==========] Running 37 tests from 2 test suites. 92: [----------] Global test environment set-up. 92: [----------] 1 test from VirtualSiteVelocityTest 92: [ RUN ] VirtualSiteVelocityTest.ReferenceIsCorrect 92: [ OK ] VirtualSiteVelocityTest.ReferenceIsCorrect (0 ms) 92: [----------] 1 test from VirtualSiteVelocityTest (8 ms total) 92: 92: [----------] 36 tests from VelocitiesConformToExpectations/VirtualSiteTest 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/0 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 92: NVE simulation with an initial temperature of zero: will use a Verlet 92: buffer of 10%. Check your energy drift! 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: This run will generate roughly 0 Mb of data 92: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI processes 92: Using 1 OpenMP thread per MPI process 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: 92: Dynamic load balancing report: 92: DLB was off during the run due to low measured imbalance. 92: Average load imbalance: 7.5%. 92: The balanceable part of the MD step is 36%, load imbalance is computed from this. 92: Part of the total run time spent waiting due to load imbalance: 2.7%. 92: 92: 92: NOTE: 50 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.376 0.188 199.9 92: (ns/day) (hour/ns) 92: Performance: 4.135 5.804 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading virtual site types... 92: trr version: GMX_trn_file (single precision) 92: 92: Reading virtual site types... 92: trr version: GMX_trn_file (single precision) 92: 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/0 (199 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/1 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 92: NVE simulation with an initial temperature of zero: will use a Verlet 92: buffer of 10%. Check your energy drift! 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: This run will generate roughly 0 Mb of data 92: 92: There were 4 NOTEs 92: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI processes 92: Using 1 OpenMP thread per MPI process 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: 92: Dynamic load balancing report: 92: DLB was off during the run due to low measured imbalance. 92: Average load imbalance: 21.2%. 92: The balanceable part of the MD step is 17%, load imbalance is computed from this. 92: Part of the total run time spent waiting due to load imbalance: 3.6%. 92: 92: 92: NOTE: 47 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.027 0.013 198.1 92: (ns/day) (hour/ns) 92: Performance: 57.714 0.416 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading virtual site types... 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: 92: Reading virtual site types... 92: 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/1 (25 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/2 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: This run will generate roughly 0 Mb of data 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 92: NVE simulation with an initial temperature of zero: will use a Verlet 92: buffer of 10%. Check your energy drift! 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI processes 92: Using 1 OpenMP thread per MPI process 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: 92: Dynamic load balancing report: 92: DLB was off during the run due to low measured imbalance. 92: Average load imbalance: 23.8%. 92: The balanceable part of the MD step is 17%, load imbalance is computed from this. 92: Part of the total run time spent waiting due to load imbalance: 4.0%. 92: 92: 92: NOTE: 47 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.032 0.016 198.0 92: (ns/day) (hour/ns) 92: Performance: 48.290 0.497 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading virtual site types... 92: 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading virtual site types... 92: 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/2 (26 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/3 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 92: artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: You are using a plain Coulomb cut-off, which might produce 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI processes 92: Using 1 OpenMP thread per MPI process 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: NOTE: 47 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.021 0.011 197.4 92: (ns/day) (hour/ns) 92: Performance: 72.935 0.329 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading virtual site types... 92: 92: Reading virtual site types... 92: 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/3 (32 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/4 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI processes 92: Using 1 OpenMP thread per MPI process 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: NOTE: 47 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.019 0.009 197.8 92: (ns/day) (hour/ns) 92: Performance: 82.433 0.291 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading virtual site types... 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: 92: Reading virtual site types... 92: 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/4 (28 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/5 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: pectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToEx 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI processes 92: Using 1 OpenMP thread per MPI process 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: NOTE: 47 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.023 0.012 197.2 92: (ns/day) (hour/ns) 92: Performance: 67.030 0.358 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading virtual site types... 92: Reading virtual site types... 92: 92: 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/5 (29 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/6 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 92: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 92: 1 92: 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 5 NOTEs 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI processes 92: Using 1 OpenMP thread per MPI process 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: NOTE: 47 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.017 0.009 197.1 92: (ns/day) (hour/ns) 92: Performance: 89.008 0.270 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading virtual site types... 92: Reading virtual site types... 92: 92: 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/6 (27 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/7 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 92: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 92: 1 92: 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 5 NOTEs 92: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI processes 92: Using 1 OpenMP thread per MPI process 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: NOTE: 47 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.020 0.010 197.5 92: (ns/day) (hour/ns) 92: Performance: 78.583 0.305 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading virtual site types... 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading virtual site types... 92: 92: 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/7 (29 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/8 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 92: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 92: 1 92: 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 5 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 5 NOTEs 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI processes 92: Using 1 OpenMP thread per MPI process 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: NOTE: 47 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.023 0.012 198.5 92: (ns/day) (hour/ns) 92: Performance: 66.818 0.359 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading virtual site types... 92: Reading virtual site types... 92: 92: 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/8 (29 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/9 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 92: NVE simulation with an initial temperature of zero: will use a Verlet 92: buffer of 10%. Check your energy drift! 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI processes 92: Using 1 OpenMP thread per MPI process 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: This run will generate roughly 0 Mb of data 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: 92: Dynamic load balancing report: 92: DLB was off during the run due to low measured imbalance. 92: Average load imbalance: 17.3%. 92: The balanceable part of the MD step is 27%, load imbalance is computed from this. 92: Part of the total run time spent waiting due to load imbalance: 4.7%. 92: 92: 92: NOTE: 47 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.030 0.015 197.9 92: (ns/day) (hour/ns) 92: Performance: 51.943 0.462 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading virtual site types... 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: 92: Reading virtual site types... 92: 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/9 (24 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/10 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: This run will generate roughly 0 Mb of data 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 92: NVE simulation with an initial temperature of zero: will use a Verlet 92: buffer of 10%. Check your energy drift! 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI processes 92: Using 1 OpenMP thread per MPI process 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: 92: Dynamic load balancing report: 92: DLB was off during the run due to low measured imbalance. 92: Average load imbalance: 6.8%. 92: The balanceable part of the MD step is 40%, load imbalance is computed from this. 92: Part of the total run time spent waiting due to load imbalance: 2.7%. 92: 92: 92: NOTE: 47 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.022 0.011 197.1 92: (ns/day) (hour/ns) 92: Performance: 71.186 0.337 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading virtual site types... 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/10 (21 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/11 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/11 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/12 92: 92: 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI processes 92: Using 1 OpenMP thread per MPI process 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: NOTE: 47 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.018 0.009 197.9 92: (ns/day) (hour/ns) 92: Performance: 84.965 0.282 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: 92: Reading virtual site types... 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/12 (28 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/13 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI processes 92: Using 1 OpenMP thread per MPI process 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: NOTE: 46 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.025 0.013 197.3 92: (ns/day) (hour/ns) 92: Performance: 61.282 0.392 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading virtual site types... 92: 92: Reading virtual site types... 92: 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/13 (32 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/14 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/14 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/15 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI processes 92: Using 1 OpenMP thread per MPI process 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: NOTE: 47 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.026 0.013 197.7 92: (ns/day) (hour/ns) 92: Performance: 59.900 0.401 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading virtual site types... 92: 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading virtual site types... 92: 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/15 (33 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/16 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI processes 92: Using 1 OpenMP thread per MPI process 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: NOTE: 47 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.023 0.012 196.9 92: (ns/day) (hour/ns) 92: Performance: 65.331 0.367 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading virtual site types... 92: 92: Reading virtual site types... 92: 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/16 (31 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/17 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/17 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/18 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: 92: This run will generate roughly 0 Mb of data 92: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI processes 92: Using 1 OpenMP thread per MPI process 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: NOTE: 47 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.023 0.012 198.4 92: (ns/day) (hour/ns) 92: Performance: 66.645 0.360 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading virtual site types... 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExp 92: ectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading virtual site types... 92: 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/18 (29 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/19 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI processes 92: Using 1 OpenMP thread per MPI process 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: NOTE: 47 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.022 0.011 198.2 92: (ns/day) (hour/ns) 92: Performance: 71.023 0.338 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading virtual site types... 92: 92: Reading virtual site types... 92: 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/19 (28 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/20 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2025.0/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: 92: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI processes 92: Using 1 OpenMP thread per MPI process 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: NOTE: 48 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.024 0.012 198.5 92: (ns/day) (hour/ns) 92: Performance: 65.378 0.367 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading virtual site types... 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: 92: 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/20 (31 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/21 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/21 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/22 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/22 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/23 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/23 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/24 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/24 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/25 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/25 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/26 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/26 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/27 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: 92: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI processes 92: Using 1 OpenMP thread per MPI process 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: NOTE: 49 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.061 0.031 199.2 92: (ns/day) (hour/ns) 92: Performance: 25.355 0.947 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading virtual site types... 92: Reading virtual site types... 92: 92: 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/27 (60 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/28 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: There were 4 NOTEs 92: 92: This run will generate roughly 0 Mb of data 92: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI processes 92: Using 1 OpenMP thread per MPI process 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: NOTE: 47 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.022 0.011 197.8 92: (ns/day) (hour/ns) 92: Performance: 69.767 0.344 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: 92: Reading virtual site types... 92: Reading virtual site types... 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/28 (40 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/29 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 92: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 92: that with the Verlet scheme, nstlist has no effect on the accuracy of 92: your simulation. 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 92: Setting nstcalcenergy (100) equal to nstenergy (4) 92: 92: Generated 3 of the 6 non-bonded parameter combinations 92: 92: Excluding 3 bonded neighbours molecule type 'VSTEST' 92: 92: Cleaning up constraints and constant bonded interactions with virtual sites 92: 92: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 92: 92: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: 92: This run will generate roughly 0 Mb of data 92: Number of degrees of freedom in T-Coupling group System is 45.00 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 92: There are 6 non-linear virtual site constructions. Their contribution to 92: the energy error is approximated. In most cases this does not affect the 92: error significantly. 92: 92: 92: NOTE 4 [file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 92: You are using a plain Coulomb cut-off, which might produce artifacts. 92: You might want to consider using PME electrostatics. 92: 92: 92: 92: There were 4 NOTEs 92: Compiled SIMD is SSE4.1, but AVX_256 might be faster (see log). 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 92: 92: Update groups can not be used for this system because an incompatible virtual site type is used 92: 92: Using 2 MPI processes 92: Using 1 OpenMP thread per MPI process 92: 92: 92: NOTE: The number of threads is not equal to the number of (logical) cpus 92: and the -pin option is set to auto: will not pin threads to cpus. 92: This can lead to significant performance degradation. 92: Consider using -pin on (and -pinoffset in case you run multiple jobs). 92: starting mdrun 'Virtual sites test system in vacuo' 92: 8 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: NOTE: 46 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.019 0.009 196.5 92: (ns/day) (hour/ns) 92: Performance: 81.961 0.293 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading virtual site types... 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: Reading file /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2025.0-Debian_2025.0_2 (single precision) 92: 92: Reading virtual site types... 92: 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/29 (39 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/30 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/30 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/31 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/31 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/32 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/32 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/33 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/33 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/34 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/34 (0 ms) 92: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/35 92: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/35 (0 ms) 92: [----------] 36 tests from VelocitiesConformToExpectations/VirtualSiteTest (834 ms total) 92: 92: [----------] Global test environment tear-down 92: [==========] 37 tests from 2 test suites ran. (895 ms total) 92: [ PASSED ] 37 tests. 92/94 Test #92: MdrunVirtualSiteTests ........................ Passed 1.38 sec test 93 Start 93: EnsembleHistogramPotentialPlugin.ForceCalc 93: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/gmxapi_extension_histogram-test "--gtest_filter=EnsembleHistogramPotentialPlugin.ForceCalc" 93: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/tests 93: Test timeout computed to be: 1500 93: Running main() from ./src/external/googletest/googletest/src/gtest_main.cc 93: Note: Google Test filter = EnsembleHistogramPotentialPlugin.ForceCalc 93: [==========] Running 1 test from 1 test suite. 93: [----------] Global test environment set-up. 93: [----------] 1 test from EnsembleHistogramPotentialPlugin 93: [ RUN ] EnsembleHistogramPotentialPlugin.ForceCalc 93: [ OK ] EnsembleHistogramPotentialPlugin.ForceCalc (0 ms) 93: [----------] 1 test from EnsembleHistogramPotentialPlugin (0 ms total) 93: 93: [----------] Global test environment tear-down 93: [==========] 1 test from 1 test suite ran. (0 ms total) 93: [ PASSED ] 1 test. 93/94 Test #93: EnsembleHistogramPotentialPlugin.ForceCalc ... Passed 0.27 sec test 94 Start 94: EnsembleBoundingPotentialPlugin.ForceCalc 94: Test command: /build/reproducible-path/gromacs-2025.0/build/mpi/bin/gmxapi_extension_bounding-test "--gtest_filter=EnsembleBoundingPotentialPlugin.ForceCalc" 94: Working Directory: /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/tests 94: Test timeout computed to be: 1500 94: Running main() from ./src/external/googletest/googletest/src/gtest_main.cc 94: Note: Google Test filter = EnsembleBoundingPotentialPlugin.ForceCalc 94: [==========] Running 1 test from 1 test suite. 94: [----------] Global test environment set-up. 94: [----------] 1 test from EnsembleBoundingPotentialPlugin 94: [ RUN ] EnsembleBoundingPotentialPlugin.ForceCalc 94: [ OK ] EnsembleBoundingPotentialPlugin.ForceCalc (0 ms) 94: [----------] 1 test from EnsembleBoundingPotentialPlugin (0 ms total) 94: 94: [----------] Global test environment tear-down 94: [==========] 1 test from 1 test suite ran. (0 ms total) 94: [ PASSED ] 1 test. 94/94 Test #94: EnsembleBoundingPotentialPlugin.ForceCalc .... Passed 0.27 sec 100% tests passed, 0 tests failed out of 94 Label Time Summary: GTest = 474.13 sec*proc (90 tests) IntegrationTest = 213.13 sec*proc (30 tests) MpiTest = 338.42 sec*proc (23 tests) QuickGpuTest = 62.36 sec*proc (22 tests) SlowGpuTest = 316.87 sec*proc (14 tests) SlowTest = 228.93 sec*proc (14 tests) UnitTest = 32.07 sec*proc (46 tests) Total Test time (real) = 272.47 sec touch build-mpi dh_testdir (mkdir -p build/documentation ; cd build/documentation; \ LD_LIBRARY_PATH=/build/reproducible-path/gromacs-2025.0/build/documentation/lib cmake /build/reproducible-path/gromacs-2025.0 \ -DCMAKE_BUILD_TYPE=Debug -DGMX_OPENMP=OFF -DGMX_SIMD=None -DGMXAPI=ON \ -DGMX_PYTHON_PACKAGE=ON -DGMX_GPU=OFF -DCMAKE_VERBOSE_MAKEFILE=ON \ -DCMAKE_RULE_MESSAGES=OFF -DGMX_BUILD_MANUAL=ON -DGMX_BUILD_HELP=ON \ -DGMX_VERSION_STRING_OF_FORK="Debian-2025.0-2") -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Python3: /usr/bin/python3 (found suitable version "3.13.2", minimum required is "3.9") found components: Interpreter Development Development.Module Development.Embed -- Performing Test CFLAGS_PRAGMA -- Performing Test CFLAGS_PRAGMA - Success -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_PRAGMA -- Performing Test CXXFLAGS_PRAGMA - Success -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- GROMACS is being built without library MPI support (-DGMX_MPI=no). However MPI is potentially useful for the gmxapi Python API, so we will search for MPI anyway. If this causes problems, disable the check with -DCMAKE_DISABLE_FIND_PACKAGE_MPI=on. -- Found MPI_CXX: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") found components: CXX -- Performing Test HAS_WARNING_NO_OLD_STYLE_CAST -- Performing Test HAS_WARNING_NO_OLD_STYLE_CAST - Success -- Performing Test HAS_WARNING_NO_CAST_QUAL -- Performing Test HAS_WARNING_NO_CAST_QUAL - Success -- Performing Test HAS_WARNING_NO_SUGGEST_OVERRIDE -- Performing Test HAS_WARNING_NO_SUGGEST_OVERRIDE - Success -- Performing Test HAS_WARNING_NO_SUGGEST_DESTRUCTOR_OVERRIDE -- Performing Test HAS_WARNING_NO_SUGGEST_DESTRUCTOR_OVERRIDE - Success -- Performing Test HAS_WARNING_NO_ZERO_AS_NULL_POINTER_CONSTANT -- Performing Test HAS_WARNING_NO_ZERO_AS_NULL_POINTER_CONSTANT - Success -- Torch not found. Neural network potential support will be disabled. -- Using default binary suffix: "" -- Using default library suffix: "" -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Performing Test TEST_ATOMICS -- Performing Test TEST_ATOMICS - Success -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- SIMD instructions disabled -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - supported -- Detected build CPU vendor - AMD -- Detected build CPU brand - AMD Opteron 62xx class CPU -- Detected build CPU family - 21 -- Detected build CPU model - 1 -- Detected build CPU stepping - 2 -- Detected build CPU features - aes amd apic avx clfsh cmov cx8 cx16 lahf misalignsse mmx msr pclmuldq pdpe1gb popcnt pse rdtscp sse2 sse3 sse4a sse4.1 sse4.2 ssse3 x2apic -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - not present -- Checking for module 'fftw3f' -- Found fftw3f, version 3.3.10 -- Looking for fftwf_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/x86_64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- Found LAPACK: /usr/lib/x86_64-linux-gnu/liblapack.so;/usr/lib/x86_64-linux-gnu/libblas.so -- Performing Test HAS_WARNING_EVERYTHING -- Performing Test HAS_WARNING_EVERYTHING - Failed -- Found Python: /usr/bin/python3 (found version "3.13.2") found components: Interpreter -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Performing Test HAVE_NO_DEBUG_DISABLES_OPTIMIZATION -- Performing Test HAVE_NO_DEBUG_DISABLES_OPTIMIZATION - Success -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Looking for inttypes.h -- Looking for inttypes.h - found -- Performing Test HAS_WARNING_NO_DEPRECATED_NON_PROTOTYPE -- Performing Test HAS_WARNING_NO_DEPRECATED_NON_PROTOTYPE - Success -- Looking for dlopen -- Looking for dlopen - found -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success -- Performing Test COMPILER_HAS_DEPRECATED_ATTR -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success -- Performing Test HAS_FLTO -- Performing Test HAS_FLTO - Success -- Configuring Python package for gmxapi version 0.4.0 -- Using /build/reproducible-path/gromacs-2025.0/build/documentation/bin/gmx from build tree. -- Found pybind11: /usr/include (found version "2.13.6") -- Found Python interpreter: /usr/bin/python3 -- Python site-packages directory is /usr/lib/python./site-packages -- Found Doxygen: /usr/bin/doxygen (found version "1.9.8") found components: doxygen dot -- Performing Test HAVE_NO_IMPLICIT_INT_FLOAT_CONVERSION -- Performing Test HAVE_NO_IMPLICIT_INT_FLOAT_CONVERSION - Success -- Found Sphinx: /usr/bin/sphinx-build (found suitable version "8.1.3", minimum required is "4.0.0") found components: pygments -- Found LATEX: /usr/bin/latex -- Configuring done (30.2s) -- Generating done (1.7s) -- Build files have been written to: /build/reproducible-path/gromacs-2025.0/build/documentation /usr/bin/make -j20 manual -C build/documentation make[1]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/cmake -P /build/reproducible-path/gromacs-2025.0/build/documentation/CMakeFiles/VerifyGlobs.cmake /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.0 -B/build/reproducible-path/gromacs-2025.0/build/documentation --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/make -f CMakeFiles/Makefile2 manual make[2]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/cmake -P /build/reproducible-path/gromacs-2025.0/build/documentation/CMakeFiles/VerifyGlobs.cmake /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.0 -B/build/reproducible-path/gromacs-2025.0/build/documentation --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.0/build/documentation/CMakeFiles 68 /usr/bin/make -f CMakeFiles/Makefile2 docs/manual/CMakeFiles/manual.dir/all make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f docs/CMakeFiles/sphinx-image-conversion.dir/build.make docs/CMakeFiles/sphinx-image-conversion.dir/depend /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/docs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/docs /build/reproducible-path/gromacs-2025.0/build/documentation/docs/CMakeFiles/sphinx-image-conversion.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/selection /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/selection /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/CMakeFiles/release-version-info.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.0/build/documentation/src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_zlib.dir/build.make src/gromacs/CMakeFiles/tng_io_zlib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/CMakeFiles/tng_io_zlib.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f docs/CMakeFiles/sphinx-image-conversion.dir/build.make docs/CMakeFiles/sphinx-image-conversion.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/CMakeFiles/colvars_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f _deps/muparser-build/CMakeFiles/muparser.dir/build.make _deps/muparser-build/CMakeFiles/muparser.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/analysis/plots/sgangle.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/analysis/plots/sgangle.png make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/plots/decomp.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/plots/decomp.png make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/external/muparser /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/_deps/muparser-build /build/reproducible-path/gromacs-2025.0/build/documentation/_deps/muparser-build/CMakeFiles/muparser.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/plots/dih.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/plots/dih.png make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -MF CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o.d -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/lmfit/lmmin.cpp /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/plots/drift-all.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/plots/drift-all.png make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/plots/f-angle.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/plots/f-angle.png make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/options /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/options /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/plots/f-bond.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/plots/f-bond.png make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2025.0-Debian_2025.0_2 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2025.0 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.0/build/documentation/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2025.0/build/documentation/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2025.0-2 -P /build/reproducible-path/gromacs-2025.0/cmake/gmxGenerateVersionInfoWithoutGit.cmake make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/plots/fp-highres.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/plots/fp-highres.png make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/parser.cpp.o -MF CMakeFiles/scanner.dir/parser.cpp.o.d -o CMakeFiles/scanner.dir/parser.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/parser.cpp /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/plots/int-mat.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/plots/int-mat.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -isystem 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-I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -MF CMakeFiles/linearalgebra.dir/eigensolver.cpp.o.d -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/eigensolver.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/abstractoption.cpp.o -MF CMakeFiles/options.dir/abstractoption.cpp.o.d -o CMakeFiles/options.dir/abstractoption.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/options/abstractoption.cpp [ 0%] Built target release-version-info cd 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cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/docs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/docs /build/reproducible-path/gromacs-2025.0/build/documentation/docs/CMakeFiles/sphinx-input-rst.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/energyanalysis && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/energyterm.cpp.o -MF CMakeFiles/energyanalysis.dir/energyterm.cpp.o.d -o CMakeFiles/energyanalysis.dir/energyterm.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis/energyterm.cpp /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/programs /build/reproducible-path/gromacs-2025.0/build/documentation/src/programs/CMakeFiles/gmx_objlib.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f docs/CMakeFiles/sphinx-input-rst.dir/build.make docs/CMakeFiles/sphinx-input-rst.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/analysis/plots/sgangle.pdf 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-c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/atomic.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/external/rpc_xdr && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/rpc_xdr/xdr_array.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd 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CMakeFiles/gmx_objlib.dir/gmx.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/gmx.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/plots/ring.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/plots/ring.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -D VERSION_VARIABLES=/build/reproducible-path/gromacs-2025.0/build/documentation/VersionInfo.cmake -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.0/docs/conf.cmakein.py -D VERSION_OUT=/build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/conf.py -D CMAKE_MINIMUM_REQUIRED_VERSION=3.28 -D EXPECTED_DOXYGEN_VERSION=1.8.5 -D EXPECTED_SPHINX_VERSION=4.0.0 -D GMX_ADMIN_DIR=/build/reproducible-path/gromacs-2025.0/admin -D GMX_CLANG_MINIMUM_REQUIRED_VERSION=14 -D GMX_GCC_MINIMUM_REQUIRED_VERSION=11 -D GMX_LMFIT_REQUIRED_VERSION=7.0 -D "GMX_MANUAL_DOI_STRING=This is not a release build of GROMACS, so please reference one of the GROMACS papers and the base release of the manual." -D GMX_TNG_MINIMUM_REQUIRED_VERSION=1.7.10 -D "GMX_SOURCE_DOI_STRING=This is not a release build of GROMACS. Please reference one of the GROMACS papers, as well as the base release that this version is built from. Also, please state what modifcations have been performed or where the version was sourced from." -D GMXAPI_PYTHON_STAGING_DIR=/build/reproducible-path/gromacs-2025.0/build/documentation/python_packaging/gmxapi/gmxapi_staging -D IMAGE_CONVERT_STRING=gmx_image_convert_possible -D REGRESSIONTEST_VERSION=2025.0 -D GMX_CUDA_MINIMUM_REQUIRED_COMPUTE_CAPABILITY=5.0 -D GMX_CUDA_MINIMUM_REQUIRED_VERSION=12.1 -D REQUIRED_OPENCL_MIN_VERSION= -D REGRESSIONTEST_MD5SUM_STRING=unknown -D RELENG_PATH= -D SOURCE_MD5SUM=unknown -D SPHINX_EXTENSION_PATH=/build/reproducible-path/gromacs-2025.0/docs -D "GMX_CURRENT_CONTRIBUTORS_STRING=Mark Abraham, Andrey Alekseenko, Brian Andrews, Vladimir Basov, Paul Bauer, Hugh Bird, Eliane Briand, Ania Brown, Mahesh Doijade, Giacomo Fiorin, Stefan Fleischmann, Sergey Gorelov, Gilles Gouaillardet, Alan Gray, M. Eric Irrgang, Farzaneh Jalalypour, Petter Johansson, Carsten Kutzner, Grzegorz Łazarski, Justin A. Lemkul, Magnus Lundborg, Pascal Merz, Vedran Miletić, Dmitry Morozov, Lukas Müllender, Julien Nabet, Szilárd Páll, Andrea Pasquadibisceglie, Michele Pellegrino, Nicola Piasentin, Daniele Rapetti, Muhammad Umair Sadiq, Hubert Santuz, Roland Schulz, Michael Shirts, Tatiana Shugaeva, Alexey Shvetsov, Philip Turner, Alessandra Villa, Sebastian Wingbermühle" -D "GMX_PREVIOUS_CONTRIBUTORS_STRING=Emile Apol, Rossen Apostolov, James Barnett, Herman J.C. Berendsen, Cathrine Bergh, Par Bjelkmar, Christian Blau, Viacheslav Bolnykh, Kevin Boyd, Aldert van Buuren, Carlo Camilloni, Rudi van Drunen, Anton Feenstra, Oliver Fleetwood, Vytas Gapsys, Gaurav Garg, Gerrit Groenhof, Bert de Groot, Anca Hamuraru, Vincent Hindriksen, Victor Holanda, Aleksei Iupinov, Joe Jordan, Christoph Junghans, Prashanth Kanduri, Dimitrios Karkoulis, Peter Kasson, Sebastian Kehl, Sebastian Keller, Jiri Kraus, Per Larsson, Viveca Lindahl, Erik Marklund, Pieter Meulenhoff, Teemu Murtola, Sander Pronk, Alfons Sijbers, Balint Soproni, David van der Spoel, Peter Tieleman, Carsten Uphoff, Jon Vincent, Teemu Virolainen, Christian Wennberg, Maarten Wolf, Artem Zhmurov" -D "GMX_CURRENT_PROJECT_LEADERS_STRING=Berk Hess, Erik Lindahl" -P /build/reproducible-path/gromacs-2025.0/cmake/gmxConfigureVersionInfo.cmake cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/plots/shiftf.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/plots/shiftf.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -MF CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o.d -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/gmx_arpack.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E touch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/conf.py cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert 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-DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/lock.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -MF CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o.d -o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/programs/legacymodules.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/texindex.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/texindex.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-deprecated-non-prototype -MD -MT src/gromacs/CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/compress.c.o -MF CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/compress.c.o.d -o CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/compress.c.o -c 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-Wno-deprecated-non-prototype -MD -MT src/gromacs/CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/crc32.c.o -MF CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/crc32.c.o.d -o CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/crc32.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/external/zlib/crc32.c cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/api/gmxlibs.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/api/gmxlibs.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/algorithms/plots/free1.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/algorithms/plots/free1.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/src/pthreads.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/api/index.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/api/index.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/external/rpc_xdr && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/rpc_xdr/xdr_stdio.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/dev-manual/build-system.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/dev-manual/build-system.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/algorithms/plots/free2.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/algorithms/plots/free2.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/dev-manual/change-management.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/dev-manual/change-management.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy 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-I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-deprecated-non-prototype -MD -MT src/gromacs/CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/deflate.c.o -MF CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/deflate.c.o.d -o CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/deflate.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/external/zlib/deflate.c cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/bwt.c cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/algorithms/plots/lincs.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/algorithms/plots/lincs.png cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/dev-manual/contribute.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/dev-manual/contribute.rst make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/dev-manual/doxygen.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/dev-manual/doxygen.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/algorithms/plots/maxwell.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/algorithms/plots/maxwell.png [ 0%] Built target internal_rpc_xdr cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/dev-manual/error-handling.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/dev-manual/error-handling.rst /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/programs /build/reproducible-path/gromacs-2025.0/build/documentation/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/dev-manual/formatting.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/dev-manual/formatting.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2025.0/docs/reference-manual/algorithms/plots/mpmd-pme.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input//reference-manual/algorithms/plots/mpmd-pme.png make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[4]: 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/rle.c cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /build/reproducible-path/gromacs-2025.0/src/external/tng_io/src/compression/tng_compress.c cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2023/2023.5.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2023/2023.5.rst [ 1%] Built target energyanalysis cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 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/build/reproducible-path/gromacs-2025.0/docs/release-notes/2020/major/miscellaneous.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2020/major/miscellaneous.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2019/2019.6.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2019/2019.6.rst [ 2%] Built target tng_io_zlib cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o -MF 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/build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2016/major/performance.rst make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2016/major/tools.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2016/major/tools.rst [ 4%] Built target thread_mpi cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/release-notes/2016/major/bugs-fixed.rst /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2016/major/bugs-fixed.rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy 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/build/reproducible-path/gromacs-2025.0/build/documentation/_deps/muparser-build && /usr/bin/cmake -E cmake_symlink_library ../../lib/libmuparser.so.2.3.4 ../../lib/libmuparser.so.2 ../../lib/libmuparser.so cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/functions/plots/subst-im.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/functions/plots/subst-im.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/functions/plots/tetra-im.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/functions/plots/tetra-im.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/functions/plots/vcrf.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/functions/plots/vcrf.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/functions/plots/vsite-4fdn.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/functions/plots/vsite-4fdn.pdf make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/special/plots/awh-invN.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/special/plots/awh-invN.pdf [ 11%] Built target muparser /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/special/plots/awh-pmfs.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/special/plots/awh-pmfs.pdf make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/pulling /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/special/plots/awh-sampleweights.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/special/plots/awh-sampleweights.pdf make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/special/plots/awh-traj.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/special/plots/awh-traj.pdf /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/output.cpp.o -MF CMakeFiles/pulling.dir/output.cpp.o.d -o CMakeFiles/pulling.dir/output.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/output.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/special/plots/compelsetup.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/special/plots/compelsetup.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy 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/build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/special/plots/gaussians.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/special/plots/gaussians.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/special/plots/lambda-values.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/special/plots/lambda-values.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/special/plots/pulldirrel.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/special/plots/pulldirrel.pdf cd 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/build/reproducible-path/gromacs-2025.0/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pull.cpp.o -MF CMakeFiles/pulling.dir/pull.cpp.o.d -o CMakeFiles/pulling.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/pull.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/docs/reference-manual/special/plots/pull.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/reference-manual/special/plots/pull.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy 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/usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pull_rotation.cpp.o -MF CMakeFiles/pulling.dir/pull_rotation.cpp.o.d -o CMakeFiles/pulling.dir/pull_rotation.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/pull_rotation.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [ 36%] Built target sphinx-input-rst cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT 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-ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvartypes.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvartypes.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvartypes.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/external/colvars/colvartypes.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarvalue.cpp.o -MF 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src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd 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-I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o -MF CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o.d -o CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/decidesimulationworkload.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/findallgputasks.cpp.o -MF CMakeFiles/taskassignment.dir/findallgputasks.cpp.o.d -o CMakeFiles/taskassignment.dir/findallgputasks.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/findallgputasks.cpp /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/andersentemperaturecoupling.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o -MF 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src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/firstorderpressurecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/firstorderpressurecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/firstorderpressurecoupling.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/firstorderpressurecoupling.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include 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/build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/referencetemperaturemanager.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include 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Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [ 38%] Built target taskassignment cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include 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/build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/simulatoralgorithm.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include 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/build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/statepropagatordata.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include 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/build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/topologyholder.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include 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/build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/trajectoryelement.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/velocityscalingtemperaturecoupling.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [ 41%] Built target colvars_objlib make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [ 42%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/reproducible-path/gromacs-2025.0/build/documentation/VersionInfo.cmake -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /build/reproducible-path/gromacs-2025.0/cmake/gmxConfigureVersionInfo.cmake cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 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/build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/g96io.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include 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-I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/x86_64-linux-gnu/openmpi/include 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-I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem 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-Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_merge.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_permute.cpp cd 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-I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_position.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_same.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_simple.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/external/tng_io/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/tng/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2025.0/src/external -isystem /build/reproducible-path/gromacs-2025.0/src/gromacs/../external/rpc_xdr -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /build/reproducible-path/gromacs-2025.0/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/lmfit -isystem /build/reproducible-path/gromacs-2025.0/src/external/colvars -isystem /build/reproducible-path/gromacs-2025.0/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -MF CMakeFiles/libgromacs.dir/selection/symrec.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -c /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/symrec.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/cmake -E cmake_link_script CMakeFiles/libgromacs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wl,--dependency-file=CMakeFiles/libgromacs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgromacs.so.10 -o ../../lib/libgromacs.so.10.0.0 @CMakeFiles/libgromacs.dir/objects1.rsp -Wl,-rpath,"\$ORIGIN/../lib:/usr/lib/x86_64-linux-gnu/openmpi/lib" -lrt /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so -lm /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm -lm ../../lib/libmuparser.so.2.3.4 -ldl cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgromacs.so.10.0.0 ../../lib/libgromacs.so.10 ../../lib/libgromacs.so make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [ 98%] Built target 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'/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/src/programs && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmx.dir/link.txt --verbose=1 make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/gmxapi /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/api/gmxapi /build/reproducible-path/gromacs-2025.0/build/documentation/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build make[4]: Entering directory 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/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp/workflow.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2025.0/src/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/src/include -I/build/reproducible-path/gromacs-2025.0/src -I/build/reproducible-path/gromacs-2025.0/src/gromacs/math/include -I/build/reproducible-path/gromacs-2025.0/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2025.0/src/external/thread_mpi/include -isystem 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CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../bin/gmx -Wl,-rpath,"\$ORIGIN/../lib" ../../lib/libgromacs.so.10.0.0 -lm -Wl,-rpath-link,/build/reproducible-path/gromacs-2025.0/build/documentation/lib make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [ 98%] Built target gmx cd /build/reproducible-path/gromacs-2025.0/build/documentation/api/gmxapi && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wl,--dependency-file=CMakeFiles/gmxapi.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgmxapi.so.0 -o ../../lib/libgmxapi.so.0.4.0 CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o CMakeFiles/gmxapi.dir/cpp/context.cpp.o CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o CMakeFiles/gmxapi.dir/cpp/md.cpp.o CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o CMakeFiles/gmxapi.dir/cpp/session.cpp.o CMakeFiles/gmxapi.dir/cpp/status.cpp.o CMakeFiles/gmxapi.dir/cpp/system.cpp.o CMakeFiles/gmxapi.dir/cpp/version.cpp.o CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o -Wl,-rpath,"\$ORIGIN/../lib" ../../lib/libgromacs.so.10.0.0 -lm -Wl,-rpath-link,/build/reproducible-path/gromacs-2025.0/build/documentation/lib cd /build/reproducible-path/gromacs-2025.0/build/documentation/api/gmxapi && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgmxapi.so.0.4.0 ../../lib/libgmxapi.so.0 ../../lib/libgmxapi.so make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [ 98%] Built target gmxapi /usr/bin/make -f python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build.make python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/python_packaging/gmxapi /build/reproducible-path/gromacs-2025.0/build/documentation/python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build.make python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/python_packaging/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 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/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fvisibility=hidden -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/gmxpy_exceptions.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/gmxpy_exceptions.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/gmxpy_exceptions.cpp.o -c /build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi/src/cpp/gmxpy_exceptions.cpp cd /build/reproducible-path/gromacs-2025.0/build/documentation/python_packaging/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2025.0/build/documentation/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2025.0/api/gmxapi/include -I/build/reproducible-path/gromacs-2025.0/build/documentation/api/gmxapi/include -isystem /usr/include/python3.13 -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2025.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fvisibility=hidden -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/pycontext.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/pycontext.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/pycontext.cpp.o -c 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LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi.MDSes sion' on page 586 undefined on input line 64637. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi .SimulationParameters' on page 586 undefined on input line 64662. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi.Simul ationParameters' on page 586 undefined on input line 64662. [586] LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi .TprFile' on page 587 undefined on input line 64734. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi.TprFi le' on page 587 undefined on input line 64734. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi .SimulationParameters' on page 587 undefined on input line 64734. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi.Simul ationParameters' on page 587 undefined on input line 64734. [587] Chapter 7. [588] [589] [590] [591] Underfull \hbox (badness 10000) in paragraph at lines 65303--65303 []\T1/ptm/m/n/10 Bool Underfull \hbox (badness 10000) in paragraph at lines 65303--65303 []\T1/ptm/m/n/10 Ker-nel SIMD type (\T1/pcr/m/n/10 SimdAuto\T1/ptm/m/n/10 /\T1/ pcr/m/n/10 SimdNo\T1/ptm/m/n/10 /\T1/pcr/m/n/10 Simd4XM\T1/ptm/m/n/10 / Underfull \hbox (badness 10000) in paragraph at lines 65303--65303 []\T1/pcr/m/n/10 useHalfLJOptimizat Underfull \hbox (badness 10000) in paragraph at lines 65303--65303 []\T1/ptm/m/n/10 Bool Underfull \hbox (badness 10000) in paragraph at lines 65303--65303 []\T1/pcr/m/n/10 computeVirialAndEn Underfull \hbox (badness 10000) in paragraph at lines 65303--65303 []\T1/ptm/m/n/10 Bool Underfull \hbox (badness 10000) in paragraph at lines 65303--65303 []\T1/ptm/m/n/10 Coulomb in-ter-ac-tion func-tion Underfull \hbox (badness 10000) in paragraph at lines 65303--65303 []\T1/pcr/m/n/10 useTabulatedEwaldC Underfull \hbox (badness 10000) in paragraph at lines 65303--65303 []\T1/ptm/m/n/10 Bool Underfull \hbox (badness 10000) in paragraph at lines 65303--65303 []\T1/ptm/m/n/10 Bool [592] [593] [594] Chapter 8. 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[419 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.27 4}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.45729 <./vsite-4fdn.pdf>] [420] [421] [422] [423 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.28 7}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.46108 \end{equation} ] [424 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.29 4}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.46193 \paragraph{Using LJ\sphinxhyphen{}PME} pdfTeX warning (ext4): destination with the same identifier (name{equation.5.29 5}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.46193 \paragraph{Using LJ\sphinxhyphen{}PME} ] [425] [426] [427] [428] [429] [430] [431] [432] [433] [434] [435] Underfull \vbox (badness 2368) detected at line 47468 [436] [437] [438] [439] [440] [441] Underfull \hbox (badness 10000) in paragraph at lines 48166--48169 []\T1/pcr/m/n/10 resA atomA nbondsA resB atomB nbondsB length newresA newresB [ atomI atomJ Overfull \hbox (10.25368pt too wide) in paragraph at lines 48373--48375 []|\T1/pcr/m/n/10 dihedraltypes$[]$| Overfull \hbox (11.40642pt too wide) in paragraph at lines 48386--48388 []|\T1/pcr/m/n/10 constrainttypes| Underfull \hbox (badness 10000) in paragraph at lines 48402--48404 []|\T1/pcr/m/n/10 nonbond_- Underfull \hbox (badness 10000) in paragraph at lines 48418--48420 []|\T1/pcr/m/n/10 nonbond_- Underfull \hbox (badness 10000) in paragraph at lines 48427--48431 []|$\OML/cmm/m/it/10 a [][]$ \T1/ptm/m/n/10 ; Underfull \hbox (badness 10000) in paragraph at lines 48427--48431 \OML/cmm/m/it/10 b [][]$\T1/ptm/m/n/10 ; $\OML/cmm/m/it/10 c[]$ [442] Underfull \hbox (badness 10000) in paragraph at lines 48468--48470 []|\T1/ptm/m/n/10 molecule name; Underfull \hbox (badness 10000) in paragraph at lines 48481--48485 \T1/ptm/m/n/10 num-ber; residue [443] Underfull \hbox (badness 10000) in paragraph at lines 48619--48621 []|\T1/phv/m/n/10 Topol-ogy file Underfull \hbox (badness 10000) in paragraph at lines 48622--48625 []|\T1/phv/m/n/10 num. 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[546 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.47 7}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.59250 \clearpage ] [547] [548] [549] [550] [551] [552] [553] [554] [555] Chapter 6. [556] [557] [558] [559] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 61362. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 61362. [560] [561] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 61549. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 61549. [562] [563] Underfull \hbox (badness 10000) in paragraph at lines 61748--61751 []\T1/ptm/m/n/10 The fol-low-ing in-struc-tions are para-phrased from [][]$http s : / / pip . pypa . io / en / stable / user _ guide / [564] [565] [566] [567] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 62193. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 62193. [568] [569] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 62358. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 62358. 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[596] [597] [598] pdfTeX warning: /usr/bin/pdflatex (file ./graphviz-d18d8687359a04d68afb2d653619 8981190fe142.pdf): PDF inclusion: found PDF version <1.7>, but at most version <1.5> allowed [599] [600 <./graphviz-d18d8687359a04d68afb2d6536198981190fe142.pdf>] [601] [602] [603] [604] [605] [606] [607] [608] [609] [610] [611] [612] [613] [614] [615] [616] Underfull \hbox (badness 10000) in paragraph at lines 68023--68029 []\T1/ptm/m/n/10 The above logic to find the in-stal-la-tion pre-fix is in \T1/ pcr/m/n/10 src/gromacs/commandline/ [617] [618] [619] [620] [621] [622] [623] [624] [625] Underfull \hbox (badness 6575) in paragraph at lines 69147--69153 []\T1/ptm/m/n/10 Use smart point-ers for mem-ory man-age-ment. 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Underfull \hbox (badness 10000) in paragraph at lines 73462--73466 \T1/ptm/m/n/10 (page 669[]) can be found at \T1/pcr/m/n/10 $GROMACS_-ROOT/share /cmake/gromacs$GROMACS_-SUFFIX/ [668] [669] [670] Underfull \hbox (badness 7344) in paragraph at lines 73829--73833 []\T1/ptm/m/n/10 CMake tar-get \T1/pcr/m/n/10 Gromacs::libgromacs\T1/ptm/m/n/10 , en-abled by [][]\T1/pcr/m/sl/10 GMX_-INSTALL_-LEGACY_-API[][] [671] Chapter 11. 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[495] [496] [497 <./field.pdf>] [498 <./compelsetup.pdf>] [499] [500] [501] [502 <./dumtypes.pdf> <./dumaro.pdf pdfTeX warning: /usr/bin/pdflatex (file ./dumaro.pdf): PDF inclusion: multiple pdfs with page group included in a single page >] [503] [504] [505] [506] [507] [508] [509] [510] [511] [512] [513] [514] [515] [516] [517] [518] [519] [520] [521] [522] [523] [524] [525 <./rdf.pdf>] [526 <./rdfO-O.pdf>] [527] [528] [529] [530 <./msdwater.pdf>] [531 <./dih-def.pdf> <./sgangle.pdf pdfTeX warning: /usr/bin/pdflatex (file ./sgangle.pdf): PDF inclusion: multiple pdfs with page group included in a single page >] [532 <./distm.pdf>] [533] [534] [535 <./hbond.pdf> <./hbond-insert.pdf pdfTeX warning: /usr/bin/pdflatex (file ./hbond-insert.pdf): PDF inclusion: mul tiple pdfs with page group included in a single page >] [536 <./phipsi.pdf>] [537 <./rama.pdf> <./hpr-wheel.pdf pdfTeX warning: /usr/bin/pdflatex (file ./hpr-wheel.pdf): PDF inclusion: multip le pdfs with page group included in a single page >] [538] [539] [540 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.44 8}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.58763 ...ecular shift (mol\sphinxhyphen{}shift)} ] [541] [542] [543 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.46 1}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.59057 \end{equation} ] [544] [545 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.47 3}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.59212 \end{equation} pdfTeX warning (ext4): destination with the same identifier (name{equation.5.47 3}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.59212 \end{equation} ] pdfTeX warning (ext4): destination with the same identifier (name{equation.5.47 7}) has been already used, duplicate ignored \relax l.59215 \begin{equation} \label{equation:reference-manual/averages:eqnsigmate... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.47 7}) has been already used, duplicate ignored \relax l.59215 \begin{equation} \label{equation:reference-manual/averages:eqnsigmate... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.47 7}) has been already used, duplicate ignored \relax l.59215 \begin{equation} \label{equation:reference-manual/averages:eqnsigmate... pdfTeX warning (ext4): destination with the same identifier (name{equation.5.47 7}) has been already used, duplicate ignored \relax l.59215 \begin{equation} \label{equation:reference-manual/averages:eqnsigmate... [546 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.47 7}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.59250 \clearpage ] [547] [548] [549] [550] [551] [552] [553] [554] [555] Chapter 6. [556] [557] [558] [559] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 61362. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 61362. [560] [561] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 61549. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 61549. [562] [563] Underfull \hbox (badness 10000) in paragraph at lines 61748--61751 []\T1/ptm/m/n/10 The fol-low-ing in-struc-tions are para-phrased from [][]$http s : / / pip . pypa . io / en / stable / user _ guide / [564] [565] [566] [567] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 62193. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 62193. [568] [569] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 62358. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 62358. 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[589] [590] [591] [592] Underfull \hbox (badness 10000) in paragraph at lines 65303--65303 []\T1/ptm/m/n/10 Bool Underfull \hbox (badness 10000) in paragraph at lines 65303--65303 []\T1/ptm/m/n/10 Ker-nel SIMD type (\T1/pcr/m/n/10 SimdAuto\T1/ptm/m/n/10 /\T1/ pcr/m/n/10 SimdNo\T1/ptm/m/n/10 /\T1/pcr/m/n/10 Simd4XM\T1/ptm/m/n/10 / Underfull \hbox (badness 10000) in paragraph at lines 65303--65303 []\T1/pcr/m/n/10 useHalfLJOptimizat Underfull \hbox (badness 10000) in paragraph at lines 65303--65303 []\T1/ptm/m/n/10 Bool Underfull \hbox (badness 10000) in paragraph at lines 65303--65303 []\T1/pcr/m/n/10 computeVirialAndEn Underfull \hbox (badness 10000) in paragraph at lines 65303--65303 []\T1/ptm/m/n/10 Bool Underfull \hbox (badness 10000) in paragraph at lines 65303--65303 []\T1/ptm/m/n/10 Coulomb in-ter-ac-tion func-tion Underfull \hbox (badness 10000) in paragraph at lines 65303--65303 []\T1/pcr/m/n/10 useTabulatedEwaldC Underfull \hbox (badness 10000) in paragraph at lines 65303--65303 []\T1/ptm/m/n/10 Bool Underfull \hbox (badness 10000) in paragraph at lines 65303--65303 []\T1/ptm/m/n/10 Bool [593] [594] [595] Chapter 8. [596] [597] [598] pdfTeX warning: /usr/bin/pdflatex (file ./graphviz-d18d8687359a04d68afb2d653619 8981190fe142.pdf): PDF inclusion: found PDF version <1.7>, but at most version <1.5> allowed [599] [600 <./graphviz-d18d8687359a04d68afb2d6536198981190fe142.pdf>] [601] [602] [603] [604] [605] [606] [607] [608] [609] [610] [611] [612] [613] [614] [615] [616] Underfull \hbox (badness 10000) in paragraph at lines 68023--68029 []\T1/ptm/m/n/10 The above logic to find the in-stal-la-tion pre-fix is in \T1/ pcr/m/n/10 src/gromacs/commandline/ [617] [618] [619] [620] [621] [622] [623] [624] [625] Underfull \hbox (badness 6575) in paragraph at lines 69147--69153 []\T1/ptm/m/n/10 Use smart point-ers for mem-ory man-age-ment. By de-fault, use \T1/pcr/m/n/10 std::unique_-ptr \T1/ptm/m/n/10 and [626] [627] [628 <./redmine-states.png>] [629] [630] [631] [632] [633] [634] [635] Overfull \vbox (2.30272pt too high) detected at line 70296 [636] [637] [638] Overfull \vbox (1.24654pt too high) detected at line 70499 [639] Underfull \vbox (badness 10000) detected at line 70499 Underfull \vbox (badness 10000) detected at line 70499 [640] [641] [642] [643] [644] [645] [646] [647] [648] [649] [650] [651] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 71788. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 71788. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 71788. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 71788. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 71792. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 71792. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 71792. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 71792. [652] [653] [654] [655] [656] [657] [658] [659] [660] [661] [662] [663] [664] [665] [666] Chapter 9. [667] Chapter 10. Underfull \hbox (badness 10000) in paragraph at lines 73462--73466 \T1/ptm/m/n/10 (page 670[]) can be found at \T1/pcr/m/n/10 $GROMACS_-ROOT/share /cmake/gromacs$GROMACS_-SUFFIX/ [668] [669] [670] Underfull \hbox (badness 7344) in paragraph at lines 73829--73833 []\T1/ptm/m/n/10 CMake tar-get \T1/pcr/m/n/10 Gromacs::libgromacs\T1/ptm/m/n/10 , en-abled by [][]\T1/pcr/m/sl/10 GMX_-INSTALL_-LEGACY_-API[][] [671] Chapter 11. [672] [673] [674] [675] [676] [677] [678] [679] [680] [681] [682] [683] [684] Underfull \hbox (badness 7168) in paragraph at lines 75153--75158 []\T1/ptm/m/n/10 In some cases, GRO-MACS could ran-domly crash on neighbor-sear ch steps with \T1/pcr/m/n/10 hip_-queue: [685] [686] Underfull \hbox (badness 10000) in paragraph at lines 75311--75315 []\T1/pcr/m/n/10 NbnxmSetupTest.CanCreateNbnxmGPU \T1/ptm/m/n/10 could crash in GPU builds with an er-ror in [687] [688] [689] [690] [691] [692] [693] [694] [695] [696] [697] [698] [699] Underfull \hbox (badness 7722) in paragraph at lines 76624--76629 []\T1/ptm/m/n/10 De-pend-ing on the build en-vi-ron-ment, GRO-MACS 2023 and 202 3.1 could in-stall a mal-formed [700] [701] [702] [703] [704] [705] [706] [707] [708] [709] [710] [711] [712] [713] [714] [715] [716] [717] [718] [719] [720] [721] [722] [723] [724] [725] [726] [727] [728] [729] [730] [731] [732] [733] [734] [735] [736] [737] [738] [739] [740] [741] [742] [743] [744] [745] [746] [747] [748] [749] [750] [751] [752] [753] [754] [755] [756] [757] [758] [759] [760] [761] [762] [763] [764] [765] [766] [767] [768] [769] [770] [771] [772] [773] [774] [775] [776] [777] [778] [779] [780] [781] [782] [783] [784] [785] [786] [787] [788] [789] [790] [791] [792] [793] [794] [795] [796] [797] [798] [799] [800] [801] [802] [803] [804] [805] [806] [807] [808] [809] [810] [811] [812] [813] [814] [815] Overfull \hbox (18.01631pt too wide) in paragraph at lines 87778--87781 []\T1/ptm/m/n/10 Changed multi-simulation nsteps be-haviour ^^P^^Q^^Q^^Q^^Q^^Q^ ^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^ Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q ^^Q^^Q^^Q^^Q^^Q^^Q^^Q- Underfull \hbox (badness 10000) in paragraph at lines 87778--87781 [816] [817] [818] [819] [820] [821] [822] [823] [824] [825] [826] [827] No file gromacs.ind. (./gromacs.aux) LaTeX Warning: There were multiply-defined labels. ) (see the transcript file for additional information) < /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/symbols/msbm10.pfb> Output written on gromacs.pdf (837 pages, 13748976 bytes). 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directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [ 5%] Built target release-version-info [ 5%] Built target scanner [ 5%] Built target internal_rpc_xdr [ 7%] Built target thread_mpi [ 8%] Built target tng_io_obj [ 10%] Built target tng_io_zlib [ 10%] Built target lmfit_objlib /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build /usr/bin/make -f docs/CMakeFiles/sphinx-input-rst.dir/build.make docs/CMakeFiles/sphinx-input-rst.dir/depend [ 10%] Built target linearalgebra /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend [ 11%] Built target muparser make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/docs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/docs /build/reproducible-path/gromacs-2025.0/build/documentation/docs/CMakeFiles/sphinx-input-rst.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/programs /build/reproducible-path/gromacs-2025.0/build/documentation/src/programs/CMakeFiles/gmx_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend [ 13%] Built target options make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/colvars_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/programs /build/reproducible-path/gromacs-2025.0/build/documentation/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f docs/CMakeFiles/sphinx-input-rst.dir/build.make docs/CMakeFiles/sphinx-input-rst.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/pulling /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build [ 16%] Built target colvars_objlib make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'docs/CMakeFiles/sphinx-input-rst.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'src/programs/CMakeFiles/gmx_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build [ 16%] Built target energyanalysis make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'src/gromacs/pulling/CMakeFiles/pulling.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [ 39%] Built target sphinx-input-rst [ 41%] Built target gmx_objlib [ 41%] Built target mdrun_objlib [ 41%] Built target pulling /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [ 41%] Built target taskassignment make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [ 42%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [ 98%] Built target libgromacs /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/gmxapi /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/api/gmxapi /build/reproducible-path/gromacs-2025.0/build/documentation/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs /build/reproducible-path/gromacs-2025.0/build/documentation 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Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [ 98%] Built target gmx [ 98%] Built target gmxapi /usr/bin/make -f python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build.make python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/python_packaging/gmxapi /build/reproducible-path/gromacs-2025.0/build/documentation/python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build.make python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [ 98%] Built target _gmxapi /usr/bin/make -f docs/CMakeFiles/sphinx-input.dir/build.make docs/CMakeFiles/sphinx-input.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/docs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/docs /build/reproducible-path/gromacs-2025.0/build/documentation/docs/CMakeFiles/sphinx-input.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f docs/CMakeFiles/sphinx-input.dir/build.make docs/CMakeFiles/sphinx-input.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'docs/CMakeFiles/sphinx-input.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [ 98%] Built target sphinx-input /usr/bin/make -f docs/CMakeFiles/sphinx-programs.dir/build.make docs/CMakeFiles/sphinx-programs.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/docs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/docs /build/reproducible-path/gromacs-2025.0/build/documentation/docs/CMakeFiles/sphinx-programs.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f docs/CMakeFiles/sphinx-programs.dir/build.make docs/CMakeFiles/sphinx-programs.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'docs/CMakeFiles/sphinx-programs.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [100%] Built target sphinx-programs /usr/bin/make -f docs/CMakeFiles/man.dir/build.make docs/CMakeFiles/man.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/docs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/docs /build/reproducible-path/gromacs-2025.0/build/documentation/docs/CMakeFiles/man.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f docs/CMakeFiles/man.dir/build.make docs/CMakeFiles/man.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/sphinx-build -q -b man -w sphinx-man.log -d /build/reproducible-path/gromacs-2025.0/build/documentation/docs/_man_doctrees -t do_man /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input /build/reproducible-path/gromacs-2025.0/build/documentation/docs/man WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://docs.python.org/3/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.python.org', port=443): Max retries exceeded with url: /3/objects.inv (Caused by NameResolutionError(": Failed to resolve 'docs.python.org' ([Errno -3] Temporary failure in name resolution)")) WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://mpi4py.readthedocs.io/en/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='mpi4py.readthedocs.io', port=443): Max retries exceeded with url: /en/stable/objects.inv (Caused by NameResolutionError(": Failed to resolve 'mpi4py.readthedocs.io' ([Errno -3] Temporary failure in name resolution)")) /build/reproducible-path/gromacs-2025.0/admin/trigger-post-merge.py:53: UserWarning: This tool requires the `gitlab` package. Try `pip install python-gitlab`. warnings.warn( make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [100%] Built target man make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.0/build/documentation/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[1]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -j20 webpage -C build/documentation make[1]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/cmake -P /build/reproducible-path/gromacs-2025.0/build/documentation/CMakeFiles/VerifyGlobs.cmake /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.0 -B/build/reproducible-path/gromacs-2025.0/build/documentation --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/make -f CMakeFiles/Makefile2 webpage make[2]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/cmake -P /build/reproducible-path/gromacs-2025.0/build/documentation/CMakeFiles/VerifyGlobs.cmake /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.0 -B/build/reproducible-path/gromacs-2025.0/build/documentation --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.0/build/documentation/CMakeFiles 69 /usr/bin/make -f CMakeFiles/Makefile2 docs/CMakeFiles/webpage.dir/all make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f docs/CMakeFiles/sphinx-image-conversion.dir/build.make docs/CMakeFiles/sphinx-image-conversion.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.0/build/documentation/src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f docs/CMakeFiles/sphinx-image-conversion.dir/build.make docs/CMakeFiles/sphinx-image-conversion.dir/build make[4]: Entering directory 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directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2025.0-Debian_2025.0_2 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2025.0 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.0/build/documentation/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2025.0/build/documentation/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2025.0-2 -P /build/reproducible-path/gromacs-2025.0/cmake/gmxGenerateVersionInfoWithoutGit.cmake /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make 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_deps/muparser-build/CMakeFiles/muparser.dir/depend /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend [ 10%] Built target tng_io_zlib make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/external/muparser /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/_deps/muparser-build /build/reproducible-path/gromacs-2025.0/build/documentation/_deps/muparser-build/CMakeFiles/muparser.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend /usr/bin/make -f docs/CMakeFiles/sphinx-input-rst.dir/build.make docs/CMakeFiles/sphinx-input-rst.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake 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'/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/docs/doxygen /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen/CMakeFiles/doxygen-version.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f _deps/muparser-build/CMakeFiles/muparser.dir/build.make 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'/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'src/gromacs/options/CMakeFiles/options.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/colvars_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'src/programs/CMakeFiles/gmx_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-source-timestamp.dir/build.make docs/doxygen/CMakeFiles/doxygen-source-timestamp.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen && /usr/bin/cmake -E touch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen/doxygen-source-timestamp.txt /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-version.dir/build.make docs/doxygen/CMakeFiles/doxygen-version.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen && /usr/bin/cmake -D VERSION_VARIABLES=/build/reproducible-path/gromacs-2025.0/build/documentation/VersionInfo.cmake -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.0/docs/doxygen/Doxyfile-version.cmakein -D VERSION_OUT=Doxyfile-version -P /build/reproducible-path/gromacs-2025.0/cmake/gmxConfigureVersionInfo.cmake make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [ 33%] Built target sphinx-input-rst [ 36%] Built target energyanalysis [ 36%] Built target muparser [ 36%] Built target linearalgebra [ 39%] Built target colvars_objlib [ 39%] Built target options /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/pulling /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" [ 39%] Built target mdrun_objlib [ 40%] Built target gmx_objlib [ 42%] Built target doxygen-source-timestamp make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'src/gromacs/pulling/CMakeFiles/pulling.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen && /usr/bin/cmake -E touch Doxyfile-version make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [ 42%] Built target pulling /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" [ 42%] Built target doxygen-version /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-xml.dir/build.make docs/doxygen/CMakeFiles/doxygen-xml.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/docs/doxygen /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen/CMakeFiles/doxygen-xml.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [ 42%] Built target taskassignment /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-xml.dir/build.make docs/doxygen/CMakeFiles/doxygen-xml.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen && /usr/bin/cmake -E make_directory /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen/depgraphs [ 43%] Built target modularsimulator cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen && /usr/bin/cmake -DDOCTYPE=xml -P RunDoxygen.cmake /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend NOTE: You are using Doxygen version 1.9.8. The documentation is designed for 1.8.5. Other versions may or may not work, but very likely produce extra warnings. Running Doxygen... warning: Tag 'MSCGEN_PATH' at line 40 of file 'Doxyfile-common' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'CLASS_DIAGRAMS' at line 15 of file 'Doxyfile-xml' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs /build/reproducible-path/gromacs-2025.0/build/documentation/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [ 98%] Built target libgromacs /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/depend /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/src/programs /build/reproducible-path/gromacs-2025.0/build/documentation/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/gmxapi /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/api/gmxapi /build/reproducible-path/gromacs-2025.0/build/documentation/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'src/programs/CMakeFiles/gmx.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'api/gmxapi/CMakeFiles/gmxapi.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [ 98%] Built target gmx [ 98%] Built target gmxapi /usr/bin/make -f python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build.make python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/python_packaging/gmxapi /build/reproducible-path/gromacs-2025.0/build/documentation/python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build.make python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [ 98%] Built target _gmxapi /usr/bin/make -f docs/CMakeFiles/sphinx-input.dir/build.make docs/CMakeFiles/sphinx-input.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/docs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/docs /build/reproducible-path/gromacs-2025.0/build/documentation/docs/CMakeFiles/sphinx-input.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f docs/CMakeFiles/sphinx-input.dir/build.make docs/CMakeFiles/sphinx-input.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'docs/CMakeFiles/sphinx-input.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [ 98%] Built target sphinx-input /usr/bin/make -f docs/CMakeFiles/sphinx-programs.dir/build.make docs/CMakeFiles/sphinx-programs.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/docs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/docs /build/reproducible-path/gromacs-2025.0/build/documentation/docs/CMakeFiles/sphinx-programs.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f docs/CMakeFiles/sphinx-programs.dir/build.make docs/CMakeFiles/sphinx-programs.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'docs/CMakeFiles/sphinx-programs.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [100%] Built target sphinx-programs /usr/bin/make -f docs/manual/CMakeFiles/pdf.dir/build.make docs/manual/CMakeFiles/pdf.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/docs/manual /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/docs/manual /build/reproducible-path/gromacs-2025.0/build/documentation/docs/manual/CMakeFiles/pdf.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f docs/manual/CMakeFiles/pdf.dir/build.make docs/manual/CMakeFiles/pdf.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'docs/manual/CMakeFiles/pdf.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [100%] Built target pdf /usr/bin/make -f docs/manual/CMakeFiles/manual.dir/build.make docs/manual/CMakeFiles/manual.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/docs/manual /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/docs/manual /build/reproducible-path/gromacs-2025.0/build/documentation/docs/manual/CMakeFiles/manual.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f docs/manual/CMakeFiles/manual.dir/build.make docs/manual/CMakeFiles/manual.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'docs/manual/CMakeFiles/manual.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [100%] Built target manual /usr/bin/make -f docs/CMakeFiles/webpage-sphinx.dir/build.make docs/CMakeFiles/webpage-sphinx.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/docs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/docs /build/reproducible-path/gromacs-2025.0/build/documentation/docs/CMakeFiles/webpage-sphinx.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f docs/CMakeFiles/webpage-sphinx.dir/build.make docs/CMakeFiles/webpage-sphinx.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/sphinx-build -q -b html -w sphinx-html.log -d /build/reproducible-path/gromacs-2025.0/build/documentation/docs/_html_doctrees -t do_html /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input /build/reproducible-path/gromacs-2025.0/build/documentation/docs/html WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://docs.python.org/3/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.python.org', port=443): Max retries exceeded with url: /3/objects.inv (Caused by NameResolutionError(": Failed to resolve 'docs.python.org' ([Errno -3] Temporary failure in name resolution)")) WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://mpi4py.readthedocs.io/en/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='mpi4py.readthedocs.io', port=443): Max retries exceeded with url: /en/stable/objects.inv (Caused by NameResolutionError(": Failed to resolve 'mpi4py.readthedocs.io' ([Errno -3] Temporary failure in name resolution)")) /build/reproducible-path/gromacs-2025.0/admin/trigger-post-merge.py:53: UserWarning: This tool requires the `gitlab` package. Try `pip install python-gitlab`. warnings.warn( The following warnings were produced by Doxygen: /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/biasgrid.h:279: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/biasgrid.h:279: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/energyhistory.cpp:48: warning: Conditional section with label 'INTERNAL' does not have a corresponding \endcond command within this file. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_utils.h:63: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_utils.h:63: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2025.0/src/gromacs/restraint/restraintmdmodule.cpp:64: warning: no matching class member found for gmx::RestraintForceProvider::RestraintForceProvider(std::shared_ptr< gmx::IRestraintPotential > restraint, const std::vector< int > &sites) Possible candidates: 'gmx::RestraintForceProvider::RestraintForceProvider()=delete' at line 212 of file /build/reproducible-path/gromacs-2025.0/src/gromacs/restraint/restraintmdmodule_impl.h 'gmx::RestraintForceProvider::RestraintForceProvider(std::shared_ptr< gmx::IRestraintPotential > restraint, const std::vector< int > &sites)' at line 223 of file /build/reproducible-path/gromacs-2025.0/src/gromacs/restraint/restraintmdmodule_impl.h /build/reproducible-path/gromacs-2025.0/src/gromacs/restraint/restraintmdmodule.cpp:168: warning: no matching class member found for gmx::RestraintMDModuleImpl::RestraintMDModuleImpl(std::shared_ptr< gmx::IRestraintPotential > restraint, const std::vector< int > &sites) Possible candidates: 'gmx::RestraintMDModuleImpl::RestraintMDModuleImpl()=delete' at line 271 of file /build/reproducible-path/gromacs-2025.0/src/gromacs/restraint/restraintmdmodule_impl.h 'gmx::RestraintMDModuleImpl::RestraintMDModuleImpl(std::shared_ptr< gmx::IRestraintPotential > restraint, const std::vector< int > &sites)' at line 278 of file /build/reproducible-path/gromacs-2025.0/src/gromacs/restraint/restraintmdmodule_impl.h 'gmx::RestraintMDModuleImpl::RestraintMDModuleImpl(RestraintMDModuleImpl &&) noexcept=default' at line 286 of file /build/reproducible-path/gromacs-2025.0/src/gromacs/restraint/restraintmdmodule_impl.h /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/arrayref.h:311: warning: @copybrief or @copydoc target 'arrayRefFromArray' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/checkpointdata.h:277: warning: @copybrief or @copydoc target 'CheckpointData::subCheckpointData' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:94: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:99: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/electricfield.cpp:186: warning: @copybrief or @copydoc target 'IForceProvider::calculateForces()' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:120: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:125: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/checkpointdata.h:256: warning: @copybrief or @copydoc target 'CheckpointData::scalar' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_insolidangle.cpp:99: warning: unable to resolve reference to 'sm_insolidangle' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/leapfrog_gpu_internal_sycl.cpp:170: warning: unable to resolve reference to 'NumTempScaleValues' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd_memory.h:154: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(pointer, pointer)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd_memory.h:163: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/requirements.cpp:59: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:295: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:398: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/optionflags.h:107: warning: explicit link request to 'OptionFlag' could not be resolved /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/selection/selectionenums.h:82: warning: explicit link request to 'SelectionFlag' could not be resolved /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/requirements.cpp:63: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:340: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:106: warning: unable to resolve reference to 'VdwType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:82: warning: unable to resolve reference to 'ElecType' for \ref command /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/optionflags.h:107: warning: explicit link request to 'OptionFlag' could not be resolved /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/selection/selectionenums.h:82: warning: explicit link request to 'SelectionFlag' could not be resolved /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/requirements.cpp:59: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/requirements.cpp:63: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/leapfrog_gpu_internal_sycl.cpp:170: warning: unable to resolve reference to 'NumTempScaleValues' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:82: warning: unable to resolve reference to 'ElecType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:106: warning: unable to resolve reference to 'VdwType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:295: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:340: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:398: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/optionflags.h:107: warning: explicit link request to 'OptionFlag' could not be resolved /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/selection/selectionenums.h:82: warning: explicit link request to 'SelectionFlag' could not be resolved /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:94: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:99: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:120: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:125: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/leapfrog_gpu_internal_sycl.cpp:170: warning: unable to resolve reference to 'NumTempScaleValues' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/requirements.cpp:59: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/requirements.cpp:63: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:82: warning: unable to resolve reference to 'ElecType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:106: warning: unable to resolve reference to 'VdwType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:295: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:340: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:398: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/checkpointdata.h:256: warning: @copybrief or @copydoc target 'CheckpointData::scalar' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/checkpointdata.h:277: warning: @copybrief or @copydoc target 'CheckpointData::subCheckpointData' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/electricfield.cpp:186: warning: @copybrief or @copydoc target 'IForceProvider::calculateForces()' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd_memory.h:154: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(pointer, pointer)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd_memory.h:163: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/electricfield.cpp:186: warning: @copybrief or @copydoc target 'IForceProvider::calculateForces()' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/electricfield.cpp:187: warning: @copydetails or @copydoc target 'IForceProvider::calculateForces()' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/checkpointdata.h:256: warning: @copybrief or @copydoc target 'CheckpointData::scalar' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/checkpointdata.h:257: warning: @copydetails or @copydoc target 'CheckpointData::scalar' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/checkpointdata.h:264: warning: @copybrief or @copydoc target 'CheckpointData::arrayRef' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/checkpointdata.h:264: warning: @copydetails or @copydoc target 'CheckpointData::arrayRef' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/checkpointdata.h:274: warning: @copybrief or @copydoc target 'CheckpointData::tensor' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/checkpointdata.h:274: warning: @copydetails or @copydoc target 'CheckpointData::tensor' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/checkpointdata.h:277: warning: @copybrief or @copydoc target 'CheckpointData::subCheckpointData' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/checkpointdata.h:278: warning: @copydetails or @copydoc target 'CheckpointData::subCheckpointData' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd_memory.h:154: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(pointer, pointer)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd_memory.h:155: warning: @copydetails or @copydoc target 'ArrayRef::ArrayRef(pointer, pointer)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd_memory.h:163: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd_memory.h:164: warning: @copydetails or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:295: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:305: warning: unable to resolve reference to 'SimdIBool' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:340: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:352: warning: unable to resolve reference to 'SimdBool' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:353: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:353: warning: unable to resolve reference to 'SimdIBool' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:354: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:356: warning: unable to resolve reference to 'cvtB2IB' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:356: warning: unable to resolve reference to 'cvtIB2B' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:398: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/optionflags.h:107: warning: explicit link request to 'OptionFlag' could not be resolved /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/selection/selectionenums.h:82: warning: explicit link request to 'SelectionFlag' could not be resolved /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/requirements.cpp:59: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/requirements.cpp:63: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:82: warning: unable to resolve reference to 'ElecType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:106: warning: unable to resolve reference to 'VdwType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/correlationhistory.h:61: warning: unable to resolve reference to 'updateCorrelationGridHistory' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:94: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:95: warning: @copydetails or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:99: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:100: warning: @copydetails or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:120: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:121: warning: @copydetails or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:125: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:126: warning: @copydetails or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/leapfrog_gpu_internal_sycl.cpp:170: warning: unable to resolve reference to 'NumTempScaleValues' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:593: warning: argument 'wcycle' from the argument list of gmx::computeSpecialForces has multiple @param documentation sections /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/index.h:123: warning: Illegal command @param found as part of a \p command /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/index.h:120: warning: The following parameter of write_index(const char *outf, gmx::ArrayRef< const IndexGroup > indexGroups, bool duplicate, int numAtoms) is not documented: parameter 'numAtoms' /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/iframeconverter.h:116: warning: invalid argument for command '\iline' /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/matio.h:297: warning: argument 'n_x' of command @param is not found in the argument list of write_xpm(FILE *out, unsigned int flags, const std::string &title, const std::string &legend, const std::string &label_x, const std::string &label_y, gmx::ArrayRef< const real > axis_x, gmx::ArrayRef< const real > axis_y, gmx::basic_mdspan< const real, gmx::dynamicExtents2D > mat, real lo, real hi, t_rgb rlo, t_rgb rhi, int *nlevels) /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/matio.h:297: warning: argument 'n_y' of command @param is not found in the argument list of write_xpm(FILE *out, unsigned int flags, const std::string &title, const std::string &legend, const std::string &label_x, const std::string &label_y, gmx::ArrayRef< const real > axis_x, gmx::ArrayRef< const real > axis_y, gmx::basic_mdspan< const real, gmx::dynamicExtents2D > mat, real lo, real hi, t_rgb rlo, t_rgb rhi, int *nlevels) /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/matio.h:297: warning: argument 'n_x' of command @param is not found in the argument list of write_xpm(FILE *out, unsigned int flags, const std::string &title, const std::string &legend, const std::string &label_x, const std::string &label_y, gmx::ArrayRef< const real > axis_x, gmx::ArrayRef< const real > axis_y, gmx::basic_mdspan< const real, gmx::dynamicExtents2D > mat, real lo, real hi, t_rgb rlo, t_rgb rhi, int *nlevels) /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/matio.h:297: warning: argument 'n_y' of command @param is not found in the argument list of write_xpm(FILE *out, unsigned int flags, const std::string &title, const std::string &legend, const std::string &label_x, const std::string &label_y, gmx::ArrayRef< const real > axis_x, gmx::ArrayRef< const real > axis_y, gmx::basic_mdspan< const real, gmx::dynamicExtents2D > mat, real lo, real hi, t_rgb rlo, t_rgb rhi, int *nlevels) /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/warninp.h:153: warning: @copybrief or @copydoc target 'warning_error_and_exit(WarningHandler*,const char *,int,const char *,int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/warninp.h:154: warning: @copydetails or @copydoc target 'warning_error_and_exit(WarningHandler*,const char *,int,const char *,int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/warninp.h:153: warning: @copybrief or @copydoc target 'warning_error_and_exit(WarningHandler*,const char *,int,const char *,int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/warninp.h:154: warning: @copydetails or @copydoc target 'warning_error_and_exit(WarningHandler*,const char *,int,const char *,int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_insolidangle.cpp:99: warning: unable to resolve reference to 'sm_insolidangle' for \ref command /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/index.h:123: warning: Illegal command @param found as part of a \p command /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/index.h:120: warning: The following parameter of write_index(const char *outf, gmx::ArrayRef< const IndexGroup > indexGroups, bool duplicate, int numAtoms) is not documented: parameter 'numAtoms' /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/impl_reference/impl_reference_util_double.h:171: warning: @copydetails or @copydoc target 'c_simdBestPairAlignmentFloat' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/impl_reference/impl_reference_util_float.h:151: warning: unable to resolve reference to 'c_simdBestPairAlignmentFloat' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/impl_reference/impl_reference_util_float.h:152: warning: unable to resolve reference to 'c_simdBestPairAlignmentDouble' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/errorcodes.h:111: warning: explicit link request to 'eeUnknownError' could not be resolved /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:113: warning: @copydetails or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:119: warning: @copydetails or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:179: warning: @copydetails or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:184: warning: @copydetails or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:189: warning: @copydetails or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:83: warning: @copydetails or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:100: warning: @copydetails or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:119: warning: @copydetails or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:144: warning: @copydetails or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:402: warning: @copydetails or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:419: warning: @copydetails or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen && /usr/bin/cmake -E touch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen/doxygen-xml-timestamp.txt make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [100%] Built target doxygen-xml /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-user.dir/build.make docs/doxygen/CMakeFiles/doxygen-user.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f docs/doxygen/CMakeFiles/dep-graphs-dot.dir/build.make docs/doxygen/CMakeFiles/dep-graphs-dot.dir/depend cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/docs/doxygen /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen/CMakeFiles/doxygen-user.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/docs/doxygen /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen/CMakeFiles/dep-graphs-dot.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-user.dir/build.make docs/doxygen/CMakeFiles/doxygen-user.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen && /usr/bin/cmake -E make_directory /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen/depgraphs make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f docs/doxygen/CMakeFiles/dep-graphs-dot.dir/build.make docs/doxygen/CMakeFiles/dep-graphs-dot.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen && /usr/bin/python3 /build/reproducible-path/gromacs-2025.0/docs/doxygen/graphbuilder.py -S /build/reproducible-path/gromacs-2025.0 -B /build/reproducible-path/gromacs-2025.0/build/documentation -o /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen/depgraphs cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen && /usr/bin/cmake -DDOCTYPE=user -P RunDoxygen.cmake NOTE: You are using Doxygen version 1.9.8. The documentation is designed for 1.8.5. Other versions may or may not work, but very likely produce extra warnings. Running Doxygen... /build/reproducible-path/gromacs-2025.0/docs/doxygen/doxygenxml.py:35: SyntaxWarning: invalid escape sequence '\l' """Doxygen XML output parser. /build/reproducible-path/gromacs-2025.0/docs/doxygen/doxygenxml.py:343: SyntaxWarning: invalid escape sequence '\i' self, "\internal does not cover whole documentation" /build/reproducible-path/gromacs-2025.0/docs/doxygen/doxygenxml.py:350: SyntaxWarning: invalid escape sequence '\l' self, "\libinternal should not be used inside \internal" warning: Tag 'MSCGEN_PATH' at line 40 of file 'Doxyfile-common' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" Scanning source tree... Reading source files... Reading Doxygen XML files... Writing graphs... cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen && /usr/bin/cmake -E touch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen/dep-graphs-dot-timestamp.txt make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [100%] Built target dep-graphs-dot /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-full.dir/build.make docs/doxygen/CMakeFiles/doxygen-full.dir/depend /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-lib.dir/build.make docs/doxygen/CMakeFiles/doxygen-lib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/docs/doxygen /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen/CMakeFiles/doxygen-full.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/docs/doxygen /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen/CMakeFiles/doxygen-lib.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-full.dir/build.make docs/doxygen/CMakeFiles/doxygen-full.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen && /usr/bin/cmake -E make_directory /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen/depgraphs make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-lib.dir/build.make docs/doxygen/CMakeFiles/doxygen-lib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen && /usr/bin/cmake -E make_directory /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen/depgraphs cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen && /usr/bin/cmake -DDOCTYPE=full -P RunDoxygen.cmake cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen && /usr/bin/cmake -DDOCTYPE=lib -P RunDoxygen.cmake NOTE: You are using Doxygen version 1.9.8. The documentation is designed for 1.8.5. Other versions may or may not work, but very likely produce extra warnings. Running Doxygen... NOTE: You are using Doxygen version 1.9.8. The documentation is designed for 1.8.5. Other versions may or may not work, but very likely produce extra warnings. Running Doxygen... warning: Tag 'MSCGEN_PATH' at line 40 of file 'Doxyfile-common' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'MSCGEN_PATH' at line 40 of file 'Doxyfile-common' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" libpath/shortest.c:324: triangulation failed libpath/shortest.c:324: triangulation failed The following warnings were produced by Doxygen: /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/biasgrid.h:279: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/biasgrid.h:279: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/energyhistory.cpp:48: warning: Conditional section with label 'INTERNAL' does not have a corresponding \endcond command within this file. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_utils.h:63: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_utils.h:63: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2025.0/src/gromacs/onlinehelp/helpwritercontext.cpp:247: warning: unbalanced grouping commands /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/testasserts.h:738: warning: unbalanced grouping commands /build/reproducible-path/gromacs-2025.0/src/testutils/testasserts.cpp:186: warning: unbalanced grouping commands /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/int64_to_int.h:57: warning: Member int64_to_int found in multiple @ingroup groups! The member will be put in group module_utility, and not in group group_libraryapi /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/basedefinitions.h:229: warning: documentation for unknown define GMX_IGNORE_RETURN_VALUE found. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:94: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:99: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:120: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:125: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:82: warning: unable to resolve reference to 'ElecType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:106: warning: unable to resolve reference to 'VdwType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/requirements.cpp:59: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/leapfrog_gpu_internal_sycl.cpp:170: warning: unable to resolve reference to 'NumTempScaleValues' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/requirements.cpp:63: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/selectioncollection.cpp:978: warning: Member swap(SelectionCollection &lhs, SelectionCollection &rhs) noexcept (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:226: warning: Member t_functype (typedef) of file idef.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:473: warning: Member printInteractionParameters(gmx::TextWriter *writer, t_functype ftype, const t_iparams &iparams) (function) of file idef.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:474: warning: Member pr_iparams(FILE *fp, t_functype ftype, const t_iparams &iparams) (function) of file idef.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:475: warning: Member pr_ilist(FILE *fp, int indent, const char *title, const t_functype *functype, const InteractionList &ilist, bool bShowNumbers, bool bShowParameters, const t_iparams *iparams) (function) of file idef.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:483: warning: Member pr_idef(FILE *fp, int indent, const char *title, const t_idef *idef, bool bShowNumbers, bool bShowParameters) (function) of file idef.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:54: warning: Member t_iatom (typedef) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:59: warning: Member rvec4[4] (typedef) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:220: warning: Member IS_RESTRAINT_TYPE(int ifunc) (function) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:239: warning: Member NRFPA(int ftype) (function) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:244: warning: Member NRFPB(int ftype) (function) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:249: warning: Member NRFP(int ftype) (function) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:254: warning: Member NRAL(int ftype) (function) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:275: warning: Member IS_VSITE(int ftype) (function) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:280: warning: Member IS_TABULATED(int ftype) (function) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:67: warning: Member IF_VSITE (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:68: warning: Member IF_CONSTRAINT (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:69: warning: Member IF_CHEMBOND (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:76: warning: Member IF_DIHEDRAL (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:77: warning: Member IF_PAIR (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:78: warning: Member IF_TABULATED (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:233: warning: Member NR_CBTDIHS (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:234: warning: Member NR_FOURDIHS (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:787: warning: Member CompileTimeStringJoin_v (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/iframeconverter.h:109: warning: invalid argument for command '\iline' /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/hip_kernel_utils.h:78: warning: Member LAUNCH_BOUNDS_EXACT(WORK_GROUP_SIZE, WAVES_PER_EU) (macro definition) of file hip_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/hip_kernel_utils.h:82: warning: Member LAUNCH_BOUNDS_EXACT_SINGLE(WORK_GROUP_SIZE) (macro definition) of file hip_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/hip_kernel_utils.h:85: warning: Member GMX_HIP_MAX_BLOCKS_PER_MP (macro definition) of file hip_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/hip_kernel_utils.h:86: warning: Member GMX_HIP_MAX_THREADS_PER_MP (macro definition) of file hip_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/hip_sycl_kernel_utils.h:82: warning: Member GMX_ALWAYS_INLINE_ATTRIBUTE (macro definition) of file hip_sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/hip_sycl_kernel_utils.h:83: warning: Member GMX_FUNC_ATTRIBUTE (macro definition) of file hip_sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/hip_sycl_kernel_utils.h:109: warning: Member idx (variable) of file hip_sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/sycl_kernel_utils.h:65: warning: Member SYCL_ASSERT(condition) (macro definition) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/sycl_kernel_utils.h:85: warning: Member compilingForHost() (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/sycl_kernel_utils.h:101: warning: Member compilingForSubGroupSize() (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/sycl_kernel_utils.h:115: warning: Member skipKernelCompilation() (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/sycl_kernel_utils.h:137: warning: Member atomicAddDefault(T &val, const T delta) (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/sycl_kernel_utils.h:174: warning: Member atomicFetchAddLocal(T &val, const T delta) (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_data_mgmt.cpp:76: warning: Member gpu_min_ci_balanced_factor (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:46: warning: Member def_bonded(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:51: warning: Member def_pair(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:56: warning: Member def_bondedt(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:61: warning: Member def_bondedtz(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:66: warning: Member def_angle(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:71: warning: Member def_dihedral(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:77: warning: Member def_dihedral_tabulated(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:82: warning: Member def_bond(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:87: warning: Member def_bondt(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:92: warning: Member def_bondnb(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:97: warning: Member def_vsite(const char *str, const char *lstr, int nra, int nrpa) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:102: warning: Member def_shk(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:107: warning: Member def_shkcb(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:112: warning: Member def_nb(const char *str, const char *lstr, int nra, int nrpa) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:117: warning: Member def_nofc(const char *str, const char *lstr) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/fatalerror.h:217: warning: Member gmx_call(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/fatalerror.h:218: warning: Member gmx_comm(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/fatalerror.h:219: warning: Member gmx_file(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/fatalerror.h:220: warning: Member gmx_impl(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/fatalerror.h:221: warning: Member gmx_incons(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/fatalerror.h:222: warning: Member gmx_input(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/fatalerror.h:223: warning: Member gmx_mem(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/fatalerror.h:224: warning: Member gmx_open(fn) (macro definition) of file fatalerror.h is not documented. :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::initOptions()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::optionsFinished()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::initAnalysis()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::initAfterFirstFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::finishAnalysis()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::writeOutput()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::startFrames()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::startFrames()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::finishFrames()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::finishFrames()' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/utility.h:109: warning: explicit link request to 'GMX_IGNORE_RETURN_VALUE' could not be resolved /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:119: warning: @copydetails or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:100: warning: @copydetails or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:144: warning: @copydetails or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/errorcodes.h:111: warning: explicit link request to 'eeUnknownError' could not be resolved /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/int64_to_int.h:48: warning: Found unknown command '\file' /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:402: warning: @copydetails or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:419: warning: @copydetails or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:83: warning: @copydetails or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/constraint_gpu_helpers.h:55: warning: Member AtomsAdjacencyListElement(int indexOfSecondConstrainedAtom, int indexOfConstraint, int signFactor) (function) of struct AtomsAdjacencyListElement is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/dlbtiming.h:215: warning: Member impl_ (variable) of class BalanceRegion is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/commrec.h:68: warning: Member bUse (variable) of struct gmx_nodecomm_t is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/commrec.h:69: warning: Member comm_intra (variable) of struct gmx_nodecomm_t is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/commrec.h:70: warning: Member rank_intra (variable) of struct gmx_nodecomm_t is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/commrec.h:71: warning: Member comm_inter (variable) of struct gmx_nodecomm_t is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:453: warning: Member fudgeQQ (variable) of struct t_idef is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:459: warning: Member iparams_fbposres (variable) of struct t_idef is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:327: warning: Member iatoms (variable) of struct t_ilist is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:328: warning: Member nalloc (variable) of struct t_ilist is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:105: warning: Member nrfpA (variable) of struct t_interaction_function is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:71: warning: Member bham (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:75: warning: Member harmonic (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:79: warning: Member linangle (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:83: warning: Member restraint (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:87: warning: Member cubic (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:91: warning: Member fene (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:95: warning: Member cross_bb (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:99: warning: Member cross_ba (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:103: warning: Member u_b (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:107: warning: Member qangle (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:111: warning: Member polarize (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:115: warning: Member anharm_polarize (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:119: warning: Member wpol (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:123: warning: Member thole (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:127: warning: Member lj (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:131: warning: Member lj14 (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:135: warning: Member ljc14 (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:139: warning: Member ljcnb (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:155: warning: Member constr (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:168: warning: Member morse (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:172: warning: Member posres (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:177: warning: Member fbposres (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:181: warning: Member rbdihs (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:185: warning: Member cbtdihs (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:189: warning: Member vsite (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:194: warning: Member vsiten (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:200: warning: Member disres (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:204: warning: Member dihres (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:209: warning: Member orires (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:215: warning: Member tab (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:219: warning: Member cmap (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:223: warning: Member generic (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/fcdata.h:216: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(t_oriresdata) (function) of struct t_oriresdata is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/warninp.h:71: warning: Member WarningHandler(bool allowWarnings, int maxNumberWarnings) (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/warninp.h:89: warning: Member errorCount() const (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/warninp.h:91: warning: Member warningCount() const (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/warninp.h:93: warning: Member noteCount() const (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/warninp.h:95: warning: Member maxWarningCount() const (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_force_sender_gpu_impl.h:76: warning: Member CacheLineAlignedFlag (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/h5md.h:55: warning: Member hid_t (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/h5md.h:57: warning: Member herr_t (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:875: warning: Member mode (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:435: warning: Member GpuPairlistByLocality (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/opencl/nbnxm_ocl_types.h:130: warning: Member cl_nbparam_params_t (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:77: warning: Member FCiFloat3 (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/oclraii.h:131: warning: Member ClCommandQueue (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/oclraii.h:132: warning: Member ClProgram (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/oclraii.h:133: warning: Member ClKernel (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft.h:67: warning: Member FftBackend (enumeration) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/h5md.h:59: warning: Member H5mdFileMode (enumeration) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/checkpointdata.h:76: warning: Member CheckpointDataOperation (enumeration) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/referencetemperaturemanager.h:67: warning: Member ReferenceTemperatureChangeAlgorithm (enumeration) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/nnpotoptions.cpp:86: warning: Member NNPotMdpTransformFromString(IKeyValueTreeTransformRules *rules, TransformWithFunctionType transformationFunction, const std::string &optionTag) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/torchmodel.cpp:60: warning: Member recordToString(std::tuple< at::DataPtr, size_t > data) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/gpuhaloexchange_impl_gpu_sycl.cpp:63: warning: Member packSendBufKernel(Float3 *__restrict__ gm_dataPacked, const Float3 *__restrict__ gm_data, const int *__restrict__ gm_map, int mapSize, Float3 coordinateShift) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/gpuhaloexchange_impl_gpu_sycl.cpp:119: warning: Member launchPackSendBufKernel(const DeviceStream &deviceStream, int xSendSize, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/gpuhaloexchange_impl_gpu_sycl.cpp:134: warning: Member launchUnpackRecvBufKernel(const DeviceStream &deviceStream, int fRecvSize, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_cufftmp.cpp:102: warning: Member handleCufftError(cufftResult_t status, const char *msg) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_sycl_vkfft.cpp:258: warning: Member launchVkFft(const DeviceBuffer< float > &realGrid, const DeviceBuffer< float > &complexGrid, NativeQueue queue, gmx_fft_direction fftDirection, VkFFTApplication *application, VkFFTLaunchParams *launchParams) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:94: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:99: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:120: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:125: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/h5md_low_level_util.h:63: warning: Member throwUponH5mdError(const bool errorExists, const std::string &message) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/massrepartitioning.cpp:57: warning: Member smallestAtomMass(const gmx_mtop_t &mtop) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces_gpu_impl_gpu.cpp:67: warning: Member chooseSubGroupSizeForDevice(const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:878: warning: Member bondedKernel(sycl::handler &cgh, const BondedGpuKernelParameters &kernelParams, const DeviceBuffer< t_iatom > gm_iatoms_[numFTypesOnGpu], float *__restrict__ gm_vTot, const t_iparams *__restrict__ gm_forceParams_, const sycl::float4 *__restrict__ gm_xq_, Float3 *__restrict__ gm_f_, Float3 *__restrict__ gm_fShift_) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:1498: warning: Member do_force(FILE *log, const t_commrec *cr, const gmx_multisim_t *ms, const t_inputrec &inputrec, const MDModulesNotifiers &mdModulesNotifiers, Awh *awh, gmx_enfrot *enforcedRotation, ImdSession *imdSession, pull_t *pull_work, int64_t step, t_nrnb *nrnb, gmx_wallcycle *wcycle, const gmx_localtop_t *top, const matrix box, ArrayRefWithPadding< RVec > coordinates, ArrayRef< RVec > velocities, const history_t *hist, ForceBuffersView *force, tensor vir_force, const t_mdatoms *mdatoms, gmx_enerdata_t *enerd, ArrayRef< const real > lambda, t_forcerec *fr, const MdrunScheduleWorkload &runScheduleWork, VirtualSitesHandler *vsite, rvec mu_tot, double t, gmx_edsam *ed, CpuPpLongRangeNonbondeds *longRangeNonbondeds, const DDBalanceRegionHandler &ddBalanceRegionHandler) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/leapfrog_gpu_internal_sycl.cpp:170: warning: unable to resolve reference to 'NumTempScaleValues' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/lincs_gpu_internal_sycl.cpp:452: warning: Member launchLincsKernel(const DeviceStream &deviceStream, const int numConstraintsThreads, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:163: warning: Member sum_forces(ArrayRef< RVec > f, ArrayRef< const RVec > forceToAdd) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:176: warning: Member calc_virial(int start, int homenr, const rvec x[], const ForceWithShiftForces &forceWithShiftForces, tensor vir_part, const matrix box, t_nrnb *nrnb, const t_forcerec *fr, PbcType pbcType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:205: warning: Member pull_potential_wrapper(const t_commrec *cr, const t_inputrec &ir, const matrix box, ArrayRef< const RVec > x, const t_mdatoms *mdatoms, gmx_enerdata_t *enerd, pull_t *pull_work, const real *lambda, double t, gmx_wallcycle *wcycle) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:238: warning: Member pme_receive_force_ener(t_forcerec *fr, const t_commrec *cr, ForceWithVirial *forceWithVirial, gmx_enerdata_t *enerd, bool useGpuPmePpComms, bool receivePmeForceToGpu, gmx_wallcycle *wcycle) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:280: warning: Member print_large_forces(FILE *fp, const t_mdatoms *md, const t_commrec *cr, int64_t step, real forceTolerance, ArrayRef< const RVec > x, ArrayRef< const RVec > f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:429: warning: Member do_nb_verlet(t_forcerec *fr, const interaction_const_t *ic, gmx_enerdata_t *enerd, const StepWorkload &stepWork, const InteractionLocality ilocality, const int clearF, const int64_t step, t_nrnb *nrnb, gmx_wallcycle *wcycle) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:476: warning: Member clearRVecs(ArrayRef< RVec > v, const bool useOpenmpThreading) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:942: warning: Member launchGpuEndOfStepTasks(nonbonded_verlet_t *nbv, ListedForcesGpu *listedForcesGpu, gmx_pme_t *pmedata, gmx_enerdata_t *enerd, const MdrunScheduleWorkload &runScheduleWork, int64_t step, gmx_wallcycle *wcycle) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:1108: warning: Member reduceAndUpdateMuTot(DipoleData *dipoleData, const t_commrec *cr, const bool haveFreeEnergy, ArrayRef< const real > lambda, rvec muTotal, const DDBalanceRegionHandler &ddBalanceRegionHandler) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/checkpointdata.h:97: warning: Member makeCheckpointArrayRef(T &container) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/checkpointdata.h:117: warning: Member makeCheckpointArrayRefFromArray(T *begin, size_t size) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/propagator.cpp:759: warning: Member hasStartVelocityScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/propagator.cpp:768: warning: Member hasEndVelocityScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/propagator.cpp:775: warning: Member hasPositionScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/propagator.cpp:781: warning: Member hasParrinelloRahmanScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/propagator.cpp:907: warning: Member getConnection(Propagator< integrationStage > *propagator, const PropagatorTag &propagatorTag) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/pullelement.cpp:125: warning: Member doCheckpointData(CheckpointData< operation > *checkpointData, ArrayRef< double > previousStepCom) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/simulatoralgorithm.h:633: warning: Member getElementPointer(LegacySimulatorData *legacySimulatorData, ModularSimulatorAlgorithmBuilderHelper *builderHelper, StatePropagatorData *statePropagatorData, EnergyData *energyData, FreeEnergyPerturbationData *freeEnergyPerturbationData, GlobalCommunicationHelper *globalCommunicationHelper, ObservablesReducer *observablesReducer, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:149: warning: Member copy_int_to_nbat_int(const int *a, int na, int na_round, const int *in, int fill, int *innb) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:289: warning: Member copyRVecToNbatXYZReal(int numAtoms, const rvec *x, real *xnb, int a0) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:330: warning: Member set_lj_parameter_data(nbnxn_atomdata_t::Params *params, gmx_bool bSIMD) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:472: warning: Member nbnxn_atomdata_params_init(const MDLogger &mdlog, nbnxn_atomdata_t::Params *params, const NbnxmKernelType kernelType, const std::optional< LJCombinationRule > &ljCombinationRule, const LJCombinationRule pmeLJCombinationRule, ArrayRef< const real > nbfp, const bool addFillerAtomType, const int numEnergyGroups) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:749: warning: Member copy_lj_to_nbat_lj_comb(ArrayRef< const real > ljparam_type, const int *type, int na, real *ljparam_at) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:766: warning: Member nbnxn_atomdata_set_atomtypes(nbnxn_atomdata_t::Params *params, const GridSet &gridSet, ArrayRef< const int > atomTypes) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:793: warning: Member nbnxn_atomdata_set_ljcombparams(nbnxn_atomdata_t::Params *params, const int XFormat, const GridSet &gridSet) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:838: warning: Member nbnxn_atomdata_set_charges(nbnxn_atomdata_t *nbat, const GridSet &gridSet, ArrayRef< const real > charges) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:896: warning: Member nbnxn_atomdata_mask_fep(nbnxn_atomdata_t *nbat, const GridSet &gridSet) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:938: warning: Member nbnxn_atomdata_set_energygroups(const GridSet &gridSet, ArrayRef< const int32_t > atomInfo, EnergyGroupsPerCluster *energyGroupsPerCluster) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:998: warning: Member getGridRange(const GridSet &gridSet, const AtomLocality locality) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:1028: warning: Member copyXToNbatXForGridPart(const Grid &grid, const Range< int > &columnRange, const rvec *coordinates, nbnxn_atomdata_t *nbat) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:1061: warning: Member copyXToNbatXForGridPartIndexed(const Grid &grid, const Range< int > &columnRange, ArrayRef< const int > atomIndices, const rvec *coordinates, nbnxn_atomdata_t *nbat) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:1139: warning: Member nbnxn_atomdata_clear_reals(ArrayRef< real > dest, int i0, int i1) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:1147: warning: Member nbnxn_atomdata_reduce_reals(real *gmx_restrict dest, gmx_bool bDestSet, const real **gmx_restrict src, int nsrc, int i0, int i1) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:1179: warning: Member nbnxn_atomdata_reduce_reals_simd(real gmx_unused *gmx_restrict dest, gmx_bool gmx_unused bDestSet, const gmx_unused real **gmx_restrict src, int gmx_unused nsrc, int gmx_unused i0, int gmx_unused i1) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:1223: warning: Member addNbatFXYZToFPart(const nbnxn_atomdata_output_t &out, const int a0, const int a1, const int *cellIndices, ArrayRef< RVec > forces) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:1363: warning: Member getAtomRange(const AtomLocality locality, const GridSet &gridSet) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/grid.cpp:151: warning: Member getMaxNumCells(const Grid::Geometry &geometry, const int numAtoms, const int numColumns) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/gridset.cpp:171: warning: Member getGridOffset(ArrayRef< const Grid > grids, int gridIndex) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:1320: warning: Member launchNbnxmKernelHelper(NbnxmGpu *nb, const StepWorkload &stepWork, InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:61: warning: Member launchNbnxmKernelHelper< false, false, false >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:62: warning: Member launchNbnxmKernelHelper< false, false, true >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:63: warning: Member launchNbnxmKernelHelper< false, true, true >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:64: warning: Member launchNbnxmKernelHelper< false, true, false >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:66: warning: Member launchNbnxmKernelHelper< true, false, false >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:67: warning: Member launchNbnxmKernelHelper< true, false, true >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:68: warning: Member launchNbnxmKernelHelper< true, true, true >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:69: warning: Member launchNbnxmKernelHelper< true, true, false >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_body.h:119: warning: Member fetchNbfpC6C12(const float2 *nbfpComb, int type) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_utils.h:85: warning: Member nb_any_internal(int predicate, int widx) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_utils.h:108: warning: Member numberOfKernelBlocksSanityCheck(int numSci, const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_utils.h:125: warning: Member requiredSharedMemorySize() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kerneldispatch.cpp:375: warning: Member accountFlops(t_nrnb *nrnb, const PairlistSet &pairlistSet, const nonbonded_verlet_t &nbv, const interaction_const_t &ic, const gmx::StepWorkload &stepWork) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_prune.cpp:148: warning: Member nbnxmRefPruneKernel< NbnxmKernelType::Cpu4x4_PlainC >(NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, ArrayRef< const RVec > shiftvec, real rlistInner) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_prune.cpp:153: warning: Member nbnxmRefPruneKernel< NbnxmKernelType::Cpu1x1_PlainC >(NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, ArrayRef< const RVec > shiftvec, real rlistInner) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:62: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:74: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:86: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:98: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:110: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:122: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:134: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:146: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:158: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:170: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:182: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:194: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:206: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:218: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:230: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:242: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:254: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:266: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:278: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:290: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:302: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:314: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:326: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:338: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:350: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:362: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:374: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:386: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:398: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:410: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:423: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:435: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:447: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:459: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:471: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:483: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:495: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:507: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:519: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:531: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:543: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:555: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:567: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:579: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:591: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:603: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:615: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:627: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:639: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:651: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:663: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:675: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:687: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:699: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:711: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:723: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:735: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:747: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:759: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:771: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:784: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:796: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:808: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:820: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:832: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:844: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:856: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:868: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:880: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:892: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:904: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:916: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:928: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:940: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:952: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:964: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:976: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:988: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1000: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1012: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1024: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1036: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1048: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1060: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1072: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1084: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1096: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1108: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1120: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1132: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:62: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:74: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:86: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:98: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:110: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:122: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:134: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:146: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:158: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:170: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:182: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:194: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:206: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:218: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:230: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:242: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:254: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:266: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:278: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:290: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:302: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:314: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:326: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:338: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:350: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:362: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:374: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:386: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:398: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:410: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:423: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:435: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:447: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:459: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:471: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:483: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:495: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:507: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:519: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:531: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:543: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:555: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:567: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:579: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:591: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:603: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:615: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:627: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:639: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:651: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:663: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:675: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:687: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:699: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:711: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:723: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:735: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:747: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:759: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:771: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:784: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:796: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:808: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:820: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:832: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:844: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:856: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:868: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:880: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:892: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:904: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:916: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:928: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:940: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:952: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:964: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:976: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:988: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1000: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1012: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1024: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1036: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1048: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1060: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1072: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1084: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1096: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1108: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1120: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1132: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:122: warning: Member isGpuKernelType(const NbnxmKernelType kernelType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_setup.cpp:261: warning: Member nbnxmKernelTypeToName(NbnxmKernelType kernelType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:149: warning: Member isGpuSpecificPairlist(const PairlistType pairlistType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:269: warning: Member sc_gpuPairlistHasSplitJCluster(const PairlistType pairlistType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_buffer_ops.cpp:65: warning: Member nbnxn_gpu_x_to_nbat_x(const Grid &grid, NbnxmGpu *nb, DeviceBuffer< RVec > d_x, GpuEventSynchronizer *xReadyOnDevice, const AtomLocality locality, int gridId, int numColumnsMax, bool mustInsertNonLocalDependency) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:95: warning: Member init_ewald_coulomb_force_table(const EwaldCorrectionTables &tables, NBParamGpu *nbp, const DeviceContext &deviceContext, const DeviceStream &deviceStream) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:114: warning: Member useTabulatedEwaldByDefault(const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:148: warning: Member nbnxn_gpu_pick_ewald_kernel_type(const interaction_const_t &ic, const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:198: warning: Member set_cutoff_parameters(NBParamGpu *nbp, const interaction_const_t &ic, const PairlistParams &listParams) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:248: warning: Member init_timings(gmx_wallclock_gpu_nbnxn_t *t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:297: warning: Member nbnxmGpuPickVdwKernelType(const interaction_const_t &ic, LJCombinationRule ljCombinationRule) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:351: warning: Member nbnxmGpuPickElectrostaticsKernelType(const interaction_const_t &ic, const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:437: warning: Member initializeGpuLists(bool localAndNonLocal) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:448: warning: Member gpu_init(const DeviceStreamManager &deviceStreamManager, const interaction_const_t *ic, const PairlistParams &listParams, const nbnxn_atomdata_t *nbat, const bool bLocalAndNonlocal) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:512: warning: Member gpu_pme_loadbal_update_param(nonbonded_verlet_t *nbv, const interaction_const_t &ic) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:530: warning: Member gpu_upload_shiftvec(NbnxmGpu *nb, const nbnxn_atomdata_t *nbatom) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:691: warning: Member gpu_init_atomdata(NbnxmGpu *nb, const nbnxn_atomdata_t *nbat) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:794: warning: Member gpu_clear_outputs(NbnxmGpu *nb, bool computeVirial) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:825: warning: Member gpu_is_kernel_ewald_analytical(const NbnxmGpu *nb) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:831: warning: Member setupGpuShortRangeWorkLow(NbnxmGpu *nb, const ListedForcesGpu *listedForcesGpu, const InteractionLocality iLocality) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:844: warning: Member haveGpuShortRangeWork(const NbnxmGpu *nb, const InteractionLocality interactionLocality) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:984: warning: Member nbnxnInsertNonlocalGpuDependency(NbnxmGpu *nb, const InteractionLocality interactionLocality) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:1079: warning: Member nbnxn_gpu_init_x_to_nbat_x(const GridSet &gridSet, NbnxmGpu *gpu_nbv) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:1261: warning: Member gpuGetNBAtomData(NbnxmGpu *nb) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:1267: warning: Member gpu_get_f(NbnxmGpu *nb) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:90: warning: Member constexpr(doCalcEnergies) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:104: warning: Member c_useSimdGpuClusterPairDistance(const PairlistType layoutType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:121: warning: Member sizeNeededForBufferFlags(const int numAtoms) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:127: warning: Member resizeAndZeroBufferFlags(std::vector< gmx_bitmask_t > *flags, const int numAtoms) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:142: warning: Member listRangeForBoundingBoxToGridCell(real rlist, const GridDimensions &gridDims) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:154: warning: Member listRangeForGridCellToGridCell(real rlist, const GridDimensions &iGridDims, const GridDimensions &jGridDims) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:166: warning: Member get_cell_range(real b0, real b1, const GridDimensions &jGridDims, real d2, real rlist, int *cf, int *cl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:194: warning: Member clusterpairInRangePlainC(const NbnxmPairlistGpuWork &work, const int si, const int csj, const int jCoordStride, const real *x_j, const real rlist2) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:346: warning: Member clusterpairInRange(const NbnxmPairlistGpuWork &work, const int si, const int csj, const int jCoordStride, const real *x_j, const real rlist2) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:414: warning: Member createGpuPairlists(int numLists) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:494: warning: Member print_nblist_statistics(FILE *fp, const NbnxnPairlistCpu &nbl, const GridSet &gridSet, const real rl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:552: warning: Member print_nblist_statistics(FILE *fp, const NbnxnPairlistGpu &nbl, const GridSet &gridSet, const real rl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:633: warning: Member get_exclusion_mask(NbnxnPairlistGpu *nbl, int cjPacked, int warp) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:656: warning: Member setSelfAndNewtonExclusionsGpu(NbnxnPairlistGpu *nbl, const int cjPackedIndex, const int jOffsetInGroup, const int iClusterInCell) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:696: warning: Member makeClusterListSimple(const Grid &jGrid, NbnxnPairlistCpu *nbl, int icluster, int jclusterFirst, int jclusterLast, bool excludeSubDiagonal, const real *gmx_restrict x_j, real rlist2, float rbb2, int *gmx_restrict numDistanceChecks) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:817: warning: Member make_cluster_list_supersub(const Grid &iGrid, const Grid &jGrid, NbnxnPairlistGpu *nbl, const int sci, const int scj, const bool excludeSubDiagonal, const int stride, const real *x, const real rlist2, const float rbb2, int *numDistanceChecks) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:969: warning: Member numContiguousJClusters(const int cjIndexStart, const int cjIndexEnd, const JClusterListType &cjList) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1024: warning: Member findJClusterInJList(int jCluster, const JListRanges &ranges, const JClusterListType &cjList) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1065: warning: Member setExclusionsForIEntry(const GridSet &gridSet, NbnxnPairlistCpu *nbl, bool diagRemoved, int na_cj_2log, const ListOfLists< int > &exclusions) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1135: warning: Member getCoordinate(const nbnxn_atomdata_t &nbat, const int a) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1260: warning: Member make_fep_list(ArrayRef< const int > atomIndices, const nbnxn_atomdata_t *nbat, NbnxnPairlistCpu *nbl, bool bDiagRemoved, const real shx, const real shy, const real shz, const real gmx_unused rlist_fep2, const Grid &iGrid, const Grid &jGrid, t_nblist *nlist) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1438: warning: Member cj_mod_cjPacked(int cj) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1445: warning: Member cj_to_cjPacked(int cj) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1452: warning: Member a_mod_wj(int a) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1459: warning: Member make_fep_list(ArrayRef< const int > atomIndices, const nbnxn_atomdata_t *nbat, NbnxnPairlistGpu *nbl, bool bDiagRemoved, real shx, real shy, real shz, real rlist_fep2, const Grid &iGrid, const Grid &jGrid, t_nblist *nlist) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1606: warning: Member setExclusionsForIEntry(const GridSet &gridSet, NbnxnPairlistGpu *nbl, bool diagRemoved, int gmx_unused na_cj_2log, const ListOfLists< int > &exclusions) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1710: warning: Member addNewIEntry(NbnxnPairlistCpu *nbl, int ci, int shift, int flags) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1724: warning: Member addNewIEntry(NbnxnPairlistGpu *nbl, int sci, int shift, int gmx_unused flags) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1738: warning: Member sort_cj_excl(nbnxn_cj_t *cj, int ncj, NbnxmPairlistCpuWork *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1770: warning: Member closeIEntry(NbnxnPairlistCpu *nbl, int gmx_unused sp_max_av, bool gmx_unused progBal, float gmx_unused nsp_tot_est, int gmx_unused thread, int gmx_unused nthread) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1815: warning: Member split_sci_entry(NbnxnPairlistGpu *nbl, int nsp_target_av, bool progBal, float nsp_tot_est, int thread, int nthread) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1897: warning: Member closeIEntry(NbnxnPairlistGpu *nbl, int nsp_max_av, bool progBal, float nsp_tot_est, int thread, int nthread) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1927: warning: Member sync_work(NbnxnPairlistCpu gmx_unused *nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1933: warning: Member sync_work(NbnxnPairlistGpu *nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1939: warning: Member clear_pairlist(NbnxnPairlistCpu *nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1952: warning: Member clear_pairlist(NbnxnPairlistGpu *nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1961: warning: Member set_icell_bb_simple(ArrayRef< const BoundingBox > bb, int ci, const RVec &shift, BoundingBox *bb_ci) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1973: warning: Member set_icell_bb(const Grid &iGrid, int ci, const RVec &shift, NbnxmPairlistCpuWork *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2006: warning: Member set_icell_bb_supersub(ArrayRef< const BoundingBox > bb, int ci, const RVec &shift, BoundingBox *bb_ci) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2016: warning: Member set_icell_bb(const Grid &iGrid, int ci, const RVec &shift, NbnxmPairlistGpuWork *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2029: warning: Member icellSetXSimple(int ci, const RVec &shift, int stride, const real *x, NbnxmPairlistCpuWork::IClusterData *iClusterData) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2052: warning: Member icell_set_x(int ci, const RVec &shift, int stride, const real *x, const ClusterDistanceKernelType kernelType, NbnxmPairlistCpuWork *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2085: warning: Member icell_set_x(int ci, const RVec &shift, int stride, const real *x, ClusterDistanceKernelType, NbnxmPairlistGpuWork *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2129: warning: Member minimum_subgrid_size_xy(const Grid &grid) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2145: warning: Member effective_buffer_1x1_vs_MxN(const Grid &iGrid, const Grid &jGrid) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2171: warning: Member nonlocal_vol2(const gmx::DomdecZones &zones, const rvec ls, real r) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2214: warning: Member get_nsubpair_target(const GridSet &gridSet, const InteractionLocality iloc, const real rlist, const int min_ci_balanced, int *nsubpair_target, float *nsubpair_tot_est) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2313: warning: Member print_nblist_ci_cj(FILE *fp, const NbnxnPairlistCpu &nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2328: warning: Member print_nblist_sci_cj(FILE *fp, const NbnxnPairlistGpu &nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2364: warning: Member combine_nblists(ArrayRef< const NbnxnPairlistGpu > nbls, NbnxnPairlistGpu *nblc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2438: warning: Member balance_fep_lists(ArrayRef< std::unique_ptr< t_nblist > > fepLists, ArrayRef< PairsearchWork > work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2526: warning: Member next_ci(const Grid &grid, int nth, int ci_block, int *ci_x, int *ci_y, int *ci_b, int *ci) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2559: warning: Member boundingbox_only_distance2(const GridDimensions &iGridDims, const GridDimensions &jGridDims, real rlist, bool simple, const PairlistType layoutType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2597: warning: Member get_ci_block_size(const Grid &iGrid, const bool haveMultipleDomains, const int numLists) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2654: warning: Member getBufferFlagShift(int numAtomsPerCluster) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2665: warning: Member makeClusterListWrapper(NbnxnPairlistCpu *nbl, const Grid gmx_unused &iGrid, const int ci, const Grid &jGrid, const int firstCell, const int lastCell, const bool excludeSubDiagonal, const nbnxn_atomdata_t *nbat, const real rlist2, const real rbb2, const ClusterDistanceKernelType kernelType, int *numDistanceChecks) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2704: warning: Member makeClusterListWrapper(NbnxnPairlistGpu *nbl, const Grid &gmx_unused iGrid, const int ci, const Grid &jGrid, const int firstCell, const int lastCell, const bool excludeSubDiagonal, const nbnxn_atomdata_t *nbat, const real rlist2, const real rbb2, ClusterDistanceKernelType gmx_unused kernelType, int *numDistanceChecks) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2724: warning: Member getNumSimpleJClustersInList(const NbnxnPairlistCpu &nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2729: warning: Member getNumSimpleJClustersInList(const gmx_unused NbnxnPairlistGpu &nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2734: warning: Member incrementNumSimpleJClustersInList(NbnxnPairlistCpu *nbl, int ncj_old_j) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2740: warning: Member incrementNumSimpleJClustersInList(NbnxnPairlistGpu gmx_unused *nbl, int gmx_unused ncj_old_j) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2744: warning: Member checkListSizeConsistency(const NbnxnPairlistCpu &nbl, const bool haveFreeEnergy) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2752: warning: Member checkListSizeConsistency(const NbnxnPairlistGpu gmx_unused &nbl, bool gmx_unused haveFreeEnergy) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2758: warning: Member setBufferFlags(const NbnxnPairlistCpu &nbl, const int ncj_old_j, const int gridj_flag_shift, gmx_bitmask_t *gridj_flag, const int th) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2775: warning: Member setBufferFlags(const NbnxnPairlistGpu gmx_unused &nbl, int gmx_unused ncj_old_j, int gmx_unused gridj_flag_shift, gmx_bitmask_t gmx_unused *gridj_flag, int gmx_unused th) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2786: warning: Member nbnxn_make_pairlist_part(const GridSet &gridSet, const Grid &iGrid, const Grid &jGrid, PairsearchWork *work, const nbnxn_atomdata_t *nbat, const ListOfLists< int > &exclusions, real rlist, const PairlistType pairlistType, int ci_block, bool bFBufferFlag, int nsubpair_max, bool progBal, float nsubpair_tot_est, int th, int nth, T *nbl, t_nblist *nbl_fep) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:3304: warning: Member reduce_buffer_flags(ArrayRef< PairsearchWork > searchWork, int nsrc, ArrayRef< gmx_bitmask_t > dest) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:3318: warning: Member print_reduction_cost(ArrayRef< const gmx_bitmask_t > flags, int nout) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:3372: warning: Member copySelectedListRange(const nbnxn_ci_t *gmx_restrict srcCi, const NbnxnPairlistCpu *gmx_restrict src, NbnxnPairlistCpu *gmx_restrict dest, gmx_bitmask_t *flag, int iFlagShift, int jFlagShift, int t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:3408: warning: Member countClusterpairs(ArrayRef< const NbnxnPairlistCpu > pairlists) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:3430: warning: Member rebalanceSimpleLists(ArrayRef< const NbnxnPairlistCpu > srcSet, ArrayRef< NbnxnPairlistCpu > destSet, ArrayRef< PairsearchWork > searchWork) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:3505: warning: Member checkRebalanceSimpleLists(ArrayRef< const NbnxnPairlistCpu > lists) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:3539: warning: Member sort_sci(NbnxnPairlistGpu *nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:3594: warning: Member getIZoneRange(const GridSet::DomainSetup &domainSetup, const InteractionLocality locality) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:3614: warning: Member getJZoneRange(const gmx::DomdecZones *ddZones, const InteractionLocality locality, const int iZone) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:3636: warning: Member getGridList(ArrayRef< const Grid > grids, const Range< int > &ddZoneRange) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:73: warning: Member sc_iClusterSizeSimd() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:82: warning: Member sc_jClusterSizeSimd() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:252: warning: Member setICellCoordinatesSimd4xM(int gmx_unused ci, const RVec gmx_unused &shift, int gmx_unused stride, const real gmx_unused *x, NbnxmPairlistCpuWork gmx_unused *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:265: warning: Member setICellCoordinatesSimd2xMM(int gmx_unused ci, const RVec gmx_unused &shift, int gmx_unused stride, const real gmx_unused *x, NbnxmPairlistCpuWork gmx_unused *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:504: warning: Member makeClusterListSimd4xM(const Grid gmx_unused &jGrid, NbnxnPairlistCpu gmx_unused *nbl, int gmx_unused icluster, int gmx_unused firstCell, int gmx_unused lastCell, bool gmx_unused excludeSubDiagonal, const real gmx_unused *gmx_restrict x_j, real gmx_unused rlist2, float gmx_unused rbb2, int gmx_unused *gmx_restrict numDistanceChecks) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:523: warning: Member makeClusterListSimd2xMM(const Grid gmx_unused &jGrid, NbnxnPairlistCpu gmx_unused *nbl, int gmx_unused icluster, int gmx_unused firstCell, int gmx_unused lastCell, bool gmx_unused excludeSubDiagonal, const real gmx_unused *gmx_restrict x_j, real gmx_unused rlist2, float gmx_unused rbb2, int gmx_unused *gmx_restrict numDistanceChecks) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl.cpp:256: warning: Member launchSciSortOnGpu(GpuPairlist *plist, const int maxWorkGroupSize, const DeviceStream &deviceStream) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl.cpp:228: warning: Member launchPrefixSumKernel(sycl::queue &q, GpuPairlistSorting *sorting) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl.cpp:241: warning: Member launchBucketSortKernel(sycl::queue &q, GpuPairlist *plist) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel.cpp:53: warning: Member getNbnxmSubGroupSize(const DeviceInformation &deviceInfo, PairlistType layoutType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel.cpp:104: warning: Member launchNbnxmKernel(NbnxmGpu *nb, const gmx::StepWorkload &stepWork, const InteractionLocality iloc, bool doPrune) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_utils.h:58: warning: Member sc_superClInteractionMask(const PairlistType layoutType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/compiler.cpp:2598: warning: Member compileSelection(SelectionCollection *coll) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/selectioncollection.cpp:978: warning: Member swap(SelectionCollection &lhs, SelectionCollection &rhs) noexcept (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/decidegpuusage.cpp:175: warning: Member decideWhetherToUseGpusForPmeFft(const TaskTarget pmeFftTarget) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/decidegpuusage.cpp:182: warning: Member canUseGpusForPme(const bool useGpuForNonbonded, const TaskTarget pmeTarget, const TaskTarget pmeFftTarget, const t_inputrec &inputrec, std::string *errorMessage) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/template_mp.h:87: warning: Member dispatchTemplatedFunction(Function &&f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/stringutil.cpp:132: warning: Member formatString(gmx_fmtstr const char *fmt,...) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulationinput.h:120: warning: Member globalSimulationState(const SimulationInput &) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulationinput.h:121: warning: Member applyGlobalInputRecord(const SimulationInput &, t_inputrec *) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulationinput.h:122: warning: Member applyGlobalTopology(const SimulationInput &, gmx_mtop_t *) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/vec.h:625: warning: Member norm2(T *v) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/tests/colvarsoptions.cpp:87: warning: Member colvarsConfig (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/requirements.cpp:59: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/requirements.cpp:63: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:161: warning: Member c_disableAlternatingWait (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/nosehooverchains.cpp:67: warning: Member nhcUsageNames (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/gpu_types_common.h:88: warning: Member c_sciSortingItemsPerThread (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/gpu_types_common.h:463: warning: Member elecEwald (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/gpu_types_common.h:466: warning: Member elecEwaldTab (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/gpu_types_common.h:469: warning: Member ljEwald (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_data_mgmt.cpp:76: warning: Member gpu_min_ci_balanced_factor (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_body.h:574: warning: Member nbparam (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_body.h:574: warning: Member plist (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_utils.h:70: warning: Member c_subWarp (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_utils.h:82: warning: Member c_fbufStride (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp:59: warning: Member refPairlistLayoutType (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp:61: warning: Member c_clSize (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:82: warning: unable to resolve reference to 'ElecType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:106: warning: unable to resolve reference to 'VdwType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_geometry.cpp:49: warning: Member c_nbnxnRlistIncreaseOutsideFactor (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:56: warning: Member epsilon (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:59: warning: Member sigma6 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:60: warning: Member c6 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:61: warning: Member c12 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:63: warning: Member return (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:69: warning: Member repulsionShift (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:70: warning: Member rVdwSwitch (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:73: warning: Member rInv (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:74: warning: Member r2 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:75: warning: Member fInvR (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:76: warning: Member eLJ (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:80: warning: Member dispShiftV3 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:81: warning: Member repuShiftV2 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:82: warning: Member repuShiftV3 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:84: warning: Member r (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:85: warning: Member rSwitch (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:104: warning: Member typeI (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:119: warning: Member c_pbcShiftBackward (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1224: warning: Member max_nrj_fep (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:55: warning: Member c_centralShiftIndex (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:56: warning: Member c_numShiftVectors (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/decidegpuusage.cpp:126: warning: Member c_gpuBuildSyclWithoutGpuFft (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:83: warning: Member c_angstrom (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:84: warning: Member c_kilo (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:85: warning: Member c_nano (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:86: warning: Member c_pico (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:87: warning: Member c_nm2A (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:88: warning: Member c_cal2Joule (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:89: warning: Member c_electronCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:91: warning: Member c_amu (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:92: warning: Member c_boltzmann (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:93: warning: Member c_avogadro (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:94: warning: Member c_universalGasConstant (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:95: warning: Member c_boltz (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:96: warning: Member c_faraday (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:97: warning: Member c_planck1 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:98: warning: Member c_planck (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:100: warning: Member c_epsilon0Si (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:102: warning: Member c_epsilon0 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:105: warning: Member c_speedOfLight (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:107: warning: Member c_rydberg (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:109: warning: Member c_one4PiEps0 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:114: warning: Member c_barMdunits (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:115: warning: Member c_presfac (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:120: warning: Member c_debye2Enm (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:121: warning: Member c_enm2Debye (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:125: warning: Member c_fieldfac (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:128: warning: Member c_hartree2Kj (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:129: warning: Member c_bohr2Nm (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:130: warning: Member c_hartreeBohr2Md (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:132: warning: Member c_rad2Deg (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:133: warning: Member c_deg2Rad (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:787: warning: Member CompileTimeStringJoin_v (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:64: warning: Member sc_atomInfo_HasPerturbedCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:65: warning: Member sc_atomInfo_Exclusion (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:66: warning: Member sc_atomInfo_Constraint (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:67: warning: Member sc_atomInfo_Settle (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:68: warning: Member sc_atomInfo_BondCommunication (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:69: warning: Member sc_atomInfo_HasVdw (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:70: warning: Member sc_atomInfo_HasCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:71: warning: Member sc_atomInfo_IsFillerParticle (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:53: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:54: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:55: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:56: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:57: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJ_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:58: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:59: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:60: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:61: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:62: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJ_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:63: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:64: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:65: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:66: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:68: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:69: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:70: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:71: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:72: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:73: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:74: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:75: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:76: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:77: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:78: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:79: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:80: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:81: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:82: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:84: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:85: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:86: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:87: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:88: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:89: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:90: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:91: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:92: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:93: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:94: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:95: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:96: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:97: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:98: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:54: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:55: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:56: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:57: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:58: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJ_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:59: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:60: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:61: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:62: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:63: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJ_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:64: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:65: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:66: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:67: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:69: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:70: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:71: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:72: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:73: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:74: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:75: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:76: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:77: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:78: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:79: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:80: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:81: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:82: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:83: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:85: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:86: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:87: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:88: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:89: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:90: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:91: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:92: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:93: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:94: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:95: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:96: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:97: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:98: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:99: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:44: warning: Member c_dBoxY (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:45: warning: Member c_dBoxX (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:593: warning: argument 'wcycle' from the argument list of gmx::computeSpecialForces has multiple @param documentation sections /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/correlationhistory.h:61: warning: unable to resolve reference to 'updateCorrelationGridHistory' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:99: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:100: warning: @copydetails or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:94: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:95: warning: @copydetails or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:125: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:126: warning: @copydetails or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:120: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:121: warning: @copydetails or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/requirements.cpp:63: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/requirements.cpp:59: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/booltype.h:72: warning: Member value_ (variable) of struct gmx::BoolType is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:765: warning: Member impl() noexcept (function) of struct gmx::CompileTimeStringJoin is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:781: warning: Member stringArray (variable) of struct gmx::CompileTimeStringJoin is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:783: warning: Member value (variable) of struct gmx::CompileTimeStringJoin is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_coulomb_functions.h:134: warning: Member CoulombCalculator(const interaction_const_t &ic) (function) of class gmx::CoulombCalculator< KernelCoulombType::EwaldAnalytical > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_coulomb_functions.h:145: warning: Member force(const std::array< SimdReal, nR > &rSquaredV, const std::array< SimdReal, nR > gmx_unused &dummyRInvV, const std::array< SimdReal, nR > &rInvExclV, const std::array< SimdBool, nR > &withinCutoffV) (function) of class gmx::CoulombCalculator< KernelCoulombType::EwaldAnalytical > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_coulomb_functions.h:194: warning: Member CoulombCalculator(const interaction_const_t &ic) (function) of class gmx::CoulombCalculator< KernelCoulombType::EwaldTabulated > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_coulomb_functions.h:83: warning: Member CoulombCalculator(const interaction_const_t &ic) (function) of class gmx::CoulombCalculator< KernelCoulombType::RF > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_diagonal_masker.h:106: warning: Member DiagonalMasker(const nbnxn_atomdata_t::SimdMasks &simdMasks) (function) of class gmx::DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeEqualsISize > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_diagonal_masker.h:132: warning: Member DiagonalMasker(const nbnxn_atomdata_t::SimdMasks &simdMasks) (function) of class gmx::DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeIsDoubleISize > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_diagonal_masker.h:165: warning: Member DiagonalMasker(const nbnxn_atomdata_t::SimdMasks &simdMasks) (function) of class gmx::DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeIsHalfISize > is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/enumerationhelpers.h:333: warning: Member value (variable) of class gmx::EnumClassSuitsEnumerationArray is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:441: warning: Member operator()(const std::string &lhs, const std::string &rhs) const (function) of class gmx::EqualCaseInsensitive is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/haloexchange.h:93: warning: Member HaloExchange(PbcType pbcType) (function) of class gmx::HaloExchange is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/nnpotmodel.h:76: warning: Member prepareAtomNumbers(std::vector< int > &)=0 (function) of class gmx::INNPotModel is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/nnpotmodel.h:77: warning: Member prepareBox(matrix &)=0 (function) of class gmx::INNPotModel is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/nnpotmodel.h:78: warning: Member preparePbcType(PbcType &)=0 (function) of class gmx::INNPotModel is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/checkpointdata.h:146: warning: Member value (variable) of struct gmx::IsSerializableEnum is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_lennardjones_functions.h:328: warning: Member LennardJonesCalculator(const interaction_const_t &ic) (function) of class gmx::LennardJonesCalculator< calculateEnergies, InteractionModifiers::ForceSwitch > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_lennardjones_functions.h:488: warning: Member LennardJonesCalculator(const interaction_const_t &ic) (function) of class gmx::LennardJonesCalculator< calculateEnergies, InteractionModifiers::PotSwitch > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_lennardjones_functions.h:175: warning: Member LennardJonesCalculator(const interaction_const_t gmx_unused &ic) (function) of class gmx::LennardJonesCalculator< false, InteractionModifiers::PotShift > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_lennardjones_functions.h:205: warning: Member forceSigmaEpsilon(const std::array< SimdReal, inputSize > &rInvV, const std::array< SimdBool, interactSize > &interactV, SimdBool *withinCutoffV, const std::array< SimdReal, nR > &sigmaV, const std::array< SimdReal, nR > &epsilonV, SimdReal sixth, SimdReal twelfth, std::array< SimdReal, nR > &frLJV, std::array< SimdReal, vljvSize > &vLJV) (function) of class gmx::LennardJonesCalculator< false, InteractionModifiers::PotShift > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_lennardjones_functions.h:227: warning: Member LennardJonesCalculator(const interaction_const_t &ic) (function) of class gmx::LennardJonesCalculator< true, InteractionModifiers::PotShift > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_lennardjones_functions.h:266: warning: Member forceSigmaEpsilon(const std::array< SimdReal, inputSize > &rInvV, const std::array< SimdBool, interactSize > &interactV, SimdBool *withinCutoffV, const std::array< SimdReal, nR > &sigmaV, const std::array< SimdReal, nR > &epsilonV, SimdReal sixth, SimdReal twelfth, std::array< SimdReal, nR > &frLJV, std::array< SimdReal, vljvSize > &vLJV) (function) of class gmx::LennardJonesCalculator< true, InteractionModifiers::PotShift > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlistwork.h:62: warning: Member NbnxmPairlistCpuWork(const int iClusterSize) (function) of struct gmx::NbnxmPairlistCpuWork is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlistwork.h:67: warning: Member IClusterData(const int iClusterSize) (function) of struct gmx::NbnxmPairlistCpuWork::IClusterData is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.h:286: warning: Member NbnxnPairlistCpu(int iClusterSize) (function) of struct gmx::NbnxnPairlistCpu is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.h:237: warning: Member PackedJClusterList(const PinningPolicy pinningPolicy) (function) of class gmx::PackedJClusterList is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:218: warning: Member allocator_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:219: warning: Member size_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:220: warning: Member reference (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:221: warning: Member const_reference (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:222: warning: Member storage_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:223: warning: Member pointer (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:224: warning: Member const_pointer (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:225: warning: Member iterator (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:226: warning: Member const_iterator (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:227: warning: Member difference_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:351: warning: Member data() const noexcept (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:353: warning: Member begin() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:354: warning: Member end() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:356: warning: Member cbegin() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:357: warning: Member cend() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:359: warning: Member begin() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:360: warning: Member end() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:362: warning: Member cbegin() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:363: warning: Member cend() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairsearch.h:216: warning: Member setNonLocalGrid(int gridIndex, int zone, const GridDimensions &gridDimensions, ArrayRef< const std::pair< int, int > > columns, ArrayRef< const int32_t > atomInfo, ArrayRef< const RVec > x, nbnxn_atomdata_t *nbat) (function) of class gmx::PairSearch is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/range.h:75: warning: Member iterator_category (typedef) of struct gmx::Range::iterator is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/range.h:76: warning: Member difference_type (typedef) of struct gmx::Range::iterator is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/range.h:77: warning: Member value_type (typedef) of struct gmx::Range::iterator is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/range.h:78: warning: Member pointer (typedef) of struct gmx::Range::iterator is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/range.h:79: warning: Member reference (typedef) of struct gmx::Range::iterator is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/selection/selectioncollection.h:145: warning: Member SelectionCollection(const SelectionCollection &rhs) (function) of class gmx::SelectionCollection is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/selection/selectioncollection.h:146: warning: Member operator=(SelectionCollection rhs) (function) of class gmx::SelectionCollection is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/selection/selectioncollection.h:147: warning: Member swap(SelectionCollection &rhs) noexcept (function) of class gmx::SelectionCollection is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/torchmodel.h:91: warning: Member prepareAtomNumbers(std::vector< int > &atomTypes) override (function) of class gmx::TorchModel is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/torchmodel.h:92: warning: Member prepareBox(matrix &box) override (function) of class gmx::TorchModel is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/torchmodel.h:93: warning: Member preparePbcType(PbcType &pbcType) override (function) of class gmx::TorchModel is not documented. cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen && /usr/bin/cmake -E touch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen/doxygen-user-timestamp.txt make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [100%] Built target doxygen-user libpath/shortest.c:324: triangulation failed libpath/shortest.c:324: triangulation failed libpath/shortest.c:324: triangulation failed libpath/shortest.c:324: triangulation failed The following warnings were produced by Doxygen: /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/biasgrid.h:279: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/biasgrid.h:279: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/energyhistory.cpp:48: warning: Conditional section with label 'INTERNAL' does not have a corresponding \endcond command within this file. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_utils.h:63: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_utils.h:63: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2025.0/src/gromacs/onlinehelp/helpwritercontext.cpp:247: warning: unbalanced grouping commands /build/reproducible-path/gromacs-2025.0/src/testutils/testasserts.cpp:186: warning: unbalanced grouping commands /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/basedefinitions.h:229: warning: documentation for unknown define GMX_IGNORE_RETURN_VALUE found. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:94: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:99: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:120: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:125: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:82: warning: unable to resolve reference to 'ElecType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:106: warning: unable to resolve reference to 'VdwType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/requirements.cpp:59: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/leapfrog_gpu_internal_sycl.cpp:170: warning: unable to resolve reference to 'NumTempScaleValues' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/requirements.cpp:63: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:398: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:295: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:340: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme.h:323: warning: unable to resolve reference to 'pme_gpu_supports_input' for \ref command /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/optionflags.h:107: warning: explicit link request to 'OptionFlag' could not be resolved /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/optionflags.h:107: warning: explicit link request to 'OptionFlag' could not be resolved /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/selectioncollection.cpp:978: warning: Member swap(SelectionCollection &lhs, SelectionCollection &rhs) noexcept (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:226: warning: Member t_functype (typedef) of file idef.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:473: warning: Member printInteractionParameters(gmx::TextWriter *writer, t_functype ftype, const t_iparams &iparams) (function) of file idef.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:474: warning: Member pr_iparams(FILE *fp, t_functype ftype, const t_iparams &iparams) (function) of file idef.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:475: warning: Member pr_ilist(FILE *fp, int indent, const char *title, const t_functype *functype, const InteractionList &ilist, bool bShowNumbers, bool bShowParameters, const t_iparams *iparams) (function) of file idef.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:483: warning: Member pr_idef(FILE *fp, int indent, const char *title, const t_idef *idef, bool bShowNumbers, bool bShowParameters) (function) of file idef.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:54: warning: Member t_iatom (typedef) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:59: warning: Member rvec4[4] (typedef) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:220: warning: Member IS_RESTRAINT_TYPE(int ifunc) (function) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:239: warning: Member NRFPA(int ftype) (function) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:244: warning: Member NRFPB(int ftype) (function) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:249: warning: Member NRFP(int ftype) (function) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:254: warning: Member NRAL(int ftype) (function) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:275: warning: Member IS_VSITE(int ftype) (function) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:280: warning: Member IS_TABULATED(int ftype) (function) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:67: warning: Member IF_VSITE (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:68: warning: Member IF_CONSTRAINT (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:69: warning: Member IF_CHEMBOND (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:76: warning: Member IF_DIHEDRAL (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:77: warning: Member IF_PAIR (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:78: warning: Member IF_TABULATED (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:233: warning: Member NR_CBTDIHS (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:234: warning: Member NR_FOURDIHS (variable) of file ifunc.h is not documented. warning: Included by graph for 'arrayref.h' not generated, too many nodes (57), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'basedefinitions.h' not generated, too many nodes (80), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'gmxassert.h' not generated, too many nodes (58), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'real.h' not generated, too many nodes (95), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:787: warning: Member CompileTimeStringJoin_v (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/mp11.h:76: warning: Member mp_with_index(std::size_t i, F &&f) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/pointers.h:87: warning: Member Ensures(cond) (macro definition) of file pointers.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/pointers.h:194: warning: Member operator!=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() !=rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/pointers.h:200: warning: Member operator<(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get()< rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/pointers.h:206: warning: Member operator<=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get()<=rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/pointers.h:212: warning: Member operator>(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() > rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/pointers.h:218: warning: Member operator>=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() >=rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/iframeconverter.h:116: warning: invalid argument for command '\iline' /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme.h:323: warning: unable to resolve reference to 'pme_gpu_supports_input' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme.h:228: warning: unable to resolve reference to 'gmx_pme_reinit' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme.h:323: warning: unable to resolve reference to 'pme_gpu_supports_input' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_types_host.h:72: warning: Member PmeGpuHaloExchange (typedef) of file pme_gpu_types_host.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/devicebuffer_hip.h:339: warning: Member asMpiPointer(DeviceBuffer< ValueType > &buffer) (function) of file devicebuffer_hip.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/devicebuffer_ocl.h:384: warning: Member asMpiPointer(DeviceBuffer< ValueType > &) (function) of file devicebuffer_ocl.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/devicebuffer_sycl.h:434: warning: Member asMpiPointer(DeviceBuffer< ValueType > &buffer) (function) of file devicebuffer_sycl.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gmxopencl.h:56: warning: Member CL_USE_DEPRECATED_OPENCL_2_0_APIS (macro definition) of file gmxopencl.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpueventsynchronizer.h:58: warning: unable to resolve reference to 'GpuEventSynchronizer::markEvent' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpueventsynchronizer.h:59: warning: unable to resolve reference to 'GpuEventSynchronizer::waitForEvent' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpueventsynchronizer.h:60: warning: unable to resolve reference to 'GpuEventSynchronizer::enqueueWaitEvent' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpueventsynchronizer.h:74: warning: unable to resolve reference to 'GpuEventSynchronizer::reset' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpueventsynchronizer.h:76: warning: unable to resolve reference to 'GpuEventSynchronizer::consume' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpueventsynchronizer.h:78: warning: unable to resolve reference to 'GpuEventSynchronizer::markEvent' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpueventsynchronizer.h:81: warning: unable to resolve reference to 'GpuEventSynchronizer::waitForEvent' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpueventsynchronizer.h:83: warning: unable to resolve reference to 'GpuEventSynchronizer::enqueueWaitEvent' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpueventsynchronizer.h:88: warning: unable to resolve reference to 'GpuEventSynchronizer::markEvent' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpueventsynchronizer.h:89: warning: unable to resolve reference to 'GpuEventSynchronizer::enqueueWaitEvent' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpueventsynchronizer.h:89: warning: unable to resolve reference to 'GpuEventSynchronizer::enqueueWaitEvent' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gputraits.h:67: warning: Member DeviceTexture (typedef) of file gputraits.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gputraits_ocl.h:50: warning: Member DeviceTexture (typedef) of file gputraits_ocl.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/hip_kernel_utils.h:78: warning: Member LAUNCH_BOUNDS_EXACT(WORK_GROUP_SIZE, WAVES_PER_EU) (macro definition) of file hip_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/hip_kernel_utils.h:82: warning: Member LAUNCH_BOUNDS_EXACT_SINGLE(WORK_GROUP_SIZE) (macro definition) of file hip_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/hip_kernel_utils.h:85: warning: Member GMX_HIP_MAX_BLOCKS_PER_MP (macro definition) of file hip_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/hip_kernel_utils.h:86: warning: Member GMX_HIP_MAX_THREADS_PER_MP (macro definition) of file hip_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/hip_sycl_kernel_utils.h:82: warning: Member GMX_ALWAYS_INLINE_ATTRIBUTE (macro definition) of file hip_sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/hip_sycl_kernel_utils.h:83: warning: Member GMX_FUNC_ATTRIBUTE (macro definition) of file hip_sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/hip_sycl_kernel_utils.h:109: warning: Member idx (variable) of file hip_sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/oclraii.h:131: warning: Member ClCommandQueue (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/oclraii.h:132: warning: Member ClProgram (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/oclraii.h:133: warning: Member ClKernel (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/sycl_kernel_utils.h:65: warning: Member SYCL_ASSERT(condition) (macro definition) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/sycl_kernel_utils.h:85: warning: Member compilingForHost() (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/sycl_kernel_utils.h:101: warning: Member compilingForSubGroupSize() (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/sycl_kernel_utils.h:115: warning: Member skipKernelCompilation() (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/sycl_kernel_utils.h:137: warning: Member atomicAddDefault(T &val, const T delta) (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/sycl_kernel_utils.h:174: warning: Member atomicFetchAddLocal(T &val, const T delta) (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/nrjac.h:55: warning: Member jacobi(double **a, int numDimensions, double *eigenvalues, double **eigenvectors, int *numRotations) (function) of file nrjac.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/nrjac.h:65: warning: Member jacobi(gmx::ArrayRef< gmx::DVec > a, gmx::ArrayRef< double > eigenvalues, gmx::ArrayRef< gmx::DVec > eigenvectors) (function) of file nrjac.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/nrjac.h:67: warning: Member m_inv_gen(const real *m, int n, real *minv) (function) of file nrjac.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/nrjac.cpp:59: warning: Member do_rotate(MatrixType a, int i, int j, int k, int l, double tau, double s) (function) of file nrjac.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/nrjac.cpp:69: warning: Member jacobi(MatrixType a, const int n, double d[], MatrixType v) (function) of file nrjac.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/nrjac.cpp:182: warning: Member jacobi(double **a, const int numDimensions, double *eigenvalues, double **eigenvectors, int *numRotations) (function) of file nrjac.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/nrjac.cpp:192: warning: Member jacobi(gmx::ArrayRef< gmx::DVec > a, gmx::ArrayRef< double > eigenvalues, gmx::ArrayRef< gmx::DVec > eigenvectors) (function) of file nrjac.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/nrjac.cpp:201: warning: Member m_inv_gen(const real *m, int n, real *minv) (function) of file nrjac.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/energyoutput.h:87: warning: Member pvEnergyFieldName (variable) of file energyoutput.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/energyoutput.h:89: warning: Member enthalpyEnergyFieldName (variable) of file energyoutput.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/energyoutput.h:91: warning: Member virialEnergyFieldNames (variable) of file energyoutput.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulationinput.h:120: warning: Member globalSimulationState(const SimulationInput &) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulationinput.h:121: warning: Member applyGlobalInputRecord(const SimulationInput &, t_inputrec *) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulationinput.h:122: warning: Member applyGlobalTopology(const SimulationInput &, gmx_mtop_t *) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:64: warning: Member sc_atomInfo_HasPerturbedCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:65: warning: Member sc_atomInfo_Exclusion (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:66: warning: Member sc_atomInfo_Constraint (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:67: warning: Member sc_atomInfo_Settle (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:68: warning: Member sc_atomInfo_BondCommunication (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:69: warning: Member sc_atomInfo_HasVdw (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:70: warning: Member sc_atomInfo_HasCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:71: warning: Member sc_atomInfo_IsFillerParticle (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/checkpointdata.h:97: warning: Member makeCheckpointArrayRef(T &container) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/checkpointdata.h:117: warning: Member makeCheckpointArrayRefFromArray(T *begin, size_t size) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_data_mgmt.cpp:76: warning: Member gpu_min_ci_balanced_factor (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:122: warning: Member isGpuKernelType(const NbnxmKernelType kernelType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_setup.cpp:261: warning: Member nbnxmKernelTypeToName(NbnxmKernelType kernelType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:149: warning: Member isGpuSpecificPairlist(const PairlistType pairlistType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:269: warning: Member sc_gpuPairlistHasSplitJCluster(const PairlistType pairlistType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:82: warning: unable to resolve reference to 'ElecType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:106: warning: unable to resolve reference to 'VdwType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:180: warning: Member c_gpuNumClusterPerCellY (variable) of namespace gmx::detail is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:181: warning: Member c_gpuNumClusterPerCellX (variable) of namespace gmx::detail is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include/gromacs/pbcutil/pbc_aiuc_sycl.h:50: warning: Member xyzToShiftIndex(int x, int y, int z) (function) of file pbc_aiuc_sycl.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:642: warning: Member GMX_SIMD_HAVE_4NSIMD_UTIL_FLOAT (macro definition) of file simd.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:653: warning: Member GMX_SIMD4N_FLOAT_WIDTH (macro definition) of file simd.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:688: warning: Member GMX_SIMD_HAVE_4NSIMD_UTIL_DOUBLE (macro definition) of file simd.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:699: warning: Member GMX_SIMD4N_DOUBLE_WIDTH (macro definition) of file simd.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:733: warning: Member GMX_SIMD_HAVE_4NSIMD_UTIL_REAL (macro definition) of file simd.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:742: warning: Member GMX_SIMD4N_REAL_WIDTH (macro definition) of file simd.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:652: warning: Member Simd4NFloat (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:698: warning: Member Simd4NDouble (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:741: warning: Member Simd4NReal (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:512: warning: Member load(const std::enable_if_t< std::is_arithmetic_v< T >, T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:518: warning: Member load(const AlignedArray< internal::SimdTraitsT< T >, N > &m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:536: warning: Member loadU(const std::enable_if_t< std::is_arithmetic_v< T >, T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:542: warning: Member loadU(const AlignedArray< internal::SimdTraitsT< T >, N > &m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:623: warning: Member load(const internal::Simd4TraitsT< T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:628: warning: Member loadU(const internal::Simd4TraitsT< T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:657: warning: Member loadUNDuplicate4(const float *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:661: warning: Member load4DuplicateN(const float *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:665: warning: Member loadU4NOffset(const float *f, int) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:703: warning: Member loadUNDuplicate4(const double *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:707: warning: Member load4DuplicateN(const double *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:711: warning: Member loadU4NOffset(const double *f, int) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:295: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:340: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:398: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:374: warning: Member c_simdBestPairAlignment (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:479: warning: Member SimdTraitsT (typedef) of namespace gmx::internal is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:618: warning: Member Simd4TraitsT (typedef) of namespace gmx::internal is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/tables/forcetable.h:79: warning: Member TableFormat (enumeration) of file forcetable.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include/gromacs/timing/gpu_timing.h:57: warning: Member PmeStage (enumeration) of file gpu_timing.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:46: warning: Member def_bonded(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:51: warning: Member def_pair(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:56: warning: Member def_bondedt(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:61: warning: Member def_bondedtz(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:66: warning: Member def_angle(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:71: warning: Member def_dihedral(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:77: warning: Member def_dihedral_tabulated(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:82: warning: Member def_bond(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:87: warning: Member def_bondt(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:92: warning: Member def_bondnb(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:97: warning: Member def_vsite(const char *str, const char *lstr, int nra, int nrpa) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:102: warning: Member def_shk(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:107: warning: Member def_shkcb(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:112: warning: Member def_nb(const char *str, const char *lstr, int nra, int nrpa) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:117: warning: Member def_nofc(const char *str, const char *lstr) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include/gromacs/topology/mtop_atomloops.h:212: warning: Member gmx_mtop_atomloop_block_t (typedef) of file mtop_atomloops.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include/gromacs/topology/mtop_atomloops.h:216: warning: Member gmx_mtop_atomloop_block_init(const gmx_mtop_t &mtop) (function) of file mtop_atomloops.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include/gromacs/topology/mtop_atomloops.h:231: warning: Member gmx_mtop_atomloop_block_next(gmx_mtop_atomloop_block_t aloop, const t_atom **atom, int *nmol) (function) of file mtop_atomloops.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/fatalerror.h:217: warning: Member gmx_call(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/fatalerror.h:218: warning: Member gmx_comm(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/fatalerror.h:219: warning: Member gmx_file(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/fatalerror.h:220: warning: Member gmx_impl(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/fatalerror.h:221: warning: Member gmx_incons(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/fatalerror.h:222: warning: Member gmx_input(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/fatalerror.h:223: warning: Member gmx_mem(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/fatalerror.h:224: warning: Member gmx_open(fn) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:64: warning: Member ivec[3] (typedef) of file iserializer.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:200: warning: Member toString(bool t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:204: warning: Member toString(int t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:208: warning: Member toString(int64_t t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:212: warning: Member toString(float t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:216: warning: Member toString(double t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:220: warning: Member toString(unsigned char t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:224: warning: Member toString(std::string t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/template_mp.h:87: warning: Member dispatchTemplatedFunction(Function &&f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:85: warning: Member EXPECT_EQ(0, reinterpret_cast< std::size_t >(p) &this->mask(a)) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:86: warning: Member deallocate(p, 1000) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:93: warning: Member v(10) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:94: warning: Member EXPECT_EQ(0, reinterpret_cast< std::size_t >(v.data()) &this->mask(v.get_allocator())) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:99: warning: Member for(std::size_t i=1000;i<=10000;i+=1000) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:125: warning: Member v1(1) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:127: warning: Member EXPECT_NE(data, nullptr) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:128: warning: Member v2(std::move(v1)) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:129: warning: Member EXPECT_EQ(data, v2.data()) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:82: warning: Member a (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:83: warning: Member p (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:126: warning: Member data (variable) of namespace gmx::test is not documented. :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::initOptions()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::optionsFinished()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::initAnalysis()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::initAfterFirstFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::finishAnalysis()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::writeOutput()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::startFrames()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::startFrames()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::finishFrames()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::finishFrames()' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/impl_reference/impl_reference_util_float.h:151: warning: unable to resolve reference to 'c_simdBestPairAlignmentFloat' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/impl_reference/impl_reference_util_float.h:152: warning: unable to resolve reference to 'c_simdBestPairAlignmentDouble' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/impl_reference/impl_reference_util_double.h:171: warning: @copydetails or @copydoc target 'c_simdBestPairAlignmentFloat' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility.h:109: warning: explicit link request to 'GMX_IGNORE_RETURN_VALUE' could not be resolved /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:200: warning: Member toString(bool t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:204: warning: Member toString(int t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:208: warning: Member toString(int64_t t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:212: warning: Member toString(float t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:216: warning: Member toString(double t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:220: warning: Member toString(unsigned char t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:224: warning: Member toString(std::string t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:119: warning: @copydetails or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:184: warning: @copydetails or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:100: warning: @copydetails or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:144: warning: @copydetails or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:119: warning: @copydetails or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:113: warning: @copydetails or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/errorcodes.h:111: warning: explicit link request to 'eeUnknownError' could not be resolved /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:179: warning: @copydetails or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:402: warning: @copydetails or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:419: warning: @copydetails or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:83: warning: @copydetails or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:189: warning: @copydetails or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/constraint_gpu_helpers.h:55: warning: Member AtomsAdjacencyListElement(int indexOfSecondConstrainedAtom, int indexOfConstraint, int signFactor) (function) of struct AtomsAdjacencyListElement is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/dlbtiming.h:215: warning: Member impl_ (variable) of class BalanceRegion is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/device_information.h:184: warning: Member gpuAwareMpiStatus (variable) of struct DeviceInformation is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/commrec.h:68: warning: Member bUse (variable) of struct gmx_nodecomm_t is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/commrec.h:69: warning: Member comm_intra (variable) of struct gmx_nodecomm_t is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/commrec.h:70: warning: Member rank_intra (variable) of struct gmx_nodecomm_t is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/commrec.h:71: warning: Member comm_inter (variable) of struct gmx_nodecomm_t is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/grompp_impl.h:69: warning: Member aj() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/grompp_impl.h:70: warning: Member ak() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/grompp_impl.h:71: warning: Member al() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/grompp_impl.h:72: warning: Member am() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/grompp_impl.h:74: warning: Member c0() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/grompp_impl.h:75: warning: Member c1() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/grompp_impl.h:76: warning: Member c2() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/grompp_impl.h:78: warning: Member interactionTypeName() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:453: warning: Member fudgeQQ (variable) of struct t_idef is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:459: warning: Member iparams_fbposres (variable) of struct t_idef is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:327: warning: Member iatoms (variable) of struct t_ilist is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:328: warning: Member nalloc (variable) of struct t_ilist is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:105: warning: Member nrfpA (variable) of struct t_interaction_function is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:71: warning: Member bham (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:75: warning: Member harmonic (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:79: warning: Member linangle (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:83: warning: Member restraint (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:87: warning: Member cubic (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:91: warning: Member fene (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:95: warning: Member cross_bb (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:99: warning: Member cross_ba (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:103: warning: Member u_b (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:107: warning: Member qangle (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:111: warning: Member polarize (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:115: warning: Member anharm_polarize (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:119: warning: Member wpol (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:123: warning: Member thole (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:127: warning: Member lj (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:131: warning: Member lj14 (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:135: warning: Member ljc14 (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:139: warning: Member ljcnb (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:155: warning: Member constr (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:168: warning: Member morse (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:172: warning: Member posres (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:177: warning: Member fbposres (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:181: warning: Member rbdihs (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:185: warning: Member cbtdihs (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:189: warning: Member vsite (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:194: warning: Member vsiten (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:200: warning: Member disres (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:204: warning: Member dihres (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:209: warning: Member orires (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:215: warning: Member tab (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:219: warning: Member cmap (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:223: warning: Member generic (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/fcdata.h:216: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(t_oriresdata) (function) of struct t_oriresdata is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/warninp.h:71: warning: Member WarningHandler(bool allowWarnings, int maxNumberWarnings) (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/warninp.h:89: warning: Member errorCount() const (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/warninp.h:91: warning: Member warningCount() const (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/warninp.h:93: warning: Member noteCount() const (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/warninp.h:95: warning: Member maxWarningCount() const (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_force_sender_gpu_impl.h:76: warning: Member CacheLineAlignedFlag (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/h5md.h:55: warning: Member hid_t (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/h5md.h:57: warning: Member herr_t (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:875: warning: Member mode (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:435: warning: Member GpuPairlistByLocality (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/opencl/nbnxm_ocl_types.h:130: warning: Member cl_nbparam_params_t (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:77: warning: Member FCiFloat3 (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/optionflags.h:107: warning: explicit link request to 'OptionFlag' could not be resolved /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/oclraii.h:131: warning: Member ClCommandQueue (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/oclraii.h:132: warning: Member ClProgram (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/oclraii.h:133: warning: Member ClKernel (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft.h:67: warning: Member FftBackend (enumeration) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/h5md.h:59: warning: Member H5mdFileMode (enumeration) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/referencetemperaturemanager.h:67: warning: Member ReferenceTemperatureChangeAlgorithm (enumeration) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/nnpotoptions.cpp:86: warning: Member NNPotMdpTransformFromString(IKeyValueTreeTransformRules *rules, TransformWithFunctionType transformationFunction, const std::string &optionTag) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/torchmodel.cpp:60: warning: Member recordToString(std::tuple< at::DataPtr, size_t > data) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/gpuhaloexchange_impl_gpu_sycl.cpp:63: warning: Member packSendBufKernel(Float3 *__restrict__ gm_dataPacked, const Float3 *__restrict__ gm_data, const int *__restrict__ gm_map, int mapSize, Float3 coordinateShift) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/gpuhaloexchange_impl_gpu_sycl.cpp:119: warning: Member launchPackSendBufKernel(const DeviceStream &deviceStream, int xSendSize, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/gpuhaloexchange_impl_gpu_sycl.cpp:134: warning: Member launchUnpackRecvBufKernel(const DeviceStream &deviceStream, int fRecvSize, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_cufftmp.cpp:102: warning: Member handleCufftError(cufftResult_t status, const char *msg) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_sycl_vkfft.cpp:258: warning: Member launchVkFft(const DeviceBuffer< float > &realGrid, const DeviceBuffer< float > &complexGrid, NativeQueue queue, gmx_fft_direction fftDirection, VkFFTApplication *application, VkFFTLaunchParams *launchParams) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:94: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:99: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:120: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:125: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/h5md_low_level_util.h:63: warning: Member throwUponH5mdError(const bool errorExists, const std::string &message) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/massrepartitioning.cpp:57: warning: Member smallestAtomMass(const gmx_mtop_t &mtop) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/simd_support.cpp:70: warning: Member simdString(SimdType s) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/simd_support.cpp:199: warning: Member simdCompiled() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces_gpu_impl_gpu.cpp:67: warning: Member chooseSubGroupSizeForDevice(const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:878: warning: Member bondedKernel(sycl::handler &cgh, const BondedGpuKernelParameters &kernelParams, const DeviceBuffer< t_iatom > gm_iatoms_[numFTypesOnGpu], float *__restrict__ gm_vTot, const t_iparams *__restrict__ gm_forceParams_, const sycl::float4 *__restrict__ gm_xq_, Float3 *__restrict__ gm_f_, Float3 *__restrict__ gm_fShift_) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:1498: warning: Member do_force(FILE *log, const t_commrec *cr, const gmx_multisim_t *ms, const t_inputrec &inputrec, const MDModulesNotifiers &mdModulesNotifiers, Awh *awh, gmx_enfrot *enforcedRotation, ImdSession *imdSession, pull_t *pull_work, int64_t step, t_nrnb *nrnb, gmx_wallcycle *wcycle, const gmx_localtop_t *top, const matrix box, ArrayRefWithPadding< RVec > coordinates, ArrayRef< RVec > velocities, const history_t *hist, ForceBuffersView *force, tensor vir_force, const t_mdatoms *mdatoms, gmx_enerdata_t *enerd, ArrayRef< const real > lambda, t_forcerec *fr, const MdrunScheduleWorkload &runScheduleWork, VirtualSitesHandler *vsite, rvec mu_tot, double t, gmx_edsam *ed, CpuPpLongRangeNonbondeds *longRangeNonbondeds, const DDBalanceRegionHandler &ddBalanceRegionHandler) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/leapfrog_gpu_internal_sycl.cpp:170: warning: unable to resolve reference to 'NumTempScaleValues' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/lincs_gpu_internal_sycl.cpp:452: warning: Member launchLincsKernel(const DeviceStream &deviceStream, const int numConstraintsThreads, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:163: warning: Member sum_forces(ArrayRef< RVec > f, ArrayRef< const RVec > forceToAdd) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:176: warning: Member calc_virial(int start, int homenr, const rvec x[], const ForceWithShiftForces &forceWithShiftForces, tensor vir_part, const matrix box, t_nrnb *nrnb, const t_forcerec *fr, PbcType pbcType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:205: warning: Member pull_potential_wrapper(const t_commrec *cr, const t_inputrec &ir, const matrix box, ArrayRef< const RVec > x, const t_mdatoms *mdatoms, gmx_enerdata_t *enerd, pull_t *pull_work, const real *lambda, double t, gmx_wallcycle *wcycle) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:238: warning: Member pme_receive_force_ener(t_forcerec *fr, const t_commrec *cr, ForceWithVirial *forceWithVirial, gmx_enerdata_t *enerd, bool useGpuPmePpComms, bool receivePmeForceToGpu, gmx_wallcycle *wcycle) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:280: warning: Member print_large_forces(FILE *fp, const t_mdatoms *md, const t_commrec *cr, int64_t step, real forceTolerance, ArrayRef< const RVec > x, ArrayRef< const RVec > f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:429: warning: Member do_nb_verlet(t_forcerec *fr, const interaction_const_t *ic, gmx_enerdata_t *enerd, const StepWorkload &stepWork, const InteractionLocality ilocality, const int clearF, const int64_t step, t_nrnb *nrnb, gmx_wallcycle *wcycle) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:476: warning: Member clearRVecs(ArrayRef< RVec > v, const bool useOpenmpThreading) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:942: warning: Member launchGpuEndOfStepTasks(nonbonded_verlet_t *nbv, ListedForcesGpu *listedForcesGpu, gmx_pme_t *pmedata, gmx_enerdata_t *enerd, const MdrunScheduleWorkload &runScheduleWork, int64_t step, gmx_wallcycle *wcycle) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:1108: warning: Member reduceAndUpdateMuTot(DipoleData *dipoleData, const t_commrec *cr, const bool haveFreeEnergy, ArrayRef< const real > lambda, rvec muTotal, const DDBalanceRegionHandler &ddBalanceRegionHandler) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/checkpointdata.h:97: warning: Member makeCheckpointArrayRef(T &container) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/checkpointdata.h:117: warning: Member makeCheckpointArrayRefFromArray(T *begin, size_t size) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/propagator.cpp:759: warning: Member hasStartVelocityScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/propagator.cpp:768: warning: Member hasEndVelocityScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/propagator.cpp:775: warning: Member hasPositionScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/propagator.cpp:781: warning: Member hasParrinelloRahmanScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/propagator.cpp:907: warning: Member getConnection(Propagator< integrationStage > *propagator, const PropagatorTag &propagatorTag) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/pullelement.cpp:125: warning: Member doCheckpointData(CheckpointData< operation > *checkpointData, ArrayRef< double > previousStepCom) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/simulatoralgorithm.h:633: warning: Member getElementPointer(LegacySimulatorData *legacySimulatorData, ModularSimulatorAlgorithmBuilderHelper *builderHelper, StatePropagatorData *statePropagatorData, EnergyData *energyData, FreeEnergyPerturbationData *freeEnergyPerturbationData, GlobalCommunicationHelper *globalCommunicationHelper, ObservablesReducer *observablesReducer, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:149: warning: Member copy_int_to_nbat_int(const int *a, int na, int na_round, const int *in, int fill, int *innb) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:289: warning: Member copyRVecToNbatXYZReal(int numAtoms, const rvec *x, real *xnb, int a0) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:330: warning: Member set_lj_parameter_data(nbnxn_atomdata_t::Params *params, gmx_bool bSIMD) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:472: warning: Member nbnxn_atomdata_params_init(const MDLogger &mdlog, nbnxn_atomdata_t::Params *params, const NbnxmKernelType kernelType, const std::optional< LJCombinationRule > &ljCombinationRule, const LJCombinationRule pmeLJCombinationRule, ArrayRef< const real > nbfp, const bool addFillerAtomType, const int numEnergyGroups) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:749: warning: Member copy_lj_to_nbat_lj_comb(ArrayRef< const real > ljparam_type, const int *type, int na, real *ljparam_at) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:766: warning: Member nbnxn_atomdata_set_atomtypes(nbnxn_atomdata_t::Params *params, const GridSet &gridSet, ArrayRef< const int > atomTypes) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:793: warning: Member nbnxn_atomdata_set_ljcombparams(nbnxn_atomdata_t::Params *params, const int XFormat, const GridSet &gridSet) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:838: warning: Member nbnxn_atomdata_set_charges(nbnxn_atomdata_t *nbat, const GridSet &gridSet, ArrayRef< const real > charges) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:896: warning: Member nbnxn_atomdata_mask_fep(nbnxn_atomdata_t *nbat, const GridSet &gridSet) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:938: warning: Member nbnxn_atomdata_set_energygroups(const GridSet &gridSet, ArrayRef< const int32_t > atomInfo, EnergyGroupsPerCluster *energyGroupsPerCluster) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:998: warning: Member getGridRange(const GridSet &gridSet, const AtomLocality locality) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:1028: warning: Member copyXToNbatXForGridPart(const Grid &grid, const Range< int > &columnRange, const rvec *coordinates, nbnxn_atomdata_t *nbat) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:1061: warning: Member copyXToNbatXForGridPartIndexed(const Grid &grid, const Range< int > &columnRange, ArrayRef< const int > atomIndices, const rvec *coordinates, nbnxn_atomdata_t *nbat) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:1139: warning: Member nbnxn_atomdata_clear_reals(ArrayRef< real > dest, int i0, int i1) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:1147: warning: Member nbnxn_atomdata_reduce_reals(real *gmx_restrict dest, gmx_bool bDestSet, const real **gmx_restrict src, int nsrc, int i0, int i1) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:1179: warning: Member nbnxn_atomdata_reduce_reals_simd(real gmx_unused *gmx_restrict dest, gmx_bool gmx_unused bDestSet, const gmx_unused real **gmx_restrict src, int gmx_unused nsrc, int gmx_unused i0, int gmx_unused i1) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:1223: warning: Member addNbatFXYZToFPart(const nbnxn_atomdata_output_t &out, const int a0, const int a1, const int *cellIndices, ArrayRef< RVec > forces) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:1363: warning: Member getAtomRange(const AtomLocality locality, const GridSet &gridSet) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/grid.cpp:151: warning: Member getMaxNumCells(const Grid::Geometry &geometry, const int numAtoms, const int numColumns) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/gridset.cpp:171: warning: Member getGridOffset(ArrayRef< const Grid > grids, int gridIndex) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:1320: warning: Member launchNbnxmKernelHelper(NbnxmGpu *nb, const StepWorkload &stepWork, InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:61: warning: Member launchNbnxmKernelHelper< false, false, false >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:62: warning: Member launchNbnxmKernelHelper< false, false, true >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:63: warning: Member launchNbnxmKernelHelper< false, true, true >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:64: warning: Member launchNbnxmKernelHelper< false, true, false >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:66: warning: Member launchNbnxmKernelHelper< true, false, false >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:67: warning: Member launchNbnxmKernelHelper< true, false, true >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:68: warning: Member launchNbnxmKernelHelper< true, true, true >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:69: warning: Member launchNbnxmKernelHelper< true, true, false >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_body.h:119: warning: Member fetchNbfpC6C12(const float2 *nbfpComb, int type) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_utils.h:85: warning: Member nb_any_internal(int predicate, int widx) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_utils.h:108: warning: Member numberOfKernelBlocksSanityCheck(int numSci, const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_utils.h:125: warning: Member requiredSharedMemorySize() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kerneldispatch.cpp:375: warning: Member accountFlops(t_nrnb *nrnb, const PairlistSet &pairlistSet, const nonbonded_verlet_t &nbv, const interaction_const_t &ic, const gmx::StepWorkload &stepWork) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_prune.cpp:148: warning: Member nbnxmRefPruneKernel< NbnxmKernelType::Cpu4x4_PlainC >(NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, ArrayRef< const RVec > shiftvec, real rlistInner) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_prune.cpp:153: warning: Member nbnxmRefPruneKernel< NbnxmKernelType::Cpu1x1_PlainC >(NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, ArrayRef< const RVec > shiftvec, real rlistInner) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:62: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:74: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:86: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:98: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:110: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:122: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:134: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:146: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:158: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:170: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:182: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:194: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:206: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:218: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:230: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:242: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:254: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:266: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:278: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:290: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:302: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:314: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:326: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:338: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:350: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:362: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:374: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:386: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:398: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:410: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:423: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:435: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:447: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:459: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:471: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:483: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:495: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:507: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:519: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:531: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:543: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:555: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:567: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:579: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:591: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:603: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:615: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:627: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:639: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:651: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:663: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:675: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:687: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:699: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:711: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:723: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:735: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:747: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:759: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:771: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:784: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:796: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:808: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:820: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:832: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:844: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:856: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:868: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:880: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:892: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:904: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:916: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:928: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:940: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:952: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:964: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:976: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:988: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1000: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1012: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1024: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1036: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1048: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1060: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1072: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1084: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1096: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1108: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1120: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1132: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:62: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:74: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:86: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:98: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:110: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:122: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:134: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:146: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:158: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:170: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:182: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:194: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:206: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:218: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:230: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:242: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:254: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:266: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:278: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:290: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:302: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:314: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:326: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:338: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:350: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:362: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:374: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:386: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:398: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:410: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:423: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:435: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:447: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:459: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:471: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:483: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:495: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:507: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:519: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:531: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:543: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:555: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:567: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:579: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:591: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:603: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:615: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:627: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:639: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:651: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:663: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:675: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:687: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:699: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:711: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:723: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:735: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:747: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:759: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:771: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:784: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:796: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:808: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:820: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:832: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:844: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:856: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:868: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:880: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:892: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:904: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:916: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:928: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:940: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:952: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:964: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:976: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:988: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1000: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1012: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1024: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1036: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1048: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1060: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1072: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1084: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1096: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1108: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1120: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1132: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:122: warning: Member isGpuKernelType(const NbnxmKernelType kernelType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_setup.cpp:261: warning: Member nbnxmKernelTypeToName(NbnxmKernelType kernelType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:149: warning: Member isGpuSpecificPairlist(const PairlistType pairlistType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:269: warning: Member sc_gpuPairlistHasSplitJCluster(const PairlistType pairlistType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_buffer_ops.cpp:65: warning: Member nbnxn_gpu_x_to_nbat_x(const Grid &grid, NbnxmGpu *nb, DeviceBuffer< RVec > d_x, GpuEventSynchronizer *xReadyOnDevice, const AtomLocality locality, int gridId, int numColumnsMax, bool mustInsertNonLocalDependency) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:95: warning: Member init_ewald_coulomb_force_table(const EwaldCorrectionTables &tables, NBParamGpu *nbp, const DeviceContext &deviceContext, const DeviceStream &deviceStream) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:114: warning: Member useTabulatedEwaldByDefault(const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:148: warning: Member nbnxn_gpu_pick_ewald_kernel_type(const interaction_const_t &ic, const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:198: warning: Member set_cutoff_parameters(NBParamGpu *nbp, const interaction_const_t &ic, const PairlistParams &listParams) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:248: warning: Member init_timings(gmx_wallclock_gpu_nbnxn_t *t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:297: warning: Member nbnxmGpuPickVdwKernelType(const interaction_const_t &ic, LJCombinationRule ljCombinationRule) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:351: warning: Member nbnxmGpuPickElectrostaticsKernelType(const interaction_const_t &ic, const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:437: warning: Member initializeGpuLists(bool localAndNonLocal) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:448: warning: Member gpu_init(const DeviceStreamManager &deviceStreamManager, const interaction_const_t *ic, const PairlistParams &listParams, const nbnxn_atomdata_t *nbat, const bool bLocalAndNonlocal) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:512: warning: Member gpu_pme_loadbal_update_param(nonbonded_verlet_t *nbv, const interaction_const_t &ic) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:530: warning: Member gpu_upload_shiftvec(NbnxmGpu *nb, const nbnxn_atomdata_t *nbatom) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:691: warning: Member gpu_init_atomdata(NbnxmGpu *nb, const nbnxn_atomdata_t *nbat) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:794: warning: Member gpu_clear_outputs(NbnxmGpu *nb, bool computeVirial) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:825: warning: Member gpu_is_kernel_ewald_analytical(const NbnxmGpu *nb) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:831: warning: Member setupGpuShortRangeWorkLow(NbnxmGpu *nb, const ListedForcesGpu *listedForcesGpu, const InteractionLocality iLocality) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:844: warning: Member haveGpuShortRangeWork(const NbnxmGpu *nb, const InteractionLocality interactionLocality) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:984: warning: Member nbnxnInsertNonlocalGpuDependency(NbnxmGpu *nb, const InteractionLocality interactionLocality) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:1079: warning: Member nbnxn_gpu_init_x_to_nbat_x(const GridSet &gridSet, NbnxmGpu *gpu_nbv) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:1261: warning: Member gpuGetNBAtomData(NbnxmGpu *nb) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:1267: warning: Member gpu_get_f(NbnxmGpu *nb) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:90: warning: Member constexpr(doCalcEnergies) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:104: warning: Member c_useSimdGpuClusterPairDistance(const PairlistType layoutType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:121: warning: Member sizeNeededForBufferFlags(const int numAtoms) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:127: warning: Member resizeAndZeroBufferFlags(std::vector< gmx_bitmask_t > *flags, const int numAtoms) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:142: warning: Member listRangeForBoundingBoxToGridCell(real rlist, const GridDimensions &gridDims) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:154: warning: Member listRangeForGridCellToGridCell(real rlist, const GridDimensions &iGridDims, const GridDimensions &jGridDims) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:166: warning: Member get_cell_range(real b0, real b1, const GridDimensions &jGridDims, real d2, real rlist, int *cf, int *cl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:194: warning: Member clusterpairInRangePlainC(const NbnxmPairlistGpuWork &work, const int si, const int csj, const int jCoordStride, const real *x_j, const real rlist2) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:346: warning: Member clusterpairInRange(const NbnxmPairlistGpuWork &work, const int si, const int csj, const int jCoordStride, const real *x_j, const real rlist2) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:414: warning: Member createGpuPairlists(int numLists) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:494: warning: Member print_nblist_statistics(FILE *fp, const NbnxnPairlistCpu &nbl, const GridSet &gridSet, const real rl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:552: warning: Member print_nblist_statistics(FILE *fp, const NbnxnPairlistGpu &nbl, const GridSet &gridSet, const real rl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:633: warning: Member get_exclusion_mask(NbnxnPairlistGpu *nbl, int cjPacked, int warp) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:656: warning: Member setSelfAndNewtonExclusionsGpu(NbnxnPairlistGpu *nbl, const int cjPackedIndex, const int jOffsetInGroup, const int iClusterInCell) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:696: warning: Member makeClusterListSimple(const Grid &jGrid, NbnxnPairlistCpu *nbl, int icluster, int jclusterFirst, int jclusterLast, bool excludeSubDiagonal, const real *gmx_restrict x_j, real rlist2, float rbb2, int *gmx_restrict numDistanceChecks) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:817: warning: Member make_cluster_list_supersub(const Grid &iGrid, const Grid &jGrid, NbnxnPairlistGpu *nbl, const int sci, const int scj, const bool excludeSubDiagonal, const int stride, const real *x, const real rlist2, const float rbb2, int *numDistanceChecks) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:969: warning: Member numContiguousJClusters(const int cjIndexStart, const int cjIndexEnd, const JClusterListType &cjList) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1024: warning: Member findJClusterInJList(int jCluster, const JListRanges &ranges, const JClusterListType &cjList) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1065: warning: Member setExclusionsForIEntry(const GridSet &gridSet, NbnxnPairlistCpu *nbl, bool diagRemoved, int na_cj_2log, const ListOfLists< int > &exclusions) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1135: warning: Member getCoordinate(const nbnxn_atomdata_t &nbat, const int a) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1260: warning: Member make_fep_list(ArrayRef< const int > atomIndices, const nbnxn_atomdata_t *nbat, NbnxnPairlistCpu *nbl, bool bDiagRemoved, const real shx, const real shy, const real shz, const real gmx_unused rlist_fep2, const Grid &iGrid, const Grid &jGrid, t_nblist *nlist) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1438: warning: Member cj_mod_cjPacked(int cj) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1445: warning: Member cj_to_cjPacked(int cj) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1452: warning: Member a_mod_wj(int a) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1459: warning: Member make_fep_list(ArrayRef< const int > atomIndices, const nbnxn_atomdata_t *nbat, NbnxnPairlistGpu *nbl, bool bDiagRemoved, real shx, real shy, real shz, real rlist_fep2, const Grid &iGrid, const Grid &jGrid, t_nblist *nlist) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1606: warning: Member setExclusionsForIEntry(const GridSet &gridSet, NbnxnPairlistGpu *nbl, bool diagRemoved, int gmx_unused na_cj_2log, const ListOfLists< int > &exclusions) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1710: warning: Member addNewIEntry(NbnxnPairlistCpu *nbl, int ci, int shift, int flags) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1724: warning: Member addNewIEntry(NbnxnPairlistGpu *nbl, int sci, int shift, int gmx_unused flags) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1738: warning: Member sort_cj_excl(nbnxn_cj_t *cj, int ncj, NbnxmPairlistCpuWork *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1770: warning: Member closeIEntry(NbnxnPairlistCpu *nbl, int gmx_unused sp_max_av, bool gmx_unused progBal, float gmx_unused nsp_tot_est, int gmx_unused thread, int gmx_unused nthread) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1815: warning: Member split_sci_entry(NbnxnPairlistGpu *nbl, int nsp_target_av, bool progBal, float nsp_tot_est, int thread, int nthread) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1897: warning: Member closeIEntry(NbnxnPairlistGpu *nbl, int nsp_max_av, bool progBal, float nsp_tot_est, int thread, int nthread) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1927: warning: Member sync_work(NbnxnPairlistCpu gmx_unused *nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1933: warning: Member sync_work(NbnxnPairlistGpu *nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1939: warning: Member clear_pairlist(NbnxnPairlistCpu *nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1952: warning: Member clear_pairlist(NbnxnPairlistGpu *nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1961: warning: Member set_icell_bb_simple(ArrayRef< const BoundingBox > bb, int ci, const RVec &shift, BoundingBox *bb_ci) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1973: warning: Member set_icell_bb(const Grid &iGrid, int ci, const RVec &shift, NbnxmPairlistCpuWork *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2006: warning: Member set_icell_bb_supersub(ArrayRef< const BoundingBox > bb, int ci, const RVec &shift, BoundingBox *bb_ci) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2016: warning: Member set_icell_bb(const Grid &iGrid, int ci, const RVec &shift, NbnxmPairlistGpuWork *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2029: warning: Member icellSetXSimple(int ci, const RVec &shift, int stride, const real *x, NbnxmPairlistCpuWork::IClusterData *iClusterData) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2052: warning: Member icell_set_x(int ci, const RVec &shift, int stride, const real *x, const ClusterDistanceKernelType kernelType, NbnxmPairlistCpuWork *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2085: warning: Member icell_set_x(int ci, const RVec &shift, int stride, const real *x, ClusterDistanceKernelType, NbnxmPairlistGpuWork *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2129: warning: Member minimum_subgrid_size_xy(const Grid &grid) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2145: warning: Member effective_buffer_1x1_vs_MxN(const Grid &iGrid, const Grid &jGrid) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2171: warning: Member nonlocal_vol2(const gmx::DomdecZones &zones, const rvec ls, real r) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2214: warning: Member get_nsubpair_target(const GridSet &gridSet, const InteractionLocality iloc, const real rlist, const int min_ci_balanced, int *nsubpair_target, float *nsubpair_tot_est) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2313: warning: Member print_nblist_ci_cj(FILE *fp, const NbnxnPairlistCpu &nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2328: warning: Member print_nblist_sci_cj(FILE *fp, const NbnxnPairlistGpu &nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2364: warning: Member combine_nblists(ArrayRef< const NbnxnPairlistGpu > nbls, NbnxnPairlistGpu *nblc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2438: warning: Member balance_fep_lists(ArrayRef< std::unique_ptr< t_nblist > > fepLists, ArrayRef< PairsearchWork > work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2526: warning: Member next_ci(const Grid &grid, int nth, int ci_block, int *ci_x, int *ci_y, int *ci_b, int *ci) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2559: warning: Member boundingbox_only_distance2(const GridDimensions &iGridDims, const GridDimensions &jGridDims, real rlist, bool simple, const PairlistType layoutType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2597: warning: Member get_ci_block_size(const Grid &iGrid, const bool haveMultipleDomains, const int numLists) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2654: warning: Member getBufferFlagShift(int numAtomsPerCluster) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2665: warning: Member makeClusterListWrapper(NbnxnPairlistCpu *nbl, const Grid gmx_unused &iGrid, const int ci, const Grid &jGrid, const int firstCell, const int lastCell, const bool excludeSubDiagonal, const nbnxn_atomdata_t *nbat, const real rlist2, const real rbb2, const ClusterDistanceKernelType kernelType, int *numDistanceChecks) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2704: warning: Member makeClusterListWrapper(NbnxnPairlistGpu *nbl, const Grid &gmx_unused iGrid, const int ci, const Grid &jGrid, const int firstCell, const int lastCell, const bool excludeSubDiagonal, const nbnxn_atomdata_t *nbat, const real rlist2, const real rbb2, ClusterDistanceKernelType gmx_unused kernelType, int *numDistanceChecks) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2724: warning: Member getNumSimpleJClustersInList(const NbnxnPairlistCpu &nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2729: warning: Member getNumSimpleJClustersInList(const gmx_unused NbnxnPairlistGpu &nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2734: warning: Member incrementNumSimpleJClustersInList(NbnxnPairlistCpu *nbl, int ncj_old_j) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2740: warning: Member incrementNumSimpleJClustersInList(NbnxnPairlistGpu gmx_unused *nbl, int gmx_unused ncj_old_j) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2744: warning: Member checkListSizeConsistency(const NbnxnPairlistCpu &nbl, const bool haveFreeEnergy) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2752: warning: Member checkListSizeConsistency(const NbnxnPairlistGpu gmx_unused &nbl, bool gmx_unused haveFreeEnergy) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2758: warning: Member setBufferFlags(const NbnxnPairlistCpu &nbl, const int ncj_old_j, const int gridj_flag_shift, gmx_bitmask_t *gridj_flag, const int th) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2775: warning: Member setBufferFlags(const NbnxnPairlistGpu gmx_unused &nbl, int gmx_unused ncj_old_j, int gmx_unused gridj_flag_shift, gmx_bitmask_t gmx_unused *gridj_flag, int gmx_unused th) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2786: warning: Member nbnxn_make_pairlist_part(const GridSet &gridSet, const Grid &iGrid, const Grid &jGrid, PairsearchWork *work, const nbnxn_atomdata_t *nbat, const ListOfLists< int > &exclusions, real rlist, const PairlistType pairlistType, int ci_block, bool bFBufferFlag, int nsubpair_max, bool progBal, float nsubpair_tot_est, int th, int nth, T *nbl, t_nblist *nbl_fep) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:3304: warning: Member reduce_buffer_flags(ArrayRef< PairsearchWork > searchWork, int nsrc, ArrayRef< gmx_bitmask_t > dest) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:3318: warning: Member print_reduction_cost(ArrayRef< const gmx_bitmask_t > flags, int nout) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:3372: warning: Member copySelectedListRange(const nbnxn_ci_t *gmx_restrict srcCi, const NbnxnPairlistCpu *gmx_restrict src, NbnxnPairlistCpu *gmx_restrict dest, gmx_bitmask_t *flag, int iFlagShift, int jFlagShift, int t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:3408: warning: Member countClusterpairs(ArrayRef< const NbnxnPairlistCpu > pairlists) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:3430: warning: Member rebalanceSimpleLists(ArrayRef< const NbnxnPairlistCpu > srcSet, ArrayRef< NbnxnPairlistCpu > destSet, ArrayRef< PairsearchWork > searchWork) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:3505: warning: Member checkRebalanceSimpleLists(ArrayRef< const NbnxnPairlistCpu > lists) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:3539: warning: Member sort_sci(NbnxnPairlistGpu *nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:3594: warning: Member getIZoneRange(const GridSet::DomainSetup &domainSetup, const InteractionLocality locality) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:3614: warning: Member getJZoneRange(const gmx::DomdecZones *ddZones, const InteractionLocality locality, const int iZone) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:3636: warning: Member getGridList(ArrayRef< const Grid > grids, const Range< int > &ddZoneRange) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:73: warning: Member sc_iClusterSizeSimd() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:82: warning: Member sc_jClusterSizeSimd() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:252: warning: Member setICellCoordinatesSimd4xM(int gmx_unused ci, const RVec gmx_unused &shift, int gmx_unused stride, const real gmx_unused *x, NbnxmPairlistCpuWork gmx_unused *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:265: warning: Member setICellCoordinatesSimd2xMM(int gmx_unused ci, const RVec gmx_unused &shift, int gmx_unused stride, const real gmx_unused *x, NbnxmPairlistCpuWork gmx_unused *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:504: warning: Member makeClusterListSimd4xM(const Grid gmx_unused &jGrid, NbnxnPairlistCpu gmx_unused *nbl, int gmx_unused icluster, int gmx_unused firstCell, int gmx_unused lastCell, bool gmx_unused excludeSubDiagonal, const real gmx_unused *gmx_restrict x_j, real gmx_unused rlist2, float gmx_unused rbb2, int gmx_unused *gmx_restrict numDistanceChecks) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:523: warning: Member makeClusterListSimd2xMM(const Grid gmx_unused &jGrid, NbnxnPairlistCpu gmx_unused *nbl, int gmx_unused icluster, int gmx_unused firstCell, int gmx_unused lastCell, bool gmx_unused excludeSubDiagonal, const real gmx_unused *gmx_restrict x_j, real gmx_unused rlist2, float gmx_unused rbb2, int gmx_unused *gmx_restrict numDistanceChecks) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl.cpp:256: warning: Member launchSciSortOnGpu(GpuPairlist *plist, const int maxWorkGroupSize, const DeviceStream &deviceStream) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl.cpp:228: warning: Member launchPrefixSumKernel(sycl::queue &q, GpuPairlistSorting *sorting) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl.cpp:241: warning: Member launchBucketSortKernel(sycl::queue &q, GpuPairlist *plist) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel.cpp:53: warning: Member getNbnxmSubGroupSize(const DeviceInformation &deviceInfo, PairlistType layoutType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel.cpp:104: warning: Member launchNbnxmKernel(NbnxmGpu *nb, const gmx::StepWorkload &stepWork, const InteractionLocality iloc, bool doPrune) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_utils.h:58: warning: Member sc_superClInteractionMask(const PairlistType layoutType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/compiler.cpp:2598: warning: Member compileSelection(SelectionCollection *coll) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/selectioncollection.cpp:978: warning: Member swap(SelectionCollection &lhs, SelectionCollection &rhs) noexcept (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/decidegpuusage.cpp:175: warning: Member decideWhetherToUseGpusForPmeFft(const TaskTarget pmeFftTarget) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/decidegpuusage.cpp:182: warning: Member canUseGpusForPme(const bool useGpuForNonbonded, const TaskTarget pmeTarget, const TaskTarget pmeFftTarget, const t_inputrec &inputrec, std::string *errorMessage) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/template_mp.h:87: warning: Member dispatchTemplatedFunction(Function &&f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/stringutil.cpp:132: warning: Member formatString(gmx_fmtstr const char *fmt,...) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulationinput.h:120: warning: Member globalSimulationState(const SimulationInput &) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulationinput.h:121: warning: Member applyGlobalInputRecord(const SimulationInput &, t_inputrec *) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulationinput.h:122: warning: Member applyGlobalTopology(const SimulationInput &, gmx_mtop_t *) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:200: warning: Member toString(bool t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:204: warning: Member toString(int t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:208: warning: Member toString(int64_t t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:212: warning: Member toString(float t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:216: warning: Member toString(double t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:220: warning: Member toString(unsigned char t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:224: warning: Member toString(std::string t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/vec.h:625: warning: Member norm2(T *v) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/tests/colvarsoptions.cpp:87: warning: Member colvarsConfig (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/requirements.cpp:59: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/requirements.cpp:63: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:161: warning: Member c_disableAlternatingWait (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/nosehooverchains.cpp:67: warning: Member nhcUsageNames (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/gpu_types_common.h:88: warning: Member c_sciSortingItemsPerThread (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/gpu_types_common.h:463: warning: Member elecEwald (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/gpu_types_common.h:466: warning: Member elecEwaldTab (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/gpu_types_common.h:469: warning: Member ljEwald (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_data_mgmt.cpp:76: warning: Member gpu_min_ci_balanced_factor (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_body.h:574: warning: Member nbparam (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_body.h:574: warning: Member plist (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_utils.h:70: warning: Member c_subWarp (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_utils.h:82: warning: Member c_fbufStride (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp:59: warning: Member refPairlistLayoutType (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp:61: warning: Member c_clSize (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:82: warning: unable to resolve reference to 'ElecType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:106: warning: unable to resolve reference to 'VdwType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_geometry.cpp:49: warning: Member c_nbnxnRlistIncreaseOutsideFactor (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:56: warning: Member epsilon (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:59: warning: Member sigma6 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:60: warning: Member c6 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:61: warning: Member c12 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:63: warning: Member return (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:69: warning: Member repulsionShift (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:70: warning: Member rVdwSwitch (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:73: warning: Member rInv (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:74: warning: Member r2 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:75: warning: Member fInvR (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:76: warning: Member eLJ (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:80: warning: Member dispShiftV3 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:81: warning: Member repuShiftV2 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:82: warning: Member repuShiftV3 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:84: warning: Member r (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:85: warning: Member rSwitch (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:104: warning: Member typeI (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:119: warning: Member c_pbcShiftBackward (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1224: warning: Member max_nrj_fep (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:55: warning: Member c_centralShiftIndex (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:56: warning: Member c_numShiftVectors (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/decidegpuusage.cpp:126: warning: Member c_gpuBuildSyclWithoutGpuFft (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:83: warning: Member c_angstrom (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:84: warning: Member c_kilo (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:85: warning: Member c_nano (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:86: warning: Member c_pico (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:87: warning: Member c_nm2A (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:88: warning: Member c_cal2Joule (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:89: warning: Member c_electronCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:91: warning: Member c_amu (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:92: warning: Member c_boltzmann (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:93: warning: Member c_avogadro (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:94: warning: Member c_universalGasConstant (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:95: warning: Member c_boltz (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:96: warning: Member c_faraday (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:97: warning: Member c_planck1 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:98: warning: Member c_planck (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:100: warning: Member c_epsilon0Si (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:102: warning: Member c_epsilon0 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:105: warning: Member c_speedOfLight (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:107: warning: Member c_rydberg (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:109: warning: Member c_one4PiEps0 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:114: warning: Member c_barMdunits (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:115: warning: Member c_presfac (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:120: warning: Member c_debye2Enm (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:121: warning: Member c_enm2Debye (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:125: warning: Member c_fieldfac (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:128: warning: Member c_hartree2Kj (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:129: warning: Member c_bohr2Nm (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:130: warning: Member c_hartreeBohr2Md (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:132: warning: Member c_rad2Deg (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:133: warning: Member c_deg2Rad (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:787: warning: Member CompileTimeStringJoin_v (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:64: warning: Member sc_atomInfo_HasPerturbedCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:65: warning: Member sc_atomInfo_Exclusion (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:66: warning: Member sc_atomInfo_Constraint (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:67: warning: Member sc_atomInfo_Settle (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:68: warning: Member sc_atomInfo_BondCommunication (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:69: warning: Member sc_atomInfo_HasVdw (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:70: warning: Member sc_atomInfo_HasCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:71: warning: Member sc_atomInfo_IsFillerParticle (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:53: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:54: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:55: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:56: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:57: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJ_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:58: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:59: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:60: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:61: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:62: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJ_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:63: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:64: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:65: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:66: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:68: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:69: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:70: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:71: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:72: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:73: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:74: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:75: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:76: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:77: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:78: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:79: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:80: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:81: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:82: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:84: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:85: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:86: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:87: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:88: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:89: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:90: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:91: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:92: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:93: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:94: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:95: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:96: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:97: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:98: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:54: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:55: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:56: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:57: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:58: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJ_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:59: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:60: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:61: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:62: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:63: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJ_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:64: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:65: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:66: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:67: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:69: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:70: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:71: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:72: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:73: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:74: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:75: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:76: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:77: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:78: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:79: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:80: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:81: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:82: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:83: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:85: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:86: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:87: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:88: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:89: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:90: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:91: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:92: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:93: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:94: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:95: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:96: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:97: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:98: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:99: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:44: warning: Member c_dBoxY (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:45: warning: Member c_dBoxX (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:295: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:340: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:398: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:374: warning: Member c_simdBestPairAlignment (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:652: warning: Member Simd4NFloat (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:698: warning: Member Simd4NDouble (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:741: warning: Member Simd4NReal (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:512: warning: Member load(const std::enable_if_t< std::is_arithmetic_v< T >, T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:518: warning: Member load(const AlignedArray< internal::SimdTraitsT< T >, N > &m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:536: warning: Member loadU(const std::enable_if_t< std::is_arithmetic_v< T >, T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:542: warning: Member loadU(const AlignedArray< internal::SimdTraitsT< T >, N > &m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:623: warning: Member load(const internal::Simd4TraitsT< T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:628: warning: Member loadU(const internal::Simd4TraitsT< T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:657: warning: Member loadUNDuplicate4(const float *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:661: warning: Member load4DuplicateN(const float *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:665: warning: Member loadU4NOffset(const float *f, int) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:703: warning: Member loadUNDuplicate4(const double *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:707: warning: Member load4DuplicateN(const double *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:711: warning: Member loadU4NOffset(const double *f, int) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:398: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:295: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:305: warning: unable to resolve reference to 'SimdIBool' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:340: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:352: warning: unable to resolve reference to 'SimdBool' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:353: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:353: warning: unable to resolve reference to 'SimdIBool' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:354: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:356: warning: unable to resolve reference to 'cvtB2IB' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:356: warning: unable to resolve reference to 'cvtIB2B' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:593: warning: argument 'wcycle' from the argument list of gmx::computeSpecialForces has multiple @param documentation sections /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/correlationhistory.h:61: warning: unable to resolve reference to 'updateCorrelationGridHistory' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:99: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:100: warning: @copydetails or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:94: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:95: warning: @copydetails or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:125: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:126: warning: @copydetails or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:120: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:121: warning: @copydetails or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/requirements.cpp:63: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/requirements.cpp:59: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/booltype.h:72: warning: Member value_ (variable) of struct gmx::BoolType is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/clfftinitializer.h:96: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(ClfftInitializer) (function) of class gmx::ClfftInitializer is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:765: warning: Member impl() noexcept (function) of struct gmx::CompileTimeStringJoin is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:781: warning: Member stringArray (variable) of struct gmx::CompileTimeStringJoin is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:783: warning: Member value (variable) of struct gmx::CompileTimeStringJoin is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/mdmodulesnotifiers.h:173: warning: Member coordinates_ (variable) of struct gmx::CoordinatesAndBoxPreprocessed is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/mdmodulesnotifiers.h:174: warning: Member box_ (variable) of struct gmx::CoordinatesAndBoxPreprocessed is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/mdmodulesnotifiers.h:175: warning: Member pbc_ (variable) of struct gmx::CoordinatesAndBoxPreprocessed is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_coulomb_functions.h:134: warning: Member CoulombCalculator(const interaction_const_t &ic) (function) of class gmx::CoulombCalculator< KernelCoulombType::EwaldAnalytical > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_coulomb_functions.h:145: warning: Member force(const std::array< SimdReal, nR > &rSquaredV, const std::array< SimdReal, nR > gmx_unused &dummyRInvV, const std::array< SimdReal, nR > &rInvExclV, const std::array< SimdBool, nR > &withinCutoffV) (function) of class gmx::CoulombCalculator< KernelCoulombType::EwaldAnalytical > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_coulomb_functions.h:194: warning: Member CoulombCalculator(const interaction_const_t &ic) (function) of class gmx::CoulombCalculator< KernelCoulombType::EwaldTabulated > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_coulomb_functions.h:83: warning: Member CoulombCalculator(const interaction_const_t &ic) (function) of class gmx::CoulombCalculator< KernelCoulombType::RF > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_diagonal_masker.h:106: warning: Member DiagonalMasker(const nbnxn_atomdata_t::SimdMasks &simdMasks) (function) of class gmx::DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeEqualsISize > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_diagonal_masker.h:132: warning: Member DiagonalMasker(const nbnxn_atomdata_t::SimdMasks &simdMasks) (function) of class gmx::DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeIsDoubleISize > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_diagonal_masker.h:165: warning: Member DiagonalMasker(const nbnxn_atomdata_t::SimdMasks &simdMasks) (function) of class gmx::DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeIsHalfISize > is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/enumerationhelpers.h:333: warning: Member value (variable) of class gmx::EnumClassSuitsEnumerationArray is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/enumerationhelpers.h:250: warning: Member const_iterator (typedef) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/enumerationhelpers.h:251: warning: Member reverse_iterator (typedef) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/enumerationhelpers.h:252: warning: Member const_reverse_iterator (typedef) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/enumerationhelpers.h:274: warning: Member const_pointer (typedef) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/enumerationhelpers.h:229: warning: Member operator[](const std::size_t arrayIndex) const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/enumerationhelpers.h:235: warning: Member operator[](const EnumType enumIndex) (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/enumerationhelpers.h:240: warning: Member operator[](const EnumType enumIndex) const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/enumerationhelpers.h:258: warning: Member end() (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/enumerationhelpers.h:259: warning: Member begin() const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/enumerationhelpers.h:260: warning: Member end() const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/enumerationhelpers.h:266: warning: Member rend() (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/enumerationhelpers.h:267: warning: Member rbegin() const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/enumerationhelpers.h:268: warning: Member rend() const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/enumerationhelpers.h:181: warning: Member end() const (function) of class gmx::EnumerationWrapper is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:441: warning: Member operator()(const std::string &lhs, const std::string &rhs) const (function) of class gmx::EqualCaseInsensitive is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/iforceprovider.h:112: warning: Member homenr_ (variable) of class gmx::ForceProviderInput is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/iforceprovider.h:113: warning: Member chargeA_ (variable) of class gmx::ForceProviderInput is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/iforceprovider.h:114: warning: Member massT_ (variable) of class gmx::ForceProviderInput is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/gpuhaloexchange.h:105: warning: Member GpuHaloExchange(GpuHaloExchange &&source) noexcept (function) of class gmx::GpuHaloExchange is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/gpuhaloexchange.h:106: warning: Member operator=(GpuHaloExchange &&source) noexcept (function) of class gmx::GpuHaloExchange is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/haloexchange.h:93: warning: Member HaloExchange(PbcType pbcType) (function) of class gmx::HaloExchange is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/nnpotmodel.h:76: warning: Member prepareAtomNumbers(std::vector< int > &)=0 (function) of class gmx::INNPotModel is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/nnpotmodel.h:77: warning: Member prepareBox(matrix &)=0 (function) of class gmx::INNPotModel is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/nnpotmodel.h:78: warning: Member preparePbcType(PbcType &)=0 (function) of class gmx::INNPotModel is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:86: warning: Member doUChar(unsigned char *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:87: warning: Member doChar(char *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:88: warning: Member doUShort(unsigned short *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:89: warning: Member doInt(int *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:90: warning: Member doInt32(int32_t *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:91: warning: Member doInt64(int64_t *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:92: warning: Member doFloat(float *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:93: warning: Member doDouble(double *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:94: warning: Member doReal(real *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:95: warning: Member doIvec(ivec *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:96: warning: Member doRvec(rvec *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:97: warning: Member doString(std::string *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:98: warning: Member doOpaque(char *data, std::size_t size)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:112: warning: Member doCharArray(char *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:119: warning: Member doUCharArray(unsigned char *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:126: warning: Member doUShortArray(unsigned short *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:133: warning: Member doIntArray(int *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:140: warning: Member doInt32Array(int32_t *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:147: warning: Member doInt64Array(int64_t *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:154: warning: Member doFloatArray(float *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:161: warning: Member doDoubleArray(double *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:168: warning: Member doRealArray(real *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:175: warning: Member doIvecArray(ivec *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:182: warning: Member doRvecArray(rvec *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/checkpointdata.h:146: warning: Member value (variable) of struct gmx::IsSerializableEnum is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/legacymdrunoptions.h:155: warning: Member ddrank_opt_choices[static_cast< int >(DdRankOrder::Count)+1] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/legacymdrunoptions.h:160: warning: Member dddlb_opt_choices[static_cast< int >(DlbOption::Count)+1] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/legacymdrunoptions.h:165: warning: Member thread_aff_opt_choices[static_cast< int >(ThreadAffinity::Count)+1] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/legacymdrunoptions.h:170: warning: Member nbpu_opt_choices[5] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/legacymdrunoptions.h:171: warning: Member pme_opt_choices[5] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/legacymdrunoptions.h:172: warning: Member pme_fft_opt_choices[5] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/legacymdrunoptions.h:173: warning: Member bonded_opt_choices[5] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/legacymdrunoptions.h:174: warning: Member update_opt_choices[5] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/legacymdrunoptions.h:175: warning: Member devicesSelectedByUser (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/legacymdrunoptions.h:176: warning: Member userGpuTaskAssignment (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/legacymdrunoptions.h:179: warning: Member imdOptions (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/legacymdrunoptions.h:181: warning: Member pa[48] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_lennardjones_functions.h:328: warning: Member LennardJonesCalculator(const interaction_const_t &ic) (function) of class gmx::LennardJonesCalculator< calculateEnergies, InteractionModifiers::ForceSwitch > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_lennardjones_functions.h:488: warning: Member LennardJonesCalculator(const interaction_const_t &ic) (function) of class gmx::LennardJonesCalculator< calculateEnergies, InteractionModifiers::PotSwitch > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_lennardjones_functions.h:175: warning: Member LennardJonesCalculator(const interaction_const_t gmx_unused &ic) (function) of class gmx::LennardJonesCalculator< false, InteractionModifiers::PotShift > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_lennardjones_functions.h:205: warning: Member forceSigmaEpsilon(const std::array< SimdReal, inputSize > &rInvV, const std::array< SimdBool, interactSize > &interactV, SimdBool *withinCutoffV, const std::array< SimdReal, nR > &sigmaV, const std::array< SimdReal, nR > &epsilonV, SimdReal sixth, SimdReal twelfth, std::array< SimdReal, nR > &frLJV, std::array< SimdReal, vljvSize > &vLJV) (function) of class gmx::LennardJonesCalculator< false, InteractionModifiers::PotShift > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_lennardjones_functions.h:227: warning: Member LennardJonesCalculator(const interaction_const_t &ic) (function) of class gmx::LennardJonesCalculator< true, InteractionModifiers::PotShift > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_lennardjones_functions.h:266: warning: Member forceSigmaEpsilon(const std::array< SimdReal, inputSize > &rInvV, const std::array< SimdBool, interactSize > &interactV, SimdBool *withinCutoffV, const std::array< SimdReal, nR > &sigmaV, const std::array< SimdReal, nR > &epsilonV, SimdReal sixth, SimdReal twelfth, std::array< SimdReal, nR > &frLJV, std::array< SimdReal, vljvSize > &vLJV) (function) of class gmx::LennardJonesCalculator< true, InteractionModifiers::PotShift > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/mdmodulesnotifiers.h:91: warning: Member MDModulesAtomsRedistributedSignal(const matrix box, gmx::ArrayRef< const RVec > x) (function) of struct gmx::MDModulesAtomsRedistributedSignal is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/runner.h:148: warning: Member operator=(Mdrunner &&handle) noexcept (function) of class gmx::Mdrunner is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/runner.h:394: warning: Member operator=(MdrunnerBuilder &&builder) noexcept (function) of class gmx::MdrunnerBuilder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/message_string_collector.h:67: warning: Member MessageStringCollector(MessageStringCollector &&) noexcept (function) of class gmx::MessageStringCollector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/message_string_collector.h:68: warning: Member operator=(MessageStringCollector &&) noexcept (function) of class gmx::MessageStringCollector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlistwork.h:62: warning: Member NbnxmPairlistCpuWork(const int iClusterSize) (function) of struct gmx::NbnxmPairlistCpuWork is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlistwork.h:67: warning: Member IClusterData(const int iClusterSize) (function) of struct gmx::NbnxmPairlistCpuWork::IClusterData is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.h:286: warning: Member NbnxnPairlistCpu(int iClusterSize) (function) of struct gmx::NbnxnPairlistCpu is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm.h:406: warning: Member setupFepThreadedForceBuffer(int numAtomsForce) (function) of struct gmx::nonbonded_verlet_t is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm.h:417: warning: Member localGrid() const (function) of struct gmx::nonbonded_verlet_t is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm.h:419: warning: Member setNonLocalGrid(int gridIndex, int ddZone, const GridDimensions &gridDimensions, ArrayRef< const std::pair< int, int > > columns, ArrayRef< const int32_t > atomInfo, ArrayRef< const RVec > x) (function) of struct gmx::nonbonded_verlet_t is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.h:237: warning: Member PackedJClusterList(const PinningPolicy pinningPolicy) (function) of class gmx::PackedJClusterList is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:218: warning: Member allocator_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:219: warning: Member size_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:220: warning: Member reference (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:221: warning: Member const_reference (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:222: warning: Member storage_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:223: warning: Member pointer (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:224: warning: Member const_pointer (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:225: warning: Member iterator (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:226: warning: Member const_iterator (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:227: warning: Member difference_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:351: warning: Member data() const noexcept (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:353: warning: Member begin() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:354: warning: Member end() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:356: warning: Member cbegin() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:357: warning: Member cend() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:359: warning: Member begin() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:360: warning: Member end() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:362: warning: Member cbegin() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:363: warning: Member cend() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairsearch.h:216: warning: Member setNonLocalGrid(int gridIndex, int zone, const GridDimensions &gridDimensions, ArrayRef< const std::pair< int, int > > columns, ArrayRef< const int32_t > atomInfo, ArrayRef< const RVec > x, nbnxn_atomdata_t *nbat) (function) of class gmx::PairSearch is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_force_sender_gpu.h:112: warning: Member waitForEvents() (function) of class gmx::PmeForceSenderGpu is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/range.h:75: warning: Member iterator_category (typedef) of struct gmx::Range::iterator is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/range.h:76: warning: Member difference_type (typedef) of struct gmx::Range::iterator is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/range.h:77: warning: Member value_type (typedef) of struct gmx::Range::iterator is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/range.h:78: warning: Member pointer (typedef) of struct gmx::Range::iterator is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/range.h:79: warning: Member reference (typedef) of struct gmx::Range::iterator is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/restraint/manager.h:90: warning: Member operator=(const RestraintManager &)=default (function) of class gmx::RestraintManager is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/restraint/manager.h:91: warning: Member RestraintManager(RestraintManager &&) noexcept=default (function) of class gmx::RestraintManager is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/restraint/manager.h:92: warning: Member operator=(RestraintManager &&) noexcept=default (function) of class gmx::RestraintManager is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/selection/selectioncollection.h:145: warning: Member SelectionCollection(const SelectionCollection &rhs) (function) of class gmx::SelectionCollection is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/selection/selectioncollection.h:146: warning: Member operator=(SelectionCollection rhs) (function) of class gmx::SelectionCollection is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/selection/selectioncollection.h:147: warning: Member swap(SelectionCollection &rhs) noexcept (function) of class gmx::SelectionCollection is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.h:356: warning: Member add(MembedHolder &&membedHolder) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.h:358: warning: Member add(std::unique_ptr< StopHandlerBuilder > stopHandlerBuilder) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.h:360: warning: Member add(SimulatorStateData &&simulatorStateData) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.h:365: warning: Member add(SimulatorConfig &&simulatorConfig) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.h:372: warning: Member add(SimulatorEnv &&simulatorEnv) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.h:377: warning: Member add(Profiling &&profiling) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.h:379: warning: Member add(ConstraintsParam &&constraintsParam) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.h:384: warning: Member add(LegacyInput &&legacyInput) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.h:389: warning: Member add(ReplicaExchangeParameters &&replicaExchangeParameters) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.h:391: warning: Member add(InteractiveMD &&interactiveMd) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.h:396: warning: Member add(SimulatorModules &&simulatorModules) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.h:401: warning: Member add(CenterOfMassPulling &¢erOfMassPulling) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.h:406: warning: Member add(IonSwapping &&ionSwapping) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.h:411: warning: Member add(TopologyData &&topologyData) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.h:416: warning: Member add(BoxDeformationHandle &&boxDeformation) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/torchmodel.h:91: warning: Member prepareAtomNumbers(std::vector< int > &atomTypes) override (function) of class gmx::TorchModel is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/torchmodel.h:92: warning: Member prepareBox(matrix &box) override (function) of class gmx::TorchModel is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/torchmodel.h:93: warning: Member preparePbcType(PbcType &pbcType) override (function) of class gmx::TorchModel is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/updategroups.h:113: warning: Member useUpdateGroups() const (function) of class gmx::UpdateGroups is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/updategroups.h:114: warning: Member maxUpdateGroupRadius() const (function) of class gmx::UpdateGroups is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/updategroups.h:115: warning: Member updateGroupingPerMoleculeType() const (function) of class gmx::UpdateGroups is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/checkpointdata.h:421: warning: Member empty() const (function) of class gmx::WriteCheckpointDataHolder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/mp11.h:76: warning: Member mp_with_index(std::size_t i, F &&f) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/pointers.h:194: warning: Member operator!=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() !=rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/pointers.h:200: warning: Member operator<(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get()< rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/pointers.h:206: warning: Member operator<=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get()<=rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/pointers.h:212: warning: Member operator>(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() > rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/pointers.h:218: warning: Member operator>=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() >=rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/pointers.h:134: warning: Member not_null(const not_null &other)=default (function) of class gmx::compat::not_null is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/pointers.h:135: warning: Member operator=(const not_null &other)=default (function) of class gmx::compat::not_null is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/pointers.h:146: warning: Member operator T() const (function) of class gmx::compat::not_null is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/pointers.h:147: warning: Member operator->() const (function) of class gmx::compat::not_null is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/tests/fft_mpi.cpp:72: warning: Member GpuFftTestParams (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/tests/fft_mpi.cpp:77: warning: Member GpuFftTestGridParams (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/gyrate.cpp:71: warning: Member GyrateTestParamsMerge (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/hbond.cpp:71: warning: Member HbondTestParamsMerge (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/simulatorcomparison.h:62: warning: Member SimulationOptionTuple (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/moduletest.h:70: warning: Member SimulationRunnerMdpSource (enumeration) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/awh_setup.cpp:71: warning: Member awhDimParamSerialized(AwhCoordinateProviderType inputCoordinateProvider, int inputCoordIndex, double inputOrigin, double inputEnd, double inputPeriod, double inputDiffusion) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/awh_setup.cpp:113: warning: Member awhBiasParamSerialized(AwhHistogramGrowthType eawhgrowth, double beta, double inputErrorScaling, ArrayRef< const std::vector< char > > dimensionParameterBuffers, int shareGroup, bool inputUserData, AwhTargetType eTargetType, bool scaleTargetByMetric) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/awh_setup.cpp:170: warning: Member awhParamSerialized(AwhHistogramGrowthType eawhgrowth, AwhPotentialType eawhpotential, double beta, double inputErrorScaling, int64_t inputSeed, ArrayRef< const std::vector< char > > dimensionParameterBuffers, int biasShareGroup, bool inputUserData, AwhTargetType eTargetType, bool scaleTargetByMetric) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/plumed/tests/plumedTestUtils.cpp:62: warning: Member plumedKernelAvailable() (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/tests/fft_mpi.cpp:79: warning: Member getGpuAwareMpiStatusForFftBackend(const FftBackend fftBackend) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/tests/device_availability.cpp:73: warning: Member getRequiredNumberOfDevices() (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/tests/typecasts_runner_hip.cpp:64: warning: Member saveFloat3InRVecFormat(ArrayRef< gmx::RVec > rVecOutput, const float3 *float3Output, int numElements) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:85: warning: Member EXPECT_EQ(0, reinterpret_cast< std::size_t >(p) &this->mask(a)) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:86: warning: Member deallocate(p, 1000) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:93: warning: Member v(10) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:94: warning: Member EXPECT_EQ(0, reinterpret_cast< std::size_t >(v.data()) &this->mask(v.get_allocator())) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:99: warning: Member for(std::size_t i=1000;i<=10000;i+=1000) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:125: warning: Member v1(1) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:127: warning: Member EXPECT_NE(data, nullptr) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:128: warning: Member v2(std::move(v1)) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:129: warning: Member EXPECT_EQ(data, v2.data()) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/moduletest.cpp:402: warning: Member getNumberOfTestOpenMPThreads() (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/simulatorcomparison.cpp:72: warning: Member runGrompp(SimulationRunner *runner, const std::vector< SimulationOptionTuple > &options) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/simulatorcomparison.cpp:85: warning: Member runMdrun(SimulationRunner *runner, const std::vector< SimulationOptionTuple > &options) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/simulatorcomparison.cpp:98: warning: Member compareEnergies(const std::string &edr1Name, const std::string &edr2Name, const EnergyTermsToCompare &energyTermsToCompare, const MaxNumFrames maxNumFrames) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/simulatorcomparison.cpp:119: warning: Member compareTrajectories(const std::string &trajectory1Name, const std::string &trajectory2Name, const TrajectoryComparison &trajectoryComparison) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/tests/pmegathertest.cpp:445: warning: Member registerDynamicalPmeGatherTests(const Range< int > hardwareContextIndexRange) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/tests/pmesolvetest.cpp:435: warning: Member registerDynamicalPmeSolveTests(const Range< int > hardwareContextIndexRange) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/trajectorycomparison.cpp:417: warning: Member checkTrajectoryAgainstReferenceData(const std::string &trajectoryFilename, const TrajectoryComparison &trajectoryComparison, TestReferenceChecker *checker) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/trajectorycomparison.cpp:425: warning: Member checkTrajectoryAgainstReferenceData(const std::string &trajectoryFilename, const TrajectoryComparison &trajectoryComparison, TestReferenceChecker *checker, MaxNumFrames maxNumFrames) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/friction_metric.cpp:82: warning: Member g_sampleWeightCentral (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/friction_metric.cpp:83: warning: Member g_sampleWeightNeighbor (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/friction_metric.cpp:84: warning: Member g_sampleTimeStep (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/friction_metric.cpp:85: warning: Member g_numPointsPerDim (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/tests/fft_mpi.cpp:266: warning: Member inputGrids (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/tests/fft_mpi.cpp:270: warning: Member inputBackends (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:82: warning: Member a (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:83: warning: Member p (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:126: warning: Member data (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/naming.h:414: warning: Member Formatters (typedef) of class gmx::test::NameOfTestFromTuple is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/naming.h:530: warning: Member operator()(const T &t) (function) of struct gmx::test::PrefixFormatter is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/naming.h:529: warning: Member prefix (variable) of struct gmx::test::PrefixFormatter is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/naming.h:464: warning: Member Formatters (typedef) of class gmx::test::RefDataFilenameMaker is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/naming.h:195: warning: Member Variant (typedef) of struct gmx::test::detail::FormatterVariant is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/naming.h:211: warning: Member Variant (typedef) of struct gmx::test::detail::FormatterVariant< Enum, typename std::enable_if_t< std::is_enum_v< Enum > > > is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/naming.h:228: warning: Member type (typedef) of struct gmx::test::detail::ParamsToFormatterVariants< std::tuple< Ts... > > is not documented. cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen && /usr/bin/cmake -E touch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen/doxygen-lib-timestamp.txt make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [100%] Built target doxygen-lib /build/reproducible-path/gromacs-2025.0/build/documentation/python_packaging/gmxapi/gmxapi_staging/gmxapi/commandline.py:docstring of gmxapi.commandline.commandline_operation:60: WARNING: 'any' reference target not found: os.getenv [ref.any] /build/reproducible-path/gromacs-2025.0/build/documentation/python_packaging/gmxapi/gmxapi_staging/gmxapi/_logging.py:docstring of gmxapi._logging:6: WARNING: 'any' reference target not found: sys.stderr [ref.any] /build/reproducible-path/gromacs-2025.0/build/documentation/python_packaging/gmxapi/gmxapi_staging/gmxapi/_logging.py:docstring of gmxapi._logging:6: WARNING: 'any' reference target not found: logging [ref.any] /build/reproducible-path/gromacs-2025.0/build/documentation/python_packaging/gmxapi/gmxapi_staging/gmxapi/_logging.py:docstring of gmxapi._logging:6: WARNING: 'any' reference target not found: logging.basicConfig [ref.any] /build/reproducible-path/gromacs-2025.0/build/documentation/python_packaging/gmxapi/gmxapi_staging/gmxapi/_logging.py:docstring of gmxapi._logging:13: WARNING: 'any' reference target not found: logging.StreamHandler [ref.any] /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/gmxapi/userguide/usage.rst:131: WARNING: 'any' reference target not found: os.environ [ref.any] /build/reproducible-path/gromacs-2025.0/build/documentation/docs/sphinx-input/release-notes/2022/2022.1.rst:181: WARNING: 'any' reference target not found: subprocess.run [ref.any] make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [100%] Built target webpage-sphinx The following warnings were produced by Doxygen: /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/biasgrid.h:279: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/biasgrid.h:279: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/energyhistory.cpp:48: warning: Conditional section with label 'INTERNAL' does not have a corresponding \endcond command within this file. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_utils.h:63: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_utils.h:63: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/arrayref.h:311: warning: @copybrief or @copydoc target 'arrayRefFromArray' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/options/abstractoptionstorage.h:144: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:94: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:99: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/electricfield.cpp:186: warning: @copybrief or @copydoc target 'IForceProvider::calculateForces()' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:120: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:125: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:82: warning: unable to resolve reference to 'ElecType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:106: warning: unable to resolve reference to 'VdwType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/requirements.cpp:59: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/leapfrog_gpu_internal_sycl.cpp:170: warning: unable to resolve reference to 'NumTempScaleValues' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/requirements.cpp:63: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:398: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd_memory.h:154: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(pointer, pointer)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd_memory.h:163: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:295: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_insolidangle.cpp:99: warning: unable to resolve reference to 'sm_insolidangle' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:340: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/optionflags.h:107: warning: explicit link request to 'OptionFlag' could not be resolved /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/selection/selectionenums.h:82: warning: explicit link request to 'SelectionFlag' could not be resolved warning: Included by graph for 'functions.h' not generated, too many nodes (80), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'md_enums.h' not generated, too many nodes (106), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'basicoptions.h' not generated, too many nodes (52), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/optionflags.h:107: warning: explicit link request to 'OptionFlag' could not be resolved /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/selectioncollection.cpp:978: warning: Member swap(SelectionCollection &lhs, SelectionCollection &rhs) noexcept (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/selection/selectionenums.h:82: warning: explicit link request to 'SelectionFlag' could not be resolved warning: Included by graph for 'idef.h' not generated, too many nodes (59), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:226: warning: Member t_functype (typedef) of file idef.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:473: warning: Member printInteractionParameters(gmx::TextWriter *writer, t_functype ftype, const t_iparams &iparams) (function) of file idef.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:474: warning: Member pr_iparams(FILE *fp, t_functype ftype, const t_iparams &iparams) (function) of file idef.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:475: warning: Member pr_ilist(FILE *fp, int indent, const char *title, const t_functype *functype, const InteractionList &ilist, bool bShowNumbers, bool bShowParameters, const t_iparams *iparams) (function) of file idef.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:483: warning: Member pr_idef(FILE *fp, int indent, const char *title, const t_idef *idef, bool bShowNumbers, bool bShowParameters) (function) of file idef.h is not documented. warning: Included by graph for 'ifunc.h' not generated, too many nodes (91), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:54: warning: Member t_iatom (typedef) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:59: warning: Member rvec4[4] (typedef) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:220: warning: Member IS_RESTRAINT_TYPE(int ifunc) (function) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:239: warning: Member NRFPA(int ftype) (function) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:244: warning: Member NRFPB(int ftype) (function) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:249: warning: Member NRFP(int ftype) (function) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:254: warning: Member NRAL(int ftype) (function) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:275: warning: Member IS_VSITE(int ftype) (function) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:280: warning: Member IS_TABULATED(int ftype) (function) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:67: warning: Member IF_VSITE (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:68: warning: Member IF_CONSTRAINT (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:69: warning: Member IF_CHEMBOND (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:76: warning: Member IF_DIHEDRAL (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:77: warning: Member IF_PAIR (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:78: warning: Member IF_TABULATED (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:233: warning: Member NR_CBTDIHS (variable) of file ifunc.h is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:234: warning: Member NR_FOURDIHS (variable) of file ifunc.h is not documented. warning: Included by graph for 'arrayref.h' not generated, too many nodes (371), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'basedefinitions.h' not generated, too many nodes (252), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'classhelpers.h' not generated, too many nodes (62), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'enumerationhelpers.h' not generated, too many nodes (106), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'exceptions.h' not generated, too many nodes (270), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'gmxassert.h' not generated, too many nodes (321), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'real.h' not generated, too many nodes (324), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'smalloc.h' not generated, too many nodes (106), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'stringutil.h' not generated, too many nodes (230), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:787: warning: Member CompileTimeStringJoin_v (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/colvarproxy_gromacs_version.h:42: warning: Member COLVARPROXY_VERSION (macro definition) of file colvarproxy_gromacs_version.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/tests/colvarsoptions.cpp:87: warning: Member colvarsConfig (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/plumed/plumedforceprovider.cpp:55: warning: Member __PLUMED_WRAPPER_FORTRAN (macro definition) of file plumedforceprovider.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/plumed/plumedforceprovider.cpp:57: warning: Member __PLUMED_WRAPPER_LINK_RUNTIME (macro definition) of file plumedforceprovider.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/plumed/plumedforceprovider.cpp:58: warning: Member __PLUMED_WRAPPER_EXTERN (macro definition) of file plumedforceprovider.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/plumed/plumedforceprovider.cpp:60: warning: Member __PLUMED_WRAPPER_CXX (macro definition) of file plumedforceprovider.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/plumed/plumedforceprovider.cpp:61: warning: Member __PLUMED_WRAPPER_LIBCXX11 (macro definition) of file plumedforceprovider.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/plumed/plumedforceprovider.cpp:62: warning: Member __PLUMED_WRAPPER_LIBCXX17 (macro definition) of file plumedforceprovider.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/plumed/plumedforceprovider.cpp:63: warning: Member __PLUMED_WRAPPER_IMPLEMENTATION (macro definition) of file plumedforceprovider.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/plumed/plumedforceprovider.cpp:64: warning: Member __PLUMED_HAS_DLOPEN (macro definition) of file plumedforceprovider.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/plumed/tests/plumedOptions.cpp:191: warning: Member getTopologyFromSimulationDatabase(gmx_mtop_t *const mtop, const std::string &fileName) (function) of namespace gmx::anonymous_namespace{plumedOptions.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/plumed/tests/plumedTestUtils.cpp:45: warning: Member __PLUMED_WRAPPER_FORTRAN (macro definition) of file plumedTestUtils.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/plumed/tests/plumedTestUtils.cpp:47: warning: Member __PLUMED_WRAPPER_LINK_RUNTIME (macro definition) of file plumedTestUtils.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/plumed/tests/plumedTestUtils.cpp:48: warning: Member __PLUMED_WRAPPER_EXTERN (macro definition) of file plumedTestUtils.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/plumed/tests/plumedTestUtils.cpp:50: warning: Member __PLUMED_WRAPPER_CXX (macro definition) of file plumedTestUtils.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/plumed/tests/plumedTestUtils.cpp:51: warning: Member __PLUMED_WRAPPER_LIBCXX11 (macro definition) of file plumedTestUtils.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/plumed/tests/plumedTestUtils.cpp:52: warning: Member __PLUMED_WRAPPER_LIBCXX17 (macro definition) of file plumedTestUtils.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/plumed/tests/plumedTestUtils.cpp:53: warning: Member __PLUMED_WRAPPER_IMPLEMENTATION (macro definition) of file plumedTestUtils.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/plumed/tests/plumedTestUtils.cpp:54: warning: Member __PLUMED_HAS_DLOPEN (macro definition) of file plumedTestUtils.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/pointers.h:87: warning: Member Ensures(cond) (macro definition) of file pointers.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/pointers.h:194: warning: Member operator!=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() !=rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/pointers.h:200: warning: Member operator<(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get()< rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/pointers.h:206: warning: Member operator<=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get()<=rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/pointers.h:212: warning: Member operator>(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() > rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/pointers.h:218: warning: Member operator>=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() >=rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/iframeconverter.h:116: warning: invalid argument for command '\iline' /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/requirements.cpp:59: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/requirements.cpp:63: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/computemultibodycutoffs.cpp:278: warning: Member dd_bonded_cg_distance(const gmx::MDLogger &mdlog, const gmx_mtop_t &mtop, const t_inputrec &inputrec, ArrayRef< const RVec > x, const matrix box, const DDBondedChecking ddBondedChecking, real *r_2b, real *r_mb) (function) of file computemultibodycutoffs.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec_network.cpp:144: warning: Member dd_sendrecv2_rvec(const struct gmx_domdec_t gmx_unused *dd, int gmx_unused ddimind, rvec gmx_unused *buf_s_fw, int gmx_unused n_s_fw, rvec gmx_unused *buf_r_fw, int gmx_unused n_r_fw, rvec gmx_unused *buf_s_bw, int gmx_unused n_s_bw, rvec gmx_unused *buf_r_bw, int gmx_unused n_r_bw) (function) of file domdec_network.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec_network.cpp:230: warning: Member dd_bcast(const gmx_domdec_t gmx_unused *dd, int gmx_unused nbytes, void gmx_unused *data) (function) of file domdec_network.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec_network.cpp:240: warning: Member dd_scatter(const gmx_domdec_t gmx_unused *dd, int gmx_unused nbytes, const void gmx_unused *src, void *dest) (function) of file domdec_network.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec_network.cpp:259: warning: Member dd_gather(const gmx_domdec_t gmx_unused *dd, int gmx_unused nbytes, const void gmx_unused *src, void gmx_unused *dest) (function) of file domdec_network.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec_network.cpp:278: warning: Member dd_scatterv(const gmx_domdec_t gmx_unused *dd, gmx::ArrayRef< const int > gmx_unused scounts, gmx::ArrayRef< const int > gmx_unused disps, const T *sbuf, int rcount, T *rbuf) (function) of file domdec_network.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec_network.cpp:321: warning: Member dd_scatterv(const gmx_domdec_t *dd, gmx::ArrayRef< const int > scounts, gmx::ArrayRef< const int > disps, const int *sbuf, int rcount, int *rbuf) (function) of file domdec_network.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec_network.cpp:328: warning: Member dd_scatterv(const gmx_domdec_t *dd, gmx::ArrayRef< const int > scounts, gmx::ArrayRef< const int > disps, const gmx::RVec *sbuf, int rcount, gmx::RVec *rbuf) (function) of file domdec_network.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec_network.cpp:336: warning: Member dd_gatherv(const gmx_domdec_t gmx_unused &dd, gmx::ArrayRef< const T > sendBuffer, gmx::ArrayRef< const int > rcounts, gmx::ArrayRef< const int > gmx_unused disps, gmx::ArrayRef< T > receiveBuffer) (function) of file domdec_network.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec_network.cpp:383: warning: Member dd_gatherv(const gmx_domdec_t &dd, gmx::ArrayRef< const int > sendBuffer, gmx::ArrayRef< const int > rcounts, gmx::ArrayRef< const int > disps, gmx::ArrayRef< int > receiveBuffer) (function) of file domdec_network.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec_network.cpp:389: warning: Member dd_gatherv(const gmx_domdec_t &dd, gmx::ArrayRef< const gmx::RVec > sendBuffer, gmx::ArrayRef< const int > rcounts, gmx::ArrayRef< const int > disps, gmx::ArrayRef< gmx::RVec > receiveBuffer) (function) of file domdec_network.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/gpuhaloexchange_impl_gpu.cpp:70: warning: Member supportedLibMpiBuild (variable) of file gpuhaloexchange_impl_gpu.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/gpuhaloexchange_impl_gpu.cpp:73: warning: Member supportedThreadMpiBuild (variable) of file gpuhaloexchange_impl_gpu.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/gpuhaloexchange_impl_gpu_sycl.cpp:63: warning: Member packSendBufKernel(Float3 *__restrict__ gm_dataPacked, const Float3 *__restrict__ gm_data, const int *__restrict__ gm_map, int mapSize, Float3 coordinateShift) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/gpuhaloexchange_impl_gpu_sycl.cpp:119: warning: Member launchPackSendBufKernel(const DeviceStream &deviceStream, int xSendSize, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/gpuhaloexchange_impl_gpu_sycl.cpp:134: warning: Member launchUnpackRecvBufKernel(const DeviceStream &deviceStream, int fRecvSize, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/haloexchangesetup.cpp:157: warning: Member isMissingALink(const ArrayRef< const int > &links, const gmx_ga2la_t &ga2la) (function) of namespace gmx::anonymous_namespace{haloexchangesetup.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/localtopology.cpp:959: warning: Member dd_make_local_top(const gmx_domdec_t &dd, const gmx::DomdecZones &zones, int npbcdim, matrix box, rvec cellsize_min, const ivec npulse, t_forcerec *fr, ArrayRef< const RVec > coordinates, const gmx_mtop_t &mtop, gmx::ArrayRef< const int32_t > atomInfo, gmx_localtop_t *ltop) (function) of file localtopology.cpp is not documented. warning: Include graph for 'partition.cpp' not generated, too many nodes (61), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/reversetopology.cpp:412: warning: Member dd_make_reverse_top(FILE *fplog, gmx_domdec_t *dd, const gmx_mtop_t &mtop, const gmx::VirtualSitesHandler *vsite, const t_inputrec &inputrec, const DDBondedChecking ddBondedChecking) (function) of file reversetopology.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/ewald.cpp:73: warning: Member cvec (typedef) of file ewald.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme.cpp:578: warning: Member initGrids(gmx::ArrayRef< PmeAndFftGrids > gridsSet, const gmx_pme_t &pme, const bool requestReproducibility, gmx::ArrayRef< std::vector< AlignedVector< real > > > gridsStorage) (function) of file pme.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme.cpp:1799: warning: Member parallel_3dfft_destroy(gmx_parallel_3dfft *pfft_setup) (function) of file pme.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_force_sender_gpu_impl.h:58: warning: Member hardware_destructive_interference_size (variable) of file pme_force_sender_gpu_impl.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gather_sycl.cpp:702: warning: Member INSTANTIATE_2(order, numGrids, threadsPerAtom, subGroupSize) (macro definition) of file pme_gather_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gather_sycl.cpp:706: warning: Member INSTANTIATE(order, subGroupSize) (macro definition) of file pme_gather_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu.cpp:280: warning: Member pme_gpu_launch_gather(gmx_pme_t *pme, gmx_wallcycle gmx_unused *wcycle, const real lambdaQ, const bool computeVirial) (function) of file pme_gpu.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_calculate_splines_sycl.h:90: warning: Member mode (typedef) of file pme_gpu_calculate_splines_sycl.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_calculate_splines_sycl.h:74: warning: Member assertIsFinite(Float3 gmx_unused arg) (function) of namespace anonymous_namespace{pme_gpu_calculate_splines_sycl.h} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_calculate_splines_sycl.h:82: warning: Member assertIsFinite(T gmx_unused arg) (function) of namespace anonymous_namespace{pme_gpu_calculate_splines_sycl.h} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_grid.h:102: warning: Member convertPmeGridToFftGrid< true >(const PmeGpu *, float *, gmx_parallel_3dfft *, int) (function) of file pme_gpu_grid.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_grid.h:107: warning: Member convertPmeGridToFftGrid< false >(const PmeGpu *, float *, gmx_parallel_3dfft *, int) (function) of file pme_gpu_grid.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_grid.h:112: warning: Member convertPmeGridToFftGrid< true >(const PmeGpu *, DeviceBuffer< float > *, int) (function) of file pme_gpu_grid.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_grid.h:116: warning: Member convertPmeGridToFftGrid< false >(const PmeGpu *, DeviceBuffer< float > *, int) (function) of file pme_gpu_grid.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_grid_sycl.cpp:61: warning: Member mode (typedef) of file pme_gpu_grid_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_grid_sycl.cpp:1404: warning: Member convertPmeGridToFftGrid< true >(const PmeGpu *pmeGpu, float *h_fftRealGrid, gmx_parallel_3dfft *fftSetup, const int gridIndex) (function) of file pme_gpu_grid_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_grid_sycl.cpp:1409: warning: Member convertPmeGridToFftGrid< false >(const PmeGpu *pmeGpu, float *h_fftRealGrid, gmx_parallel_3dfft *fftSetup, const int gridIndex) (function) of file pme_gpu_grid_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_grid_sycl.cpp:1414: warning: Member convertPmeGridToFftGrid< true >(const PmeGpu *pmeGpu, DeviceBuffer< float > *d_fftRealGrid, const int gridIndex) (function) of file pme_gpu_grid_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_grid_sycl.cpp:1418: warning: Member convertPmeGridToFftGrid< false >(const PmeGpu *pmeGpu, DeviceBuffer< float > *d_fftRealGrid, const int gridIndex) (function) of file pme_gpu_grid_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_hip_stubs.cpp:107: warning: Member pme_gpu_set_kernelparam_useNvshmem(const PmeGpu *, bool) (function) of file pme_gpu_hip_stubs.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_internal.cpp:1127: warning: Member pme_gpu_update_input_box(PmeGpu gmx_unused *pmeGpu, const matrix gmx_unused box) (function) of file pme_gpu_internal.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_internal.cpp:2550: warning: Member pme_gpu_set_kernelparam_useNvshmem(const PmeGpu *pmeGpu, bool useNvshmem) (function) of file pme_gpu_internal.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_internal.h:70: warning: Member gmx_parallel_3dfft_t (typedef) of file pme_gpu_internal.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_internal.h:447: warning: Member pme_gpu_set_kernelparam_useNvshmem(const PmeGpu *pmeGpu, bool useNvshmem) (function) of file pme_gpu_internal.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_ocl_stubs.cpp:80: warning: Member convertPmeGridToFftGrid< true >(const PmeGpu *, float *, gmx_parallel_3dfft *, const int) (function) of file pme_gpu_ocl_stubs.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_ocl_stubs.cpp:85: warning: Member convertPmeGridToFftGrid< false >(const PmeGpu *, float *, gmx_parallel_3dfft *, const int) (function) of file pme_gpu_ocl_stubs.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_ocl_stubs.cpp:90: warning: Member convertPmeGridToFftGrid< true >(const PmeGpu *, DeviceBuffer< float > *, const int) (function) of file pme_gpu_ocl_stubs.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_ocl_stubs.cpp:94: warning: Member convertPmeGridToFftGrid< false >(const PmeGpu *, DeviceBuffer< float > *, const int) (function) of file pme_gpu_ocl_stubs.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:91: warning: Member INSTANTIATE_SPREAD_2( order, computeSplines, spreadCharges, numGrids, writeGlobal, threadsPerAtom, subGroupSize) (macro definition) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:94: warning: Member INSTANTIATE_SPREAD(order, numGrids, threadsPerAtom, subGroupSize) (macro definition) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:100: warning: Member INSTANTIATE_GATHER_2(order, numGrids, readGlobal, threadsPerAtom, subGroupSize) (macro definition) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:103: warning: Member INSTANTIATE_GATHER(order, numGrids, threadsPerAtom, subGroupSize) (macro definition) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:107: warning: Member INSTANTIATE_X(x, order, subGroupSize) (macro definition) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:113: warning: Member INSTANTIATE_SOLVE(subGroupSize) (macro definition) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:123: warning: Member INSTANTIATE(order, subGroupSize) (macro definition) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:67: warning: Member chooseSubGroupSizeForDevice(const DeviceInformation &deviceInfo) (function) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:59: warning: Member c_pmeOrder (variable) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:61: warning: Member c_wrapX (variable) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:62: warning: Member c_wrapY (variable) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:64: warning: Member c_stateA (variable) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:65: warning: Member c_stateB (variable) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_types_host.h:72: warning: Member PmeGpuHaloExchange (typedef) of file pme_gpu_types_host.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_pp.cpp:484: warning: Member gmx_pme_send_resetcounters(const t_commrec gmx_unused *cr, int64_t gmx_unused step) (function) of file pme_pp.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_pp_communication.h:76: warning: Member PP_PME_CHARGEB (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_pp_communication.h:77: warning: Member PP_PME_SQRTC6 (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_pp_communication.h:78: warning: Member PP_PME_SQRTC6B (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_pp_communication.h:79: warning: Member PP_PME_SIGMA (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_pp_communication.h:80: warning: Member PP_PME_SIGMAB (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_pp_communication.h:81: warning: Member PP_PME_COORD (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_pp_communication.h:82: warning: Member PP_PME_ENER_VIR (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_pp_communication.h:83: warning: Member PP_PME_FINISH (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_pp_communication.h:84: warning: Member PP_PME_SWITCHGRID (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_pp_communication.h:85: warning: Member PP_PME_RESETCOUNTERS (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_pp_communication.h:86: warning: Member PP_PME_GPUCOMMS (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_pp_communication.h:88: warning: Member PP_PME_RECVFTOGPU (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_pp_communication.h:90: warning: Member PP_PME_MDGPUGRAPH (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_solve_sycl.cpp:54: warning: Member mode (typedef) of file pme_solve_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_spread_sycl.cpp:438: warning: Member INSTANTIATE_2(order, numGrids, threadsPerAtom, subGroupSize) (macro definition) of file pme_spread_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_spread_sycl.cpp:444: warning: Member INSTANTIATE(order, subGroupSize) (macro definition) of file pme_spread_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/tests/pmegathertest.cpp:445: warning: Member registerDynamicalPmeGatherTests(const Range< int > hardwareContextIndexRange) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/tests/pmesolvetest.cpp:129: warning: Member enumValueToString(PmeSolveAlgorithm enumValue) (function) of namespace gmx::test::anonymous_namespace{pmesolvetest.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/tests/pmesolvetest.cpp:136: warning: Member enumValueToString(GridOrdering enumValue) (function) of namespace gmx::test::anonymous_namespace{pmesolvetest.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/tests/pmesolvetest.cpp:435: warning: Member registerDynamicalPmeSolveTests(const Range< int > hardwareContextIndexRange) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:192: warning: Member enumValueToString(SplineAndSpreadOptions enumValue) (function) of namespace gmx::test::anonymous_namespace{pmesplinespreadtest.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:104: warning: Member c_testSystems (variable) of namespace gmx::test::anonymous_namespace{pmesplinespreadtest.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/tests/pmesolvetest.cpp:435: warning: Member registerDynamicalPmeSolveTests(const Range< int > hardwareContextIndexRange) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/tests/pmegathertest.cpp:445: warning: Member registerDynamicalPmeGatherTests(const Range< int > hardwareContextIndexRange) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/tests/fft.cpp:303: warning: Member FFTTest3DParameters (typedef) of namespace gmx::test::anonymous_namespace{fft.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_cufftmp.cpp:102: warning: Member handleCufftError(cufftResult_t status, const char *msg) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_sycl_vkfft.cpp:258: warning: Member launchVkFft(const DeviceBuffer< float > &realGrid, const DeviceBuffer< float > &complexGrid, NativeQueue queue, gmx_fft_direction fftDirection, VkFFTApplication *application, VkFFTLaunchParams *launchParams) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/tests/fft_mpi.cpp:72: warning: Member GpuFftTestParams (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/tests/fft_mpi.cpp:77: warning: Member GpuFftTestGridParams (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/tests/fft_mpi.cpp:79: warning: Member getGpuAwareMpiStatusForFftBackend(const FftBackend fftBackend) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/tests/fft_mpi.cpp:266: warning: Member inputGrids (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/tests/fft_mpi.cpp:270: warning: Member inputBackends (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/filetypes.cpp:63: warning: Member TypeAndName (typedef) of namespace gmx::test::anonymous_namespace{filetypes.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/filetypes.cpp:65: warning: Member FileTypeTestParams (typedef) of namespace gmx::test::anonymous_namespace{filetypes.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/filetypes.cpp:116: warning: Member testParams (variable) of namespace gmx::test::anonymous_namespace{filetypes.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/filetypes.cpp:125: warning: Member prefixes (variable) of namespace gmx::test::anonymous_namespace{filetypes.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/matio.cpp:76: warning: Member generateStdReferenceFile(gmx::ArrayRef< const t_mapping > refMaps) (function) of namespace gmx::test::anonymous_namespace{matio.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/matio.cpp:94: warning: Member getReferenceMapping() (function) of namespace gmx::test::anonymous_namespace{matio.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/matio.cpp:211: warning: Member generateReferenceMatrix4x3() (function) of namespace gmx::test::anonymous_namespace{matio.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/matio.cpp:234: warning: Member compareRealValues(const t_matrix &input, real **values, basic_mdspan< const float, extents< 4, 3 > > ref) (function) of namespace gmx::test::anonymous_namespace{matio.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/fileioxdrserializer.cpp:82: warning: Member c_int32Value (variable) of namespace gmx::test::anonymous_namespace{fileioxdrserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/fileioxdrserializer.cpp:83: warning: Member c_int64Value (variable) of namespace gmx::test::anonymous_namespace{fileioxdrserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/fileioxdrserializer.cpp:85: warning: Member c_intAndFloat32 (variable) of namespace gmx::test::anonymous_namespace{fileioxdrserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/fileioxdrserializer.cpp:86: warning: Member c_intAndFloat64 (variable) of namespace gmx::test::anonymous_namespace{fileioxdrserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/xvgio.cpp:76: warning: Member compareValues(basic_mdspan< const double, dynamicExtents2D > ref, basic_mdspan< const double, dynamicExtents2D > test) (function) of namespace gmx::test::anonymous_namespace{xvgio.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:110: warning: Member c_numAtomTypes (variable) of namespace gmx::test::anonymous_namespace{nb_free_energy.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:520: warning: Member c_softcoreBeutlerAlphaOrGapsysLinpointScaling (variable) of namespace gmx::test::anonymous_namespace{nb_free_energy.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:521: warning: Member c_softcoreCoulomb (variable) of namespace gmx::test::anonymous_namespace{nb_free_energy.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:522: warning: Member c_softcoreType (variable) of namespace gmx::test::anonymous_namespace{nb_free_energy.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/convparm.cpp:210: warning: Member ftypeToName(const int ftype) (function) of namespace gmx::test::anonymous_namespace{convparm.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/convparm.cpp:216: warning: Member sc_testNamer (variable) of namespace gmx::test::anonymous_namespace{convparm.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/grompp_directives.cpp:76: warning: Member ExpectedResult (enumeration) of namespace gmx::test::anonymous_namespace{grompp_directives.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/grompp_directives.cpp:222: warning: Member cmapValidInputOutput (variable) of namespace gmx::test::anonymous_namespace{grompp_directives.cpp} is not documented. warning: Included by graph for 'devicebuffer_datatype.h' not generated, too many nodes (53), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/devicebuffer_hip.h:339: warning: Member asMpiPointer(DeviceBuffer< ValueType > &buffer) (function) of file devicebuffer_hip.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/devicebuffer_ocl.h:384: warning: Member asMpiPointer(DeviceBuffer< ValueType > &) (function) of file devicebuffer_ocl.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/devicebuffer_sycl.h:434: warning: Member asMpiPointer(DeviceBuffer< ValueType > &buffer) (function) of file devicebuffer_sycl.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gmxopencl.h:56: warning: Member CL_USE_DEPRECATED_OPENCL_2_0_APIS (macro definition) of file gmxopencl.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpu_kernel_utils.h:70: warning: Member GMX_ALWAYS_INLINE (macro definition) of file gpu_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpu_kernel_utils.h:96: warning: Member __attribute__((always_inline)) float gmxGpuFDim(const float one (function) of file gpu_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpu_kernel_utils.h:96: warning: Member two (variable) of file gpu_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpu_kernel_utils.h:102: warning: Member value (variable) of file gpu_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpu_kernel_utils.h:120: warning: Member valueTwo (variable) of file gpu_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpu_kernel_utils.h:120: warning: Member valueThree (variable) of file gpu_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpu_kernel_utils.h:138: warning: Member d1 (variable) of file gpu_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpu_kernel_utils.h:138: warning: Member t (variable) of file gpu_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpu_kernel_utils.h:143: warning: Member offset (variable) of file gpu_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpueventsynchronizer.h:58: warning: unable to resolve reference to 'GpuEventSynchronizer::markEvent' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpueventsynchronizer.h:59: warning: unable to resolve reference to 'GpuEventSynchronizer::waitForEvent' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpueventsynchronizer.h:60: warning: unable to resolve reference to 'GpuEventSynchronizer::enqueueWaitEvent' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpueventsynchronizer.h:74: warning: unable to resolve reference to 'GpuEventSynchronizer::reset' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpueventsynchronizer.h:76: warning: unable to resolve reference to 'GpuEventSynchronizer::consume' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpueventsynchronizer.h:78: warning: unable to resolve reference to 'GpuEventSynchronizer::markEvent' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpueventsynchronizer.h:81: warning: unable to resolve reference to 'GpuEventSynchronizer::waitForEvent' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpueventsynchronizer.h:83: warning: unable to resolve reference to 'GpuEventSynchronizer::enqueueWaitEvent' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpueventsynchronizer.h:88: warning: unable to resolve reference to 'GpuEventSynchronizer::markEvent' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpueventsynchronizer.h:89: warning: unable to resolve reference to 'GpuEventSynchronizer::enqueueWaitEvent' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gpueventsynchronizer.h:89: warning: unable to resolve reference to 'GpuEventSynchronizer::enqueueWaitEvent' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gputraits.h:67: warning: Member DeviceTexture (typedef) of file gputraits.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/gputraits_ocl.h:50: warning: Member DeviceTexture (typedef) of file gputraits_ocl.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/hip_kernel_utils.h:78: warning: Member LAUNCH_BOUNDS_EXACT(WORK_GROUP_SIZE, WAVES_PER_EU) (macro definition) of file hip_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/hip_kernel_utils.h:82: warning: Member LAUNCH_BOUNDS_EXACT_SINGLE(WORK_GROUP_SIZE) (macro definition) of file hip_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/hip_kernel_utils.h:85: warning: Member GMX_HIP_MAX_BLOCKS_PER_MP (macro definition) of file hip_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/hip_kernel_utils.h:86: warning: Member GMX_HIP_MAX_THREADS_PER_MP (macro definition) of file hip_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/hip_sycl_kernel_utils.h:82: warning: Member GMX_ALWAYS_INLINE_ATTRIBUTE (macro definition) of file hip_sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/hip_sycl_kernel_utils.h:83: warning: Member GMX_FUNC_ATTRIBUTE (macro definition) of file hip_sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/hip_sycl_kernel_utils.h:109: warning: Member idx (variable) of file hip_sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/oclraii.h:131: warning: Member ClCommandQueue (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/oclraii.h:132: warning: Member ClProgram (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/oclraii.h:133: warning: Member ClKernel (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/pmalloc.cpp:82: warning: Member pmallocSetDefaultDeviceContext(const DeviceContext *) (function) of file pmalloc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/pmalloc.cpp:87: warning: Member pmallocClearDefaultDeviceContext() (function) of file pmalloc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/pmalloc_hip.cpp:91: warning: Member pmallocSetDefaultDeviceContext(const DeviceContext *) (function) of file pmalloc_hip.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/pmalloc_hip.cpp:95: warning: Member pmallocClearDefaultDeviceContext() (function) of file pmalloc_hip.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/pmalloc_sycl.cpp:128: warning: Member pmallocSetDefaultDeviceContext(const DeviceContext *deviceContext) (function) of file pmalloc_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/pmalloc_sycl.cpp:137: warning: Member pmallocClearDefaultDeviceContext() (function) of file pmalloc_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/sycl_kernel_utils.h:65: warning: Member SYCL_ASSERT(condition) (macro definition) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/sycl_kernel_utils.h:85: warning: Member compilingForHost() (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/sycl_kernel_utils.h:101: warning: Member compilingForSubGroupSize() (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/sycl_kernel_utils.h:115: warning: Member skipKernelCompilation() (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/sycl_kernel_utils.h:137: warning: Member atomicAddDefault(T &val, const T delta) (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/sycl_kernel_utils.h:174: warning: Member atomicFetchAddLocal(T &val, const T delta) (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/tests/device_availability.cpp:73: warning: Member getRequiredNumberOfDevices() (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/tests/typecasts_runner_hip.cpp:64: warning: Member saveFloat3InRVecFormat(ArrayRef< gmx::RVec > rVecOutput, const float3 *float3Output, int numElements) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/device_management_hip.cpp:128: warning: Member determineIfDeviceHasLargeRegisterPool(std::string deviceArch) (function) of file device_management_hip.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/device_management_sycl.cpp:68: warning: Member parseHardwareVersionNvidia(const std::string &archName) (function) of file device_management_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/device_management_sycl.cpp:105: warning: Member getHardwareVersionNvidia(const sycl::device &device) (function) of file device_management_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/device_management_sycl.cpp:140: warning: Member parseHardwareVersionAmd(const std::string &archName) (function) of file device_management_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/device_management_sycl.cpp:180: warning: Member getHardwareVersionAmd(const sycl::device &device) (function) of file device_management_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/device_management_sycl.cpp:214: warning: Member getHardwareVersionIntel(const sycl::device &device) (function) of file device_management_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/device_management_sycl.cpp:250: warning: Member getDeviceGpuAwareMpiStatus(const sycl::backend backend) (function) of file device_management_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/device_management_sycl.cpp:548: warning: Member partitionDevices(const std::vector< sycl::device > &&devices) (function) of file device_management_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/device_management_sycl_intel_device_ids.cpp:51: warning: Member IntelProductConfig (enumeration) of file device_management_sycl_intel_device_ids.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/device_management_sycl_intel_device_ids.cpp:611: warning: Member getHardwareVersionFromIntelProductConfig(const IntelProductConfig productConfig) (function) of file device_management_sycl_intel_device_ids.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/device_management_sycl_intel_device_ids.cpp:622: warning: Member getProductConfigFromPciExpressID(unsigned int pciExpressID) (function) of file device_management_sycl_intel_device_ids.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/device_management_sycl_intel_device_ids.cpp:138: warning: Member c_pciExpressIdsForProduct (variable) of file device_management_sycl_intel_device_ids.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/hardwaretopology.cpp:1103: warning: Member detectCpuLimit(const std::string &root="") (function) of namespace gmx::anonymous_namespace{hardwaretopology.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/hardwaretopology.cpp:1184: warning: Member setMaxThreads(float cpuLimit, int topologyCpus, int systemCpus) (function) of namespace gmx::anonymous_namespace{hardwaretopology.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/simd_support.cpp:70: warning: Member simdString(SimdType s) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/simd_support.cpp:199: warning: Member simdCompiled() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/tests/device_management.cpp:111: warning: Member uuidToString(const std::array< std::byte, 16 > &uuid) (function) of namespace gmx::test::anonymous_namespace{device_management.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/tests/mockhardwaretopology.cpp:166: warning: Member checkHardwareTopology(TestReferenceChecker *checker, const HardwareTopology &hwTop) (function) of namespace gmx::test::anonymous_namespace{mockhardwaretopology.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/bonded.cpp:3057: warning: Member CmapForceStructure (typedef) of namespace anonymous_namespace{bonded.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/bonded.cpp:3059: warning: Member processCmapForceComponent(const gmx::RVec a, const gmx::RVec b, const real df, const real gaa, const real fga, const real gbb, const real hgb, const int dim) (function) of namespace anonymous_namespace{bonded.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/bonded.cpp:3075: warning: Member applyCmapForceComponent(const gmx::RVec forceComponent) (function) of namespace anonymous_namespace{bonded.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/bonded.cpp:3086: warning: Member accumulateCmapForces(const rvec x[], rvec4 f[], rvec fshift[], const t_pbc *pbc, const gmx::RVec r_ij, const gmx::RVec r_kj, const gmx::RVec r_kl, const gmx::RVec a, const gmx::RVec b, gmx::RVec h, const real ra2r, const real rb2r, const real rgr, const real rg, const int ai, const int aj, const int ak, const int al, const real df, const int t1, const int t2) (function) of namespace anonymous_namespace{bonded.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces_gpu_impl_gpu.cpp:67: warning: Member chooseSubGroupSizeForDevice(const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces_gpu_impl_gpu.cpp:61: warning: Member c_threadsPerBlock (variable) of file listed_forces_gpu_impl_gpu.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:875: warning: Member mode (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:113: warning: Member staggeredAtomicAddForce(sycl::global_ptr< Float3 > gm_f, Float3 f, const int localId) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:134: warning: Member harmonic_gpu(const float kA, const float xA, const float x, sycl::private_ptr< float > V, sycl::private_ptr< float > F) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:152: warning: Member bonds_gpu(const int i, sycl::private_ptr< float > vtot_loc, const sycl::global_ptr< const t_iatom > gm_forceatoms, const sycl::global_ptr< const t_iparams > gm_forceparams, const sycl::global_ptr< const sycl::float4 > gm_xq, sycl::global_ptr< Float3 > gm_f, sycl::local_ptr< Float3 > sm_fShiftLoc, const PbcAiuc &pbcAiuc, const int localId) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:260: warning: Member bond_angle_gpu(const sycl::float4 xi, const sycl::float4 xj, const sycl::float4 xk, const PbcAiuc &pbcAiuc, sycl::private_ptr< Float3 > r_ij, sycl::private_ptr< Float3 > r_kj, sycl::private_ptr< float > costh, sycl::private_ptr< int > t1, sycl::private_ptr< int > t2) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:279: warning: Member angles_gpu(const int i, sycl::private_ptr< float > vtot_loc, const sycl::global_ptr< const t_iatom > gm_forceatoms, const sycl::global_ptr< const t_iparams > gm_forceparams, const sycl::global_ptr< const sycl::float4 > gm_xq, sycl::global_ptr< Float3 > gm_f, sycl::local_ptr< Float3 > sm_fShiftLoc, const PbcAiuc &pbcAiuc, const int localId) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:347: warning: Member urey_bradley_gpu(const int i, sycl::private_ptr< float > vtot_loc, const sycl::global_ptr< const t_iatom > gm_forceatoms, const sycl::global_ptr< const t_iparams > gm_forceparams, const sycl::global_ptr< const sycl::float4 > gm_xq, sycl::global_ptr< Float3 > gm_f, sycl::local_ptr< Float3 > sm_fShiftLoc, const PbcAiuc &pbcAiuc, const int localId) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:460: warning: Member dih_angle_gpu(const T xi, const T xj, const T xk, const T xl, const PbcAiuc &pbcAiuc, sycl::private_ptr< Float3 > r_ij, sycl::private_ptr< Float3 > r_kj, sycl::private_ptr< Float3 > r_kl, sycl::private_ptr< Float3 > m, sycl::private_ptr< Float3 > n, sycl::private_ptr< int > t1, sycl::private_ptr< int > t2, sycl::private_ptr< int > t3) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:489: warning: Member dih_angle_gpu_sincos(const T xi, const T xj, const T xk, const T xl, const PbcAiuc &pbcAiuc, sycl::private_ptr< Float3 > r_ij, sycl::private_ptr< Float3 > r_kj, sycl::private_ptr< Float3 > r_kl, sycl::private_ptr< Float3 > m, sycl::private_ptr< Float3 > n, sycl::private_ptr< int > t1, sycl::private_ptr< int > t2, sycl::private_ptr< float > cosval) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:529: warning: Member dopdihs_gpu(const float cpA, const float phiA, const int mult, const float phi, sycl::private_ptr< float > v, sycl::private_ptr< float > f) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:543: warning: Member do_dih_fup_gpu(const int i, const int j, const int k, const int l, const float ddphi, const Float3 r_ij, const Float3 r_kj, const Float3 r_kl, const Float3 m, const Float3 n, sycl::global_ptr< Float3 > gm_f, sycl::local_ptr< Float3 > sm_fShiftLoc, const PbcAiuc &pbcAiuc, const sycl::global_ptr< const Float4 > gm_xq, const int t1, const int t2, const int localId) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:603: warning: Member pdihs_gpu(const int i, sycl::private_ptr< float > vtot_loc, const sycl::global_ptr< const t_iatom > gm_forceatoms, const sycl::global_ptr< const t_iparams > gm_forceparams, const sycl::global_ptr< const sycl::float4 > gm_xq, sycl::global_ptr< Float3 > gm_f, sycl::local_ptr< Float3 > sm_fShiftLoc, const PbcAiuc &pbcAiuc, const int localId) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:649: warning: Member rbdihs_gpu(const int i, sycl::private_ptr< float > vtot_loc, const sycl::global_ptr< const t_iatom > gm_forceatoms, const sycl::global_ptr< const t_iparams > gm_forceparams, const sycl::global_ptr< const sycl::float4 > gm_xq, sycl::global_ptr< Float3 > gm_f, sycl::local_ptr< Float3 > sm_fShiftLoc, const PbcAiuc &pbcAiuc, const int localId) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:761: warning: Member idihs_gpu(const int i, sycl::private_ptr< float > vtot_loc, const sycl::global_ptr< const t_iatom > gm_forceatoms, const sycl::global_ptr< const t_iparams > gm_forceparams, const sycl::global_ptr< const sycl::float4 > gm_xq, sycl::global_ptr< Float3 > gm_f, sycl::local_ptr< Float3 > sm_fShiftLoc, const PbcAiuc &pbcAiuc, const int localId) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:814: warning: Member pairs_gpu(const int i, const sycl::global_ptr< const t_iatom > gm_forceatoms, const sycl::global_ptr< const t_iparams > gm_iparams, const sycl::global_ptr< const sycl::float4 > gm_xq, sycl::global_ptr< Float3 > gm_f, sycl::local_ptr< Float3 > sm_fShiftLoc, const PbcAiuc &pbcAiuc, const float scale_factor, sycl::private_ptr< float > vtotVdw_loc, sycl::private_ptr< float > vtotElec_loc, const int localId) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:878: warning: Member bondedKernel(sycl::handler &cgh, const BondedGpuKernelParameters &kernelParams, const DeviceBuffer< t_iatom > gm_iatoms_[numFTypesOnGpu], float *__restrict__ gm_vTot, const t_iparams *__restrict__ gm_forceParams_, const sycl::float4 *__restrict__ gm_xq_, Float3 *__restrict__ gm_f_, Float3 *__restrict__ gm_fShift_) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:64: warning: Member c_deg2RadF (variable) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:65: warning: Member c_Pi (variable) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/pairs.cpp:173: warning: Member sixthRoot(const real r) (function) of file pairs.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/tests/pairs.cpp:209: warning: Member frHelper (variable) of namespace gmx::test::anonymous_namespace{pairs.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/tests/position_restraints.cpp:159: warning: Member c_emptyLambdas (variable) of namespace gmx::test::anonymous_namespace{position_restraints.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/functions.cpp:399: warning: Member IntegerTypes (typedef) of namespace gmx::test::anonymous_namespace{functions.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/nrjac.h:55: warning: Member jacobi(double **a, int numDimensions, double *eigenvalues, double **eigenvectors, int *numRotations) (function) of file nrjac.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/nrjac.h:65: warning: Member jacobi(gmx::ArrayRef< gmx::DVec > a, gmx::ArrayRef< double > eigenvalues, gmx::ArrayRef< gmx::DVec > eigenvectors) (function) of file nrjac.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/nrjac.h:67: warning: Member m_inv_gen(const real *m, int n, real *minv) (function) of file nrjac.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/neldermead.cpp:102: warning: Member defaultNelderMeadParameters (variable) of namespace gmx::anonymous_namespace{neldermead.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/nrjac.cpp:59: warning: Member do_rotate(MatrixType a, int i, int j, int k, int l, double tau, double s) (function) of file nrjac.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/nrjac.cpp:69: warning: Member jacobi(MatrixType a, const int n, double d[], MatrixType v) (function) of file nrjac.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/nrjac.cpp:182: warning: Member jacobi(double **a, const int numDimensions, double *eigenvalues, double **eigenvectors, int *numRotations) (function) of file nrjac.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/nrjac.cpp:192: warning: Member jacobi(gmx::ArrayRef< gmx::DVec > a, gmx::ArrayRef< double > eigenvalues, gmx::ArrayRef< gmx::DVec > eigenvectors) (function) of file nrjac.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/nrjac.cpp:201: warning: Member m_inv_gen(const real *m, int n, real *minv) (function) of file nrjac.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/optimization.cpp:66: warning: Member mcCormick(ArrayRef< const real > x) (function) of namespace gmx::test::anonymous_namespace{optimization.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/constr.cpp:98: warning: Member c_pbcs (variable) of namespace gmx::test::anonymous_namespace{constr.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/constr.cpp:172: warning: Member c_constraintsTestSystemList (variable) of namespace gmx::test::anonymous_namespace{constr.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/energyoutput.h:87: warning: Member pvEnergyFieldName (variable) of file energyoutput.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/energyoutput.h:89: warning: Member enthalpyEnergyFieldName (variable) of file energyoutput.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/energyoutput.h:91: warning: Member virialEnergyFieldNames (variable) of file energyoutput.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/gpuforcereduction.h:62: warning: Member HAVE_GPU_FORCE_REDUCTION (macro definition) of file gpuforcereduction.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/leapfrog_gpu_internal_sycl.cpp:170: warning: unable to resolve reference to 'NumTempScaleValues' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/lincs_gpu_internal_sycl.cpp:452: warning: Member launchLincsKernel(const DeviceStream &deviceStream, const int numConstraintsThreads, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/constrtestrunners.h:63: warning: Member GPU_CONSTRAINTS_SUPPORTED (macro definition) of file constrtestrunners.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/energyoutput.cpp:102: warning: Member boxs_nm (variable) of file energyoutput.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/energyoutput.cpp:104: warning: Member tricl_boxs_nm (variable) of file energyoutput.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/energyoutput.cpp:107: warning: Member vol_nm[] (variable) of file energyoutput.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/energyoutput.cpp:109: warning: Member dens_nm[] (variable) of file energyoutput.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/energyoutput.cpp:111: warning: Member pvEnergyFieldName (variable) of file energyoutput.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/energyoutput.cpp:113: warning: Member enthalpyEnergyFieldName (variable) of file energyoutput.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/energyoutput.cpp:115: warning: Member virialEnergyFieldNames (variable) of file energyoutput.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/energyoutput.cpp:119: warning: Member boxvel_nm (variable) of file energyoutput.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/energyoutput.cpp:132: warning: Member haveFepLambdaMoves(const t_inputrec &inputrec) (function) of file energyoutput.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/freeenergyparameters.cpp:62: warning: Member lambdasAtState(const int stateIndex, gmx::ArrayRef< const std::vector< double > > lambdaArray, const int lambdaArrayExtent) (function) of namespace gmx::anonymous_namespace{freeenergyparameters.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/leapfrogtestrunners.h:61: warning: Member GPU_LEAPFROG_SUPPORTED (macro definition) of file leapfrogtestrunners.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/settletestrunners.h:61: warning: Member GPU_SETTLE_SUPPORTED (macro definition) of file settletestrunners.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/update_constrain_gpu_impl.cpp:69: warning: Member sc_haveGpuConstraintSupport (variable) of file update_constrain_gpu_impl.cpp is not documented. warning: Include graph for 'md.cpp' not generated, too many nodes (90), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Include graph for 'runner.cpp' not generated, too many nodes (112), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulationinput.h:120: warning: Member globalSimulationState(const SimulationInput &) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulationinput.h:121: warning: Member applyGlobalInputRecord(const SimulationInput &, t_inputrec *) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulationinput.h:122: warning: Member applyGlobalTopology(const SimulationInput &, gmx_mtop_t *) (function) of namespace gmx is not documented. warning: Include graph for 'tpi.cpp' not generated, too many nodes (50), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:64: warning: Member sc_atomInfo_HasPerturbedCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:65: warning: Member sc_atomInfo_Exclusion (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:66: warning: Member sc_atomInfo_Constraint (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:67: warning: Member sc_atomInfo_Settle (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:68: warning: Member sc_atomInfo_BondCommunication (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:69: warning: Member sc_atomInfo_HasVdw (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:70: warning: Member sc_atomInfo_HasCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:71: warning: Member sc_atomInfo_IsFillerParticle (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/awh_history.cpp:71: warning: Member doCheckpoint(CheckpointData< operation > checkpointData, AwhPointStateHistory *awhPointStateHistory) (function) of namespace gmx::anonymous_namespace{awh_history.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/awh_history.cpp:88: warning: Member doCheckpoint(CheckpointData< operation > checkpointData, AwhBiasStateHistory *awhBiasStateHistory) (function) of namespace gmx::anonymous_namespace{awh_history.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/awh_history.cpp:102: warning: Member doCheckpoint(CheckpointData< operation > checkpointData, CorrelationBlockDataHistory *correlationBlockDataHistory) (function) of namespace gmx::anonymous_namespace{awh_history.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/awh_history.cpp:123: warning: Member doCheckpoint(CheckpointData< operation > checkpointData, CorrelationGridHistory *correlationGridHistory) (function) of namespace gmx::anonymous_namespace{awh_history.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/awh_history.cpp:144: warning: Member doCheckpointData(CheckpointData< operation > checkpointData, AwhBiasHistory *awhBiasHistory) (function) of namespace gmx::anonymous_namespace{awh_history.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/awh_history.cpp:68: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{awh_history.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/enerdata.cpp:78: warning: Member makeFepvals(const std::vector< double > &lambdaVdw, const std::vector< double > &lambdaCoul) (function) of namespace gmx::test::anonymous_namespace{enerdata.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/enerdata.cpp:69: warning: Member c_numLambdas (variable) of namespace gmx::test::anonymous_namespace{enerdata.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/enerdata.cpp:71: warning: Member dhdlVdw (variable) of namespace gmx::test::anonymous_namespace{enerdata.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/enerdata.cpp:72: warning: Member dhdlCoul (variable) of namespace gmx::test::anonymous_namespace{enerdata.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/enerdata.cpp:74: warning: Member dhdlLinearZero (variable) of namespace gmx::test::anonymous_namespace{enerdata.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/forcebuffers.cpp:66: warning: Member c_forces (variable) of namespace gmx::test::anonymous_namespace{forcebuffers.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/multipletimestepping.cpp:147: warning: Member simpleMtsOpts() (function) of namespace gmx::test::anonymous_namespace{multipletimestepping.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/energydata.cpp:402: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{energydata.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/expandedensembleelement.cpp:129: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{expandedensembleelement.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/firstorderpressurecoupling.cpp:183: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{firstorderpressurecoupling.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/freeenergyperturbationdata.cpp:176: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{freeenergyperturbationdata.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/mttk.cpp:281: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{mttk.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/nosehooverchains.cpp:67: warning: Member nhcUsageNames (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp:298: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{parrinellorahmanbarostat.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/propagator.cpp:759: warning: Member hasStartVelocityScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/propagator.cpp:768: warning: Member hasEndVelocityScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/propagator.cpp:775: warning: Member hasPositionScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/propagator.cpp:781: warning: Member hasParrinelloRahmanScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/propagator.cpp:907: warning: Member getConnection(Propagator< integrationStage > *propagator, const PropagatorTag &propagatorTag) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/propagator.cpp:63: warning: Member integrationStepNames (variable) of namespace gmx::anonymous_namespace{propagator.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/pullelement.cpp:125: warning: Member doCheckpointData(CheckpointData< operation > *checkpointData, ArrayRef< double > previousStepCom) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/pullelement.cpp:121: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{pullelement.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/gpu_types_common.h:88: warning: Member c_sciSortingItemsPerThread (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/gpu_types_common.h:463: warning: Member elecEwald (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/gpu_types_common.h:466: warning: Member elecEwaldTab (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/gpu_types_common.h:469: warning: Member ljEwald (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/grid.cpp:151: warning: Member getMaxNumCells(const Grid::Geometry &geometry, const int numAtoms, const int numColumns) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/gridset.cpp:171: warning: Member getGridOffset(ArrayRef< const Grid > grids, int gridIndex) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_data_mgmt.cpp:97: warning: Member hipRocprimWrapper(size_t temporaryBufferSize, char *temporaryBuffer, gmx::GpuPairlist *plist, const DeviceStream &deviceStream) (function) of namespace gmx::anonymous_namespace{nbnxm_hip_data_mgmt.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_data_mgmt.cpp:76: warning: Member gpu_min_ci_balanced_factor (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:1320: warning: Member launchNbnxmKernelHelper(NbnxmGpu *nb, const StepWorkload &stepWork, InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:61: warning: Member launchNbnxmKernelHelper< false, false, false >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:62: warning: Member launchNbnxmKernelHelper< false, false, true >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:63: warning: Member launchNbnxmKernelHelper< false, true, true >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:64: warning: Member launchNbnxmKernelHelper< false, true, false >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:66: warning: Member launchNbnxmKernelHelper< true, false, false >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:67: warning: Member launchNbnxmKernelHelper< true, false, true >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:68: warning: Member launchNbnxmKernelHelper< true, true, true >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:69: warning: Member launchNbnxmKernelHelper< true, true, false >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_body.h:119: warning: Member fetchNbfpC6C12(const float2 *nbfpComb, int type) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_body.h:574: warning: Member nbparam (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_body.h:574: warning: Member plist (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:66: warning: Member launchNbnxmKernelHelper< true, false, false >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:61: warning: Member launchNbnxmKernelHelper< false, false, false >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:69: warning: Member launchNbnxmKernelHelper< true, true, false >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:64: warning: Member launchNbnxmKernelHelper< false, true, false >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:67: warning: Member launchNbnxmKernelHelper< true, false, true >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:62: warning: Member launchNbnxmKernelHelper< false, false, true >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:68: warning: Member launchNbnxmKernelHelper< true, true, true >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:63: warning: Member launchNbnxmKernelHelper< false, true, true >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_utils.h:85: warning: Member nb_any_internal(int predicate, int widx) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_utils.h:108: warning: Member numberOfKernelBlocksSanityCheck(int numSci, const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_utils.h:125: warning: Member requiredSharedMemorySize() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_utils.h:70: warning: Member c_subWarp (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_utils.h:82: warning: Member c_fbufStride (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:53: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:54: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:55: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:56: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:57: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJ_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:58: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:59: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:60: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:61: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:62: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJ_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:63: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:64: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:65: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:66: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:68: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:69: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:70: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:71: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:72: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:73: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:74: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:75: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:76: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:77: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:78: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:79: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:80: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:81: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:82: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:84: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:85: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:86: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:87: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:88: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:89: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:90: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:91: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:92: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:93: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:94: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:95: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:96: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:97: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:98: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:54: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:55: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:56: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:57: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:58: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJ_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:59: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:60: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:61: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:62: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:63: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJ_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:64: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:65: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:66: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:67: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:69: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:70: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:71: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:72: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:73: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:74: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:75: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:76: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:77: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:78: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:79: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:80: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:81: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:82: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:83: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:85: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:86: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:87: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:88: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:89: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:90: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:91: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:92: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:93: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:94: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:95: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:96: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:97: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:98: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:99: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_prune.cpp:148: warning: Member nbnxmRefPruneKernel< NbnxmKernelType::Cpu4x4_PlainC >(NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, ArrayRef< const RVec > shiftvec, real rlistInner) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_prune.cpp:153: warning: Member nbnxmRefPruneKernel< NbnxmKernelType::Cpu1x1_PlainC >(NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, ArrayRef< const RVec > shiftvec, real rlistInner) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:122: warning: Member isGpuKernelType(const NbnxmKernelType kernelType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_setup.cpp:261: warning: Member nbnxmKernelTypeToName(NbnxmKernelType kernelType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:149: warning: Member isGpuSpecificPairlist(const PairlistType pairlistType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:269: warning: Member sc_gpuPairlistHasSplitJCluster(const PairlistType pairlistType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:82: warning: unable to resolve reference to 'ElecType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:106: warning: unable to resolve reference to 'VdwType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:180: warning: Member c_gpuNumClusterPerCellY (variable) of namespace gmx::detail is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:181: warning: Member c_gpuNumClusterPerCellX (variable) of namespace gmx::detail is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_buffer_ops.cpp:65: warning: Member nbnxn_gpu_x_to_nbat_x(const Grid &grid, NbnxmGpu *nb, DeviceBuffer< RVec > d_x, GpuEventSynchronizer *xReadyOnDevice, const AtomLocality locality, int gridId, int numColumnsMax, bool mustInsertNonLocalDependency) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:435: warning: Member GpuPairlistByLocality (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:95: warning: Member init_ewald_coulomb_force_table(const EwaldCorrectionTables &tables, NBParamGpu *nbp, const DeviceContext &deviceContext, const DeviceStream &deviceStream) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:114: warning: Member useTabulatedEwaldByDefault(const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:148: warning: Member nbnxn_gpu_pick_ewald_kernel_type(const interaction_const_t &ic, const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:198: warning: Member set_cutoff_parameters(NBParamGpu *nbp, const interaction_const_t &ic, const PairlistParams &listParams) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:248: warning: Member init_timings(gmx_wallclock_gpu_nbnxn_t *t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:297: warning: Member nbnxmGpuPickVdwKernelType(const interaction_const_t &ic, LJCombinationRule ljCombinationRule) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:351: warning: Member nbnxmGpuPickElectrostaticsKernelType(const interaction_const_t &ic, const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:437: warning: Member initializeGpuLists(bool localAndNonLocal) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:448: warning: Member gpu_init(const DeviceStreamManager &deviceStreamManager, const interaction_const_t *ic, const PairlistParams &listParams, const nbnxn_atomdata_t *nbat, const bool bLocalAndNonlocal) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:512: warning: Member gpu_pme_loadbal_update_param(nonbonded_verlet_t *nbv, const interaction_const_t &ic) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:530: warning: Member gpu_upload_shiftvec(NbnxmGpu *nb, const nbnxn_atomdata_t *nbatom) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:691: warning: Member gpu_init_atomdata(NbnxmGpu *nb, const nbnxn_atomdata_t *nbat) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:794: warning: Member gpu_clear_outputs(NbnxmGpu *nb, bool computeVirial) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:825: warning: Member gpu_is_kernel_ewald_analytical(const NbnxmGpu *nb) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:831: warning: Member setupGpuShortRangeWorkLow(NbnxmGpu *nb, const ListedForcesGpu *listedForcesGpu, const InteractionLocality iLocality) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:844: warning: Member haveGpuShortRangeWork(const NbnxmGpu *nb, const InteractionLocality interactionLocality) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:984: warning: Member nbnxnInsertNonlocalGpuDependency(NbnxmGpu *nb, const InteractionLocality interactionLocality) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:1079: warning: Member nbnxn_gpu_init_x_to_nbat_x(const GridSet &gridSet, NbnxmGpu *gpu_nbv) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:1261: warning: Member gpuGetNBAtomData(NbnxmGpu *nb) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:1267: warning: Member gpu_get_f(NbnxmGpu *nb) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:90: warning: Member constexpr(doCalcEnergies) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:56: warning: Member epsilon (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:59: warning: Member sigma6 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:60: warning: Member c6 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:61: warning: Member c12 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:63: warning: Member return (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:69: warning: Member repulsionShift (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:70: warning: Member rVdwSwitch (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:73: warning: Member rInv (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:74: warning: Member r2 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:75: warning: Member fInvR (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:76: warning: Member eLJ (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:80: warning: Member dispShiftV3 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:81: warning: Member repuShiftV2 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:82: warning: Member repuShiftV3 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:84: warning: Member r (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:85: warning: Member rSwitch (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:104: warning: Member typeI (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_setup.cpp:261: warning: Member nbnxmKernelTypeToName(NbnxmKernelType kernelType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_simd.h:137: warning: Member GMX_HAVE_NBNXM_SIMD_4XM (macro definition) of file nbnxm_simd.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:73: warning: Member sc_iClusterSizeSimd() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:82: warning: Member sc_jClusterSizeSimd() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:252: warning: Member setICellCoordinatesSimd4xM(int gmx_unused ci, const RVec gmx_unused &shift, int gmx_unused stride, const real gmx_unused *x, NbnxmPairlistCpuWork gmx_unused *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:265: warning: Member setICellCoordinatesSimd2xMM(int gmx_unused ci, const RVec gmx_unused &shift, int gmx_unused stride, const real gmx_unused *x, NbnxmPairlistCpuWork gmx_unused *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:504: warning: Member makeClusterListSimd4xM(const Grid gmx_unused &jGrid, NbnxnPairlistCpu gmx_unused *nbl, int gmx_unused icluster, int gmx_unused firstCell, int gmx_unused lastCell, bool gmx_unused excludeSubDiagonal, const real gmx_unused *gmx_restrict x_j, real gmx_unused rlist2, float gmx_unused rbb2, int gmx_unused *gmx_restrict numDistanceChecks) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:523: warning: Member makeClusterListSimd2xMM(const Grid gmx_unused &jGrid, NbnxnPairlistCpu gmx_unused *nbl, int gmx_unused icluster, int gmx_unused firstCell, int gmx_unused lastCell, bool gmx_unused excludeSubDiagonal, const real gmx_unused *gmx_restrict x_j, real gmx_unused rlist2, float gmx_unused rbb2, int gmx_unused *gmx_restrict numDistanceChecks) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_gpu_buffer_ops_internal_sycl.cpp:50: warning: Member mode (typedef) of file nbnxm_gpu_buffer_ops_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl.cpp:256: warning: Member launchSciSortOnGpu(GpuPairlist *plist, const int maxWorkGroupSize, const DeviceStream &deviceStream) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl.cpp:228: warning: Member launchPrefixSumKernel(sycl::queue &q, GpuPairlistSorting *sorting) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl.cpp:241: warning: Member launchBucketSortKernel(sycl::queue &q, GpuPairlist *plist) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel.cpp:53: warning: Member getNbnxmSubGroupSize(const DeviceInformation &deviceInfo, PairlistType layoutType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:1320: warning: Member launchNbnxmKernelHelper(NbnxmGpu *nb, const StepWorkload &stepWork, InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel.cpp:104: warning: Member launchNbnxmKernel(NbnxmGpu *nb, const gmx::StepWorkload &stepWork, const InteractionLocality iloc, bool doPrune) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel.h:51: warning: Member SYCL_NBNXM_SUPPORTS_SUBGROUP_SIZE_8 (macro definition) of file nbnxm_sycl_kernel.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel.h:52: warning: Member SYCL_NBNXM_SUPPORTS_SUBGROUP_SIZE_32 (macro definition) of file nbnxm_sycl_kernel.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel.h:53: warning: Member SYCL_NBNXM_SUPPORTS_SUBGROUP_SIZE_64 (macro definition) of file nbnxm_sycl_kernel.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:77: warning: Member FCiFloat3 (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:1320: warning: Member launchNbnxmKernelHelper(NbnxmGpu *nb, const StepWorkload &stepWork, InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_pruneonly.cpp:55: warning: Member mode (typedef) of file nbnxm_sycl_kernel_pruneonly.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_utils.h:58: warning: Member sc_superClInteractionMask(const PairlistType layoutType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/tests/exclusions.cpp:228: warning: Member testKernelTypes (variable) of namespace gmx::test::anonymous_namespace{exclusions.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/tests/kernel_test.cpp:404: warning: Member isTabulated(const CoulombKernelType coulombKernelType) (function) of namespace gmx::test::anonymous_namespace{kernel_test.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/tests/kernel_test.cpp:357: warning: Member coulombKernelTypeName (variable) of namespace gmx::test::anonymous_namespace{kernel_test.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/tests/kernel_test.cpp:363: warning: Member vdwKernelTypeName (variable) of namespace gmx::test::anonymous_namespace{kernel_test.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include/gromacs/pbcutil/pbc_aiuc_sycl.h:50: warning: Member xyzToShiftIndex(int x, int y, int z) (function) of file pbc_aiuc_sycl.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/pbc.cpp:1433: warning: Member putAtomsInBoxTemplated(PbcType pbcType, const matrix box, const matrix boxDeformation, gmx::ArrayRef< gmx::RVec > x, gmx::ArrayRef< gmx::RVec > v) (function) of file pbc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/pbc_simd.cpp:56: warning: Member set_pbc_simd(const t_pbc gmx_unused *pbc, real gmx_unused *pbc_simd) (function) of file pbc_simd.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/tests/com.cpp:128: warning: Member COMInPlaceTestParams (typedef) of namespace gmx::test::anonymous_namespace{com.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/compiler.cpp:2029: warning: found documented return type for analyze_static that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/compiler.cpp:1844: warning: found documented return type for evaluate_boolean_static_part that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/compiler.cpp:1766: warning: found documented return type for init_method that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/compiler.cpp:1713: warning: found documented return type for process_const that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.cpp:1034: warning: found documented return type for _gmx_sel_evaluate_and that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.cpp:1149: warning: found documented return type for _gmx_sel_evaluate_arithmetic that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.cpp:491: warning: found documented return type for _gmx_sel_evaluate_children that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.cpp:924: warning: found documented return type for _gmx_sel_evaluate_method that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.cpp:889: warning: found documented return type for _gmx_sel_evaluate_method_params that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.cpp:974: warning: found documented return type for _gmx_sel_evaluate_modifier that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.cpp:1012: warning: found documented return type for _gmx_sel_evaluate_not that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.cpp:1085: warning: found documented return type for _gmx_sel_evaluate_or that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.h:102: warning: found documented return type for _gmx_sel_evaluate_root that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.h:122: warning: found documented return type for _gmx_sel_evaluate_static that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.cpp:608: warning: found documented return type for _gmx_sel_evaluate_subexpr that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.cpp:548: warning: found documented return type for _gmx_sel_evaluate_subexpr_simple that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.cpp:573: warning: found documented return type for _gmx_sel_evaluate_subexpr_staticeval that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.cpp:761: warning: found documented return type for _gmx_sel_evaluate_subexprref that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.cpp:726: warning: found documented return type for _gmx_sel_evaluate_subexprref_simple that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.cpp:1034: warning: found documented return type for _gmx_sel_evaluate_and that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.cpp:1149: warning: found documented return type for _gmx_sel_evaluate_arithmetic that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.cpp:491: warning: found documented return type for _gmx_sel_evaluate_children that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.cpp:924: warning: found documented return type for _gmx_sel_evaluate_method that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.cpp:889: warning: found documented return type for _gmx_sel_evaluate_method_params that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.cpp:974: warning: found documented return type for _gmx_sel_evaluate_modifier that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.cpp:1012: warning: found documented return type for _gmx_sel_evaluate_not that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.cpp:1085: warning: found documented return type for _gmx_sel_evaluate_or that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.h:102: warning: found documented return type for _gmx_sel_evaluate_root that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.h:122: warning: found documented return type for _gmx_sel_evaluate_static that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.cpp:608: warning: found documented return type for _gmx_sel_evaluate_subexpr that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.cpp:548: warning: found documented return type for _gmx_sel_evaluate_subexpr_simple that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.cpp:573: warning: found documented return type for _gmx_sel_evaluate_subexpr_staticeval that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.cpp:761: warning: found documented return type for _gmx_sel_evaluate_subexprref that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.cpp:726: warning: found documented return type for _gmx_sel_evaluate_subexprref_simple that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/params.cpp:905: warning: found documented return type for parse_values_enum that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_compare.cpp:364: warning: found documented return type for convert_real_int that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_compare.cpp:126: warning: found documented return type for init_compare that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_distance.cpp:102: warning: found documented return type for init_common that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_distance.cpp:120: warning: found documented return type for init_frame_common that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_insolidangle.cpp:99: warning: unable to resolve reference to 'sm_insolidangle' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_insolidangle.cpp:255: warning: found documented return type for init_insolidangle that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_keywords.cpp:353: warning: found documented return type for init_kweval that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_keywords.cpp:113: warning: found documented return type for init_kwreal that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_keywords.cpp:365: warning: found documented return type for init_output_kweval that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_merge.cpp:77: warning: found documented return type for init_merge that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_permute.cpp:90: warning: found documented return type for init_permute that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_position.cpp:100: warning: found documented return type for init_cog that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_position.cpp:110: warning: found documented return type for init_com that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_position.cpp:87: warning: found documented return type for init_kwpos that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_position.cpp:120: warning: found documented return type for init_output_pos that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_same.cpp:121: warning: found documented return type for init_same that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_simple.cpp:90: warning: found documented return type for check_molecules that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_simple.cpp:160: warning: found documented return type for check_pdbinfo that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/selectioncollection.cpp:978: warning: Member swap(SelectionCollection &lhs, SelectionCollection &rhs) noexcept (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:642: warning: Member GMX_SIMD_HAVE_4NSIMD_UTIL_FLOAT (macro definition) of file simd.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:653: warning: Member GMX_SIMD4N_FLOAT_WIDTH (macro definition) of file simd.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:688: warning: Member GMX_SIMD_HAVE_4NSIMD_UTIL_DOUBLE (macro definition) of file simd.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:699: warning: Member GMX_SIMD4N_DOUBLE_WIDTH (macro definition) of file simd.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:733: warning: Member GMX_SIMD_HAVE_4NSIMD_UTIL_REAL (macro definition) of file simd.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:742: warning: Member GMX_SIMD4N_REAL_WIDTH (macro definition) of file simd.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:652: warning: Member Simd4NFloat (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:698: warning: Member Simd4NDouble (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:741: warning: Member Simd4NReal (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:512: warning: Member load(const std::enable_if_t< std::is_arithmetic_v< T >, T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:518: warning: Member load(const AlignedArray< internal::SimdTraitsT< T >, N > &m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:536: warning: Member loadU(const std::enable_if_t< std::is_arithmetic_v< T >, T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:542: warning: Member loadU(const AlignedArray< internal::SimdTraitsT< T >, N > &m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:623: warning: Member load(const internal::Simd4TraitsT< T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:628: warning: Member loadU(const internal::Simd4TraitsT< T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:657: warning: Member loadUNDuplicate4(const float *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:661: warning: Member load4DuplicateN(const float *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:665: warning: Member loadU4NOffset(const float *f, int) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:703: warning: Member loadUNDuplicate4(const double *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:707: warning: Member load4DuplicateN(const double *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:711: warning: Member loadU4NOffset(const double *f, int) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:295: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:340: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:398: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:374: warning: Member c_simdBestPairAlignment (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:479: warning: Member SimdTraitsT (typedef) of namespace gmx::internal is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:618: warning: Member Simd4TraitsT (typedef) of namespace gmx::internal is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/tables/forcetable.h:79: warning: Member TableFormat (enumeration) of file forcetable.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/decidegpuusage.cpp:175: warning: Member decideWhetherToUseGpusForPmeFft(const TaskTarget pmeFftTarget) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/decidegpuusage.cpp:182: warning: Member canUseGpusForPme(const bool useGpuForNonbonded, const TaskTarget pmeTarget, const TaskTarget pmeFftTarget, const t_inputrec &inputrec, std::string *errorMessage) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/decidegpuusage.cpp:126: warning: Member c_gpuBuildSyclWithoutGpuFft (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/resourcedivision.cpp:123: warning: Member nthreads_omp_faster_Nehalem (variable) of file resourcedivision.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/resourcedivision.cpp:124: warning: Member nthreads_omp_faster_Intel_AVX (variable) of file resourcedivision.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/resourcedivision.cpp:125: warning: Member nthreads_omp_faster_AMD_Ryzen (variable) of file resourcedivision.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/resourcedivision.cpp:132: warning: Member nthreads_omp_faster_gpu_fac (variable) of file resourcedivision.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/resourcedivision.cpp:142: warning: Member nthreads_omp_mpi_ok_max (variable) of file resourcedivision.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/resourcedivision.cpp:143: warning: Member nthreads_omp_mpi_ok_min_cpu (variable) of file resourcedivision.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/resourcedivision.cpp:144: warning: Member nthreads_omp_mpi_ok_min_gpu (variable) of file resourcedivision.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/resourcedivision.cpp:145: warning: Member nthreads_omp_mpi_target_max (variable) of file resourcedivision.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/resourcedivision.cpp:149: warning: Member c_maxAutoTmpiRanksPerGpu (variable) of file resourcedivision.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include/gromacs/timing/instrumentation.h:216: warning: Member traceRangeStart(gmx_unused const char *rangeName, gmx_unused int rangeId) (function) of file instrumentation.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/timing/include/gromacs/timing/instrumentation.h:217: warning: Member traceSubRangeStart(gmx_unused const char *rangeName, gmx_unused int rangeId) (function) of file instrumentation.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/tests/trjconv.cpp:160: warning: Member DumpTestParameters (typedef) of namespace gmx::test::anonymous_namespace{trjconv.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/atoms.cpp:198: warning: Member SimulationParticleTestParameters (typedef) of file atoms.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/atoms.cpp:130: warning: Member checkParticleValue(TestReferenceChecker *checker, bool haveBState, const T &valueA, const T &valueB, const std::string &fieldName) (function) of file atoms.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/atoms.cpp:143: warning: Member checkParticleMiscInfo(TestReferenceChecker *checker, ParticleType type, gmx::Index resind, int atomnumber, const std::string &elem) (function) of file atoms.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/atoms.cpp:156: warning: Member checkParticle(TestReferenceChecker *checker, const SimulationParticle &particle) (function) of file atoms.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/atoms.cpp:201: warning: Member testParticleMassOneState (variable) of file atoms.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/atoms.cpp:202: warning: Member testParticleMassTwoState (variable) of file atoms.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/atoms.cpp:203: warning: Member testParticleChargeOneState (variable) of file atoms.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/atoms.cpp:204: warning: Member testParticleChargeTwoState (variable) of file atoms.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/atoms.cpp:205: warning: Member testParticleTypeValueOneState (variable) of file atoms.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/atoms.cpp:206: warning: Member testParticleTypeValueTwoState (variable) of file atoms.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:46: warning: Member def_bonded(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:51: warning: Member def_pair(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:56: warning: Member def_bondedt(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:61: warning: Member def_bondedtz(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:66: warning: Member def_angle(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:71: warning: Member def_dihedral(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:77: warning: Member def_dihedral_tabulated(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:82: warning: Member def_bond(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:87: warning: Member def_bondt(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:92: warning: Member def_bondnb(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:97: warning: Member def_vsite(const char *str, const char *lstr, int nra, int nrpa) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:102: warning: Member def_shk(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:107: warning: Member def_shkcb(const char *str, const char *lstr, int nra, int nrpa, int nrpb) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:112: warning: Member def_nb(const char *str, const char *lstr, int nra, int nrpa) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/ifunc.cpp:117: warning: Member def_nofc(const char *str, const char *lstr) (function) of file ifunc.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include/gromacs/topology/mtop_atomloops.h:212: warning: Member gmx_mtop_atomloop_block_t (typedef) of file mtop_atomloops.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include/gromacs/topology/mtop_atomloops.h:216: warning: Member gmx_mtop_atomloop_block_init(const gmx_mtop_t &mtop) (function) of file mtop_atomloops.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/include/gromacs/topology/mtop_atomloops.h:231: warning: Member gmx_mtop_atomloop_block_next(gmx_mtop_atomloop_block_t aloop, const t_atom **atom, int *nmol) (function) of file mtop_atomloops.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/symtab.cpp:332: warning: Member close_symtab(t_symtab gmx_unused *symtab) (function) of file symtab.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/index.cpp:72: warning: Member checkIndexGroup(TestReferenceChecker *checker, const IndexGroup &group) (function) of namespace gmx::test::anonymous_namespace{index.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/index.cpp:79: warning: Member checkBlocks(TestReferenceChecker *checker, ArrayRef< const IndexGroup > blocks) (function) of namespace gmx::test::anonymous_namespace{index.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/index.cpp:86: warning: Member compareBlocks(ArrayRef< const IndexGroup > one, ArrayRef< const IndexGroup > two) (function) of namespace gmx::test::anonymous_namespace{index.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/index.cpp:100: warning: Member checkFileMatch(TestReferenceChecker *checker, const std::string &fileName, const std::string &fullPath) (function) of namespace gmx::test::anonymous_namespace{index.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/dssp.cpp:76: warning: Member DsspTestParams (typedef) of namespace gmx::test::anonymous_namespace{dssp.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/gyrate.cpp:71: warning: Member GyrateTestParamsMerge (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/hbond.cpp:185: warning: Member c_maxHydrogensWithOxygen (variable) of namespace gmx::analysismodules::anonymous_namespace{hbond.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/hbond.cpp:187: warning: Member c_maxHydrogensWithNitrogen (variable) of namespace gmx::analysismodules::anonymous_namespace{hbond.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/hbond.cpp:189: warning: Member c_maxHydrogenBonds (variable) of namespace gmx::analysismodules::anonymous_namespace{hbond.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/hbond.cpp:71: warning: Member HbondTestParamsMerge (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/msd.cpp:99: warning: Member checkDiffusionCoefficientDataPoint(TestReferenceChecker *checker, const std::string &value) (function) of namespace gmx::test::anonymous_namespace{msd.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/scattering.cpp:71: warning: Member ScatteringTestDirectModeParams (typedef) of namespace gmx::test::anonymous_namespace{scattering.cpp} is not documented. warning: Included by graph for 'fatalerror.h' not generated, too many nodes (110), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/fatalerror.h:217: warning: Member gmx_call(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/fatalerror.h:218: warning: Member gmx_comm(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/fatalerror.h:219: warning: Member gmx_file(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/fatalerror.h:220: warning: Member gmx_impl(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/fatalerror.h:221: warning: Member gmx_incons(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/fatalerror.h:222: warning: Member gmx_input(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/fatalerror.h:223: warning: Member gmx_mem(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/fatalerror.h:224: warning: Member gmx_open(fn) (macro definition) of file fatalerror.h is not documented. warning: Included by graph for 'gmxmpi.h' not generated, too many nodes (62), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:64: warning: Member ivec[3] (typedef) of file iserializer.h is not documented. warning: Included by graph for 'logger.h' not generated, too many nodes (51), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:200: warning: Member toString(bool t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:204: warning: Member toString(int t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:208: warning: Member toString(int64_t t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:212: warning: Member toString(float t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:216: warning: Member toString(double t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:220: warning: Member toString(unsigned char t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:224: warning: Member toString(std::string t) (function) of namespace gmx is not documented. warning: Included by graph for 'textwriter.h' not generated, too many nodes (59), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/inmemoryserializer.cpp:80: warning: Member c_int16ValueSwapped (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/inmemoryserializer.cpp:81: warning: Member c_int32Value (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/inmemoryserializer.cpp:82: warning: Member c_int32ValueSwapped (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/inmemoryserializer.cpp:83: warning: Member c_int64Value (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/inmemoryserializer.cpp:84: warning: Member c_int64ValueSwapped (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/inmemoryserializer.cpp:86: warning: Member c_intAndFloat32 (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/inmemoryserializer.cpp:87: warning: Member c_intAndFloat64 (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/inmemoryserializer.cpp:89: warning: Member c_intAndFloat32Swapped (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/inmemoryserializer.cpp:90: warning: Member c_intAndFloat64Swapped (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:85: warning: Member EXPECT_EQ(0, reinterpret_cast< std::size_t >(p) &this->mask(a)) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:86: warning: Member deallocate(p, 1000) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:93: warning: Member v(10) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:94: warning: Member EXPECT_EQ(0, reinterpret_cast< std::size_t >(v.data()) &this->mask(v.get_allocator())) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:99: warning: Member for(std::size_t i=1000;i<=10000;i+=1000) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:125: warning: Member v1(1) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:127: warning: Member EXPECT_NE(data, nullptr) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:128: warning: Member v2(std::move(v1)) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:129: warning: Member EXPECT_EQ(data, v2.data()) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:82: warning: Member a (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:83: warning: Member p (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:126: warning: Member data (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/cstringutil.cpp:103: warning: Member testInplace(F f, const char *input, const char *expectedOutput) (function) of namespace gmx::test::anonymous_namespace{cstringutil.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/enumerationhelpers.cpp:183: warning: Member Unsuitable (enumeration) of namespace gmx::test::anonymous_namespace{enumerationhelpers.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/scope_guard.cpp:61: warning: Member DeleterType (typedef) of namespace gmx::test::anonymous_namespace{scope_guard.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/scope_guard.cpp:79: warning: Member deleterSetter(int object) (function) of namespace gmx::test::anonymous_namespace{scope_guard.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/scope_guard.cpp:105: warning: Member makeGuard(int object, DeleterType deleter) (function) of namespace gmx::test::anonymous_namespace{scope_guard.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/stringutil.cpp:132: warning: Member formatString(gmx_fmtstr const char *fmt,...) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found warning: Included by graph for 'gmxpre.h' not generated, too many nodes (792), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/domain_decomposition.cpp:127: warning: Member NonbondedFlavor (typedef) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/domain_decomposition.cpp:128: warning: Member UpdateFlavor (typedef) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/domain_decomposition.cpp:129: warning: Member PmeFlavor (typedef) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/domain_decomposition.cpp:83: warning: Member ElectrostaticsFlavor (enumeration) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/domain_decomposition.cpp:97: warning: Member CouplingFlavor (enumeration) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/domain_decomposition.cpp:112: warning: Member OffloadFlavor (enumeration) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/domain_decomposition.cpp:131: warning: Member SeparatePmeRankFlavor (enumeration) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/domain_decomposition.cpp:90: warning: Member enumValueToString(const ElectrostaticsFlavor enumValue) (function) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/domain_decomposition.cpp:104: warning: Member enumValueToString(const CouplingFlavor enumValue) (function) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/domain_decomposition.cpp:119: warning: Member enumValueToString(const OffloadFlavor enumValue) (function) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/domain_decomposition.cpp:209: warning: Member nameOfMdpFlavor(const MdpFlavor mdpFlavor) (function) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/domain_decomposition.cpp:216: warning: Member nameOfRuntimeFlavor(const RuntimeFlavor runtimeFlavor) (function) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/domain_decomposition.cpp:301: warning: Member sc_mdpFlavors (variable) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/domain_decomposition.cpp:397: warning: Member sc_offloadFlavors (variable) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/freeenergy.cpp:88: warning: Member ListOfInteractionsToTest (typedef) of namespace gmx::test::anonymous_namespace{freeenergy.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/freeenergy.cpp:89: warning: Member FreeEnergyReferenceTestParams (typedef) of namespace gmx::test::anonymous_namespace{freeenergy.cpp} is not documented. warning: Include graph for 'mimic.cpp' not generated, too many nodes (64), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Include graph for 'minimize.cpp' not generated, too many nodes (53), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/minimize.cpp:176: warning: Member minimizersToTest_g (variable) of namespace gmx::test::anonymous_namespace{minimize.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/minimize.cpp:178: warning: Member constrainedSystemsToTest_g (variable) of namespace gmx::test::anonymous_namespace{minimize.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/minimize.cpp:181: warning: Member minimizersToTestWithConstraints_g (variable) of namespace gmx::test::anonymous_namespace{minimize.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/multisim.cpp:186: warning: Member gmx_sumd_sim(int gmx_unused nr, double gmx_unused r[], const gmx_multisim_t gmx_unused *ms) (function) of file multisim.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/multisim.cpp:195: warning: Member gmx_sumf_sim(int gmx_unused nr, float gmx_unused r[], const gmx_multisim_t gmx_unused *ms) (function) of file multisim.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/multisim.cpp:204: warning: Member gmx_sumi_sim(int gmx_unused nr, int gmx_unused r[], const gmx_multisim_t gmx_unused *ms) (function) of file multisim.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/multisim.cpp:213: warning: Member gmx_sumli_sim(int gmx_unused nr, int64_t gmx_unused r[], const gmx_multisim_t gmx_unused *ms) (function) of file multisim.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/multisim.cpp:391: warning: Member multisim_int_all_are_equal(const gmx_multisim_t *ms, int64_t value) (function) of file multisim.cpp is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/normalmodes.cpp:171: warning: Member GTEST_ALLOW_UNINSTANTIATED_PARAMETERIZED_TEST(NormalModesTest) (function) of namespace gmx::test::anonymous_namespace{normalmodes.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/pmetest.cpp:116: warning: Member PmeTestParameters (typedef) of namespace gmx::test::anonymous_namespace{pmetest.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/pmetest.cpp:382: warning: Member c_reproducesEnergies (variable) of namespace gmx::test::anonymous_namespace{pmetest.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/pull.cpp:178: warning: Member isTransformationPullSetup(const std::string &pullSetupName) (function) of namespace gmx::test::anonymous_namespace{pull.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/pull.cpp:84: warning: Member c_mdpPullParams (variable) of namespace gmx::test::anonymous_namespace{pull.cpp} is not documented. warning: Include graph for 'rerun.cpp' not generated, too many nodes (66), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/rerun.cpp:126: warning: Member executeRerunTest(TestFileManager *fileManager, SimulationRunner *runner, const std::string &simulationName, int numWarningsToTolerate, const MdpFieldValues &mdpFieldValues, const EnergyTermsToCompare &energyTermsToCompare, const TrajectoryComparison &trajectoryComparison) (function) of namespace gmx::test::anonymous_namespace{rerun.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/simple_mdrun.cpp:196: warning: Member GTEST_ALLOW_UNINSTANTIATED_PARAMETERIZED_TEST(SimpleMdrunTest) (function) of namespace gmx::test::anonymous_namespace{simple_mdrun.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/simulatorcomparison.cpp:72: warning: Member runGrompp(SimulationRunner *runner, const std::vector< SimulationOptionTuple > &options) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/simulatorcomparison.cpp:85: warning: Member runMdrun(SimulationRunner *runner, const std::vector< SimulationOptionTuple > &options) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/simulatorcomparison.cpp:98: warning: Member compareEnergies(const std::string &edr1Name, const std::string &edr2Name, const EnergyTermsToCompare &energyTermsToCompare, const MaxNumFrames maxNumFrames) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/simulatorcomparison.cpp:119: warning: Member compareTrajectories(const std::string &trajectory1Name, const std::string &trajectory2Name, const TrajectoryComparison &trajectoryComparison) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/simulatorcomparison.h:62: warning: Member SimulationOptionTuple (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/simulatorcomparison.cpp:72: warning: Member runGrompp(SimulationRunner *runner, const std::vector< SimulationOptionTuple > &options) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/simulatorcomparison.cpp:85: warning: Member runMdrun(SimulationRunner *runner, const std::vector< SimulationOptionTuple > &options) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/simulatorcomparison.cpp:98: warning: Member compareEnergies(const std::string &edr1Name, const std::string &edr2Name, const EnergyTermsToCompare &energyTermsToCompare, const MaxNumFrames maxNumFrames) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/simulatorcomparison.cpp:119: warning: Member compareTrajectories(const std::string &trajectory1Name, const std::string &trajectory2Name, const TrajectoryComparison &trajectoryComparison) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/trajectorycomparison.cpp:425: warning: Member checkTrajectoryAgainstReferenceData(const std::string &trajectoryFilename, const TrajectoryComparison &trajectoryComparison, TestReferenceChecker *checker, MaxNumFrames maxNumFrames) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/trajectorycomparison.cpp:425: warning: Member checkTrajectoryAgainstReferenceData(const std::string &trajectoryFilename, const TrajectoryComparison &trajectoryComparison, TestReferenceChecker *checker, MaxNumFrames maxNumFrames) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/virtualsites.cpp:107: warning: Member VirtualSiteTestParams (typedef) of namespace gmx::test::anonymous_namespace{virtualsites.cpp} is not documented. warning: Included by graph for 'cmdlinetest.h' not generated, too many nodes (98), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'refdata.h' not generated, too many nodes (113), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'testasserts.h' not generated, too many nodes (200), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'testfilemanager.h' not generated, too many nodes (90), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2025.0/src/testutils/refdata_xml.cpp:102: warning: Member getCDataChildNode(XMLNodePtr node) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/refdata_xml.cpp:112: warning: Member hasCDataContent(XMLNodePtr node) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/refdata_xml.cpp:340: warning: Member createElementAndContents(XMLElementPtr parentElement, const ReferenceDataEntry &entry) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/refdata_xml.cpp:253: warning: Member setIdAttribute(XMLElementPtr element, const std::string &id) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/refdata_xml.cpp:261: warning: Member createElement(XMLElementPtr parentElement, const ReferenceDataEntry &entry) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/refdata_xml.cpp:269: warning: Member createChildElements(XMLElementPtr parentElement, const ReferenceDataEntry &entry) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/refdata_xml.cpp:311: warning: Member createElementContents(XMLElementPtr element, const ReferenceDataEntry &entry) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/refdata_xml.cpp:346: warning: Member createRootElement(XMLDocumentPtr document) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::initOptions()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::optionsFinished()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::initAnalysis()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::initAfterFirstFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::finishAnalysis()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::writeOutput()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::startFrames()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::startFrames()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::finishFrames()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::finishFrames()' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/impl_reference/impl_reference_util_float.h:151: warning: unable to resolve reference to 'c_simdBestPairAlignmentFloat' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/impl_reference/impl_reference_util_float.h:152: warning: unable to resolve reference to 'c_simdBestPairAlignmentDouble' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/impl_reference/impl_reference_util_double.h:171: warning: @copydetails or @copydoc target 'c_simdBestPairAlignmentFloat' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:200: warning: Member toString(bool t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:204: warning: Member toString(int t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:208: warning: Member toString(int64_t t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:212: warning: Member toString(float t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:216: warning: Member toString(double t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:220: warning: Member toString(unsigned char t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:224: warning: Member toString(std::string t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:119: warning: @copydetails or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:184: warning: @copydetails or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:100: warning: @copydetails or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:144: warning: @copydetails or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:119: warning: @copydetails or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:113: warning: @copydetails or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/errorcodes.h:111: warning: explicit link request to 'eeUnknownError' could not be resolved /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:179: warning: @copydetails or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:402: warning: @copydetails or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:419: warning: @copydetails or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:83: warning: @copydetails or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:189: warning: @copydetails or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/selection/selection.h:36: warning: unable to resolve reference to 'sm_insolidangle' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/constraint_gpu_helpers.h:55: warning: Member AtomsAdjacencyListElement(int indexOfSecondConstrainedAtom, int indexOfConstraint, int signFactor) (function) of struct AtomsAdjacencyListElement is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/dlbtiming.h:215: warning: Member impl_ (variable) of class BalanceRegion is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_internal.h:115: warning: Member GMX_DISALLOW_COPY_MOVE_AND_ASSIGN(bonded_threading_t) (function) of struct bonded_threading_t is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/device_information.h:184: warning: Member gpuAwareMpiStatus (variable) of struct DeviceInformation is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/commrec.h:68: warning: Member bUse (variable) of struct gmx_nodecomm_t is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/commrec.h:69: warning: Member comm_intra (variable) of struct gmx_nodecomm_t is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/commrec.h:70: warning: Member rank_intra (variable) of struct gmx_nodecomm_t is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/commrec.h:71: warning: Member comm_inter (variable) of struct gmx_nodecomm_t is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_pp_communication.h:121: warning: Member ewaldcoeff_q (variable) of struct gmx_pme_comm_n_box_t is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_pp_communication.h:122: warning: Member ewaldcoeff_lj (variable) of struct gmx_pme_comm_n_box_t is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_pp_communication.h:137: warning: Member vir_lj (variable) of struct gmx_pme_comm_vir_ene_t is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_pp_communication.h:138: warning: Member energy_q (variable) of struct gmx_pme_comm_vir_ene_t is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_pp_communication.h:139: warning: Member energy_lj (variable) of struct gmx_pme_comm_vir_ene_t is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_pp_communication.h:140: warning: Member dvdlambda_q (variable) of struct gmx_pme_comm_vir_ene_t is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_pp_communication.h:141: warning: Member dvdlambda_lj (variable) of struct gmx_pme_comm_vir_ene_t is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_only.cpp:106: warning: Member gmx_pme_pp(MPI_Comm simulationCommunicator, std::vector< PpRanks > &&ppRanks) (function) of struct gmx_pme_pp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_only.cpp:113: warning: Member chargeB (variable) of struct gmx_pme_pp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_only.cpp:114: warning: Member sqrt_c6A (variable) of struct gmx_pme_pp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_only.cpp:115: warning: Member sqrt_c6B (variable) of struct gmx_pme_pp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_only.cpp:116: warning: Member sigmaA (variable) of struct gmx_pme_pp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_only.cpp:117: warning: Member sigmaB (variable) of struct gmx_pme_pp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_only.cpp:124: warning: Member stat (variable) of struct gmx_pme_pp is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/replicaexchange.cpp:158: warning: Member cyclic (variable) of struct gmx_repl_ex is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/replicaexchange.cpp:159: warning: Member order (variable) of struct gmx_repl_ex is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/replicaexchange.cpp:160: warning: Member tmpswap (variable) of struct gmx_repl_ex is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/replicaexchange.cpp:161: warning: Member incycle (variable) of struct gmx_repl_ex is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/replicaexchange.cpp:162: warning: Member bEx (variable) of struct gmx_repl_ex is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/replicaexchange.cpp:168: warning: Member Epot (variable) of struct gmx_repl_ex is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/replicaexchange.cpp:169: warning: Member beta (variable) of struct gmx_repl_ex is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/replicaexchange.cpp:170: warning: Member Vol (variable) of struct gmx_repl_ex is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/replicaexchange.cpp:171: warning: Member de (variable) of struct gmx_repl_ex is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/grompp_impl.h:69: warning: Member aj() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/grompp_impl.h:70: warning: Member ak() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/grompp_impl.h:71: warning: Member al() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/grompp_impl.h:72: warning: Member am() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/grompp_impl.h:74: warning: Member c0() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/grompp_impl.h:75: warning: Member c1() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/grompp_impl.h:76: warning: Member c2() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/grompp_impl.h:78: warning: Member interactionTypeName() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_types_host.h:263: warning: Member useNvshmem (variable) of struct PmeGpu is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_types_host.h:265: warning: Member nvshmemParams (variable) of struct PmeGpu is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:175: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(PmeGpuProgramImpl) (function) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:114: warning: Member splineKernelSingle (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:115: warning: Member splineKernelThPerAtom4Single (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:116: warning: Member spreadKernelSingle (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:117: warning: Member spreadKernelThPerAtom4Single (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:118: warning: Member splineAndSpreadKernelSingle (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:119: warning: Member splineAndSpreadKernelThPerAtom4Single (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:120: warning: Member splineAndSpreadKernelWriteSplinesSingle (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:121: warning: Member splineAndSpreadKernelWriteSplinesThPerAtom4Single (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:122: warning: Member splineKernelDual (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:123: warning: Member splineKernelThPerAtom4Dual (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:124: warning: Member spreadKernelDual (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:125: warning: Member spreadKernelThPerAtom4Dual (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:126: warning: Member splineAndSpreadKernelDual (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:127: warning: Member splineAndSpreadKernelThPerAtom4Dual (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:128: warning: Member splineAndSpreadKernelWriteSplinesDual (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:129: warning: Member splineAndSpreadKernelWriteSplinesThPerAtom4Dual (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:142: warning: Member gatherKernelSingle (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:143: warning: Member gatherKernelThPerAtom4Single (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:144: warning: Member gatherKernelReadSplinesSingle (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:145: warning: Member gatherKernelReadSplinesThPerAtom4Single (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:146: warning: Member gatherKernelDual (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:147: warning: Member gatherKernelThPerAtom4Dual (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:148: warning: Member gatherKernelReadSplinesDual (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:149: warning: Member gatherKernelReadSplinesThPerAtom4Dual (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:159: warning: Member solveYZXKernelA (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:160: warning: Member solveXYZKernelA (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:161: warning: Member solveYZXEnergyKernelA (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:162: warning: Member solveXYZEnergyKernelA (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:163: warning: Member solveYZXKernelB (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:164: warning: Member solveXYZKernelB (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:165: warning: Member solveYZXEnergyKernelB (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:166: warning: Member solveXYZEnergyKernelB (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_program_impl.h:168: warning: Member nvshmemSignalKern (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/tables/forcetable.h:88: warning: Member t_forcetable(TableInteraction interaction, TableFormat format) (function) of struct t_forcetable is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:453: warning: Member fudgeQQ (variable) of struct t_idef is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:459: warning: Member iparams_fbposres (variable) of struct t_idef is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:327: warning: Member iatoms (variable) of struct t_ilist is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:328: warning: Member nalloc (variable) of struct t_ilist is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/ifunc.h:105: warning: Member nrfpA (variable) of struct t_interaction_function is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:71: warning: Member bham (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:75: warning: Member harmonic (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:79: warning: Member linangle (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:83: warning: Member restraint (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:87: warning: Member cubic (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:91: warning: Member fene (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:95: warning: Member cross_bb (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:99: warning: Member cross_ba (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:103: warning: Member u_b (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:107: warning: Member qangle (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:111: warning: Member polarize (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:115: warning: Member anharm_polarize (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:119: warning: Member wpol (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:123: warning: Member thole (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:127: warning: Member lj (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:131: warning: Member lj14 (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:135: warning: Member ljc14 (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:139: warning: Member ljcnb (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:155: warning: Member constr (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:168: warning: Member morse (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:172: warning: Member posres (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:177: warning: Member fbposres (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:181: warning: Member rbdihs (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:185: warning: Member cbtdihs (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:189: warning: Member vsite (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:194: warning: Member vsiten (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:200: warning: Member disres (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:204: warning: Member dihres (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:209: warning: Member orires (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:215: warning: Member tab (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:219: warning: Member cmap (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/topology/idef.h:223: warning: Member generic (variable) of union t_iparams is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/fcdata.h:216: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(t_oriresdata) (function) of struct t_oriresdata is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_wham.cpp:227: warning: Member fnTpr (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_wham.cpp:227: warning: Member fnPullf (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_wham.cpp:227: warning: Member fnCoordSel (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_wham.cpp:229: warning: Member bPullf (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_wham.cpp:230: warning: Member tmin (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_wham.cpp:230: warning: Member tmax (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_wham.cpp:242: warning: Member min (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_wham.cpp:242: warning: Member max (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_wham.cpp:242: warning: Member dz (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_wham.cpp:243: warning: Member Temperature (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_wham.cpp:259: warning: Member bBoundsOnly (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_wham.cpp:270: warning: Member bTauIntGiven (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_wham.cpp:281: warning: Member bHistEq (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_wham.cpp:307: warning: Member bsMethod (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_wham.cpp:310: warning: Member tauBootStrap (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_wham.cpp:314: warning: Member histBootStrapBlockLength (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_wham.cpp:320: warning: Member bs_verbose (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_wham.cpp:326: warning: Member bTab (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_wham.cpp:327: warning: Member tabX (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_wham.cpp:327: warning: Member tabY (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_wham.cpp:327: warning: Member tabMin (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_wham.cpp:327: warning: Member tabMax (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_wham.cpp:327: warning: Member tabDz (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxana/gmx_wham.cpp:328: warning: Member tabNbins (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/vsite_parm.cpp:99: warning: Member aj() const (function) of class VsiteBondedInteraction is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/vsite_parm.cpp:100: warning: Member ak() const (function) of class VsiteBondedInteraction is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/vsite_parm.cpp:101: warning: Member al() const (function) of class VsiteBondedInteraction is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/vsite_parm.cpp:103: warning: Member parameterValue() const (function) of class VsiteBondedInteraction is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/warninp.h:71: warning: Member WarningHandler(bool allowWarnings, int maxNumberWarnings) (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/warninp.h:89: warning: Member errorCount() const (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/warninp.h:91: warning: Member warningCount() const (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/warninp.h:93: warning: Member noteCount() const (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/warninp.h:95: warning: Member maxWarningCount() const (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/bonded.cpp:3057: warning: Member CmapForceStructure (typedef) of namespace anonymous_namespace{bonded.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/bonded.cpp:3059: warning: Member processCmapForceComponent(const gmx::RVec a, const gmx::RVec b, const real df, const real gaa, const real fga, const real gbb, const real hgb, const int dim) (function) of namespace anonymous_namespace{bonded.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/bonded.cpp:3075: warning: Member applyCmapForceComponent(const gmx::RVec forceComponent) (function) of namespace anonymous_namespace{bonded.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/bonded.cpp:3086: warning: Member accumulateCmapForces(const rvec x[], rvec4 f[], rvec fshift[], const t_pbc *pbc, const gmx::RVec r_ij, const gmx::RVec r_kj, const gmx::RVec r_kl, const gmx::RVec a, const gmx::RVec b, gmx::RVec h, const real ra2r, const real rb2r, const real rgr, const real rg, const int ai, const int aj, const int ak, const int al, const real df, const int t1, const int t2) (function) of namespace anonymous_namespace{bonded.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/device_management_common.cpp:272: warning: Member operator()(const std::array< std::byte, N > &a) const noexcept (function) of struct anonymous_namespace{device_management_common.cpp}::HashAnArray is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/domain_decomposition.cpp:127: warning: Member NonbondedFlavor (typedef) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/domain_decomposition.cpp:128: warning: Member UpdateFlavor (typedef) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/domain_decomposition.cpp:129: warning: Member PmeFlavor (typedef) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/domain_decomposition.cpp:83: warning: Member ElectrostaticsFlavor (enumeration) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/domain_decomposition.cpp:97: warning: Member CouplingFlavor (enumeration) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/domain_decomposition.cpp:112: warning: Member OffloadFlavor (enumeration) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/domain_decomposition.cpp:131: warning: Member SeparatePmeRankFlavor (enumeration) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/domain_decomposition.cpp:90: warning: Member enumValueToString(const ElectrostaticsFlavor enumValue) (function) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/domain_decomposition.cpp:104: warning: Member enumValueToString(const CouplingFlavor enumValue) (function) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/domain_decomposition.cpp:119: warning: Member enumValueToString(const OffloadFlavor enumValue) (function) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/domain_decomposition.cpp:209: warning: Member nameOfMdpFlavor(const MdpFlavor mdpFlavor) (function) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/domain_decomposition.cpp:216: warning: Member nameOfRuntimeFlavor(const RuntimeFlavor runtimeFlavor) (function) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/domain_decomposition.cpp:301: warning: Member sc_mdpFlavors (variable) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/domain_decomposition.cpp:397: warning: Member sc_offloadFlavors (variable) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/minimize.cpp:946: warning: Member mdModulesNotifiers (variable) of class anonymous_namespace{minimize.cpp}::EnergyEvaluator is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:147: warning: Member AspartateStates (enumeration) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:169: warning: Member GlutamateStates (enumeration) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:191: warning: Member GlutamineStates (enumeration) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:213: warning: Member LysineStates (enumeration) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:234: warning: Member ArginineStates (enumeration) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:1300: warning: Member ChainSeparationType (enumeration) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:1562: warning: Member VSitesType (enumeration) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:1573: warning: Member WaterType (enumeration) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:1589: warning: Member MergeType (enumeration) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:127: warning: Member res2bb_notermini(const std::string &name, gmx::ArrayRef< const RtpRename > rr) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:139: warning: Member enumValueToLongString(HistidineStates enumValue) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:154: warning: Member enumValueToString(AspartateStates enumValue) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:161: warning: Member enumValueToLongString(AspartateStates enumValue) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:176: warning: Member enumValueToString(GlutamateStates enumValue) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:183: warning: Member enumValueToLongString(GlutamateStates enumValue) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:198: warning: Member enumValueToString(GlutamineStates enumValue) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:205: warning: Member enumValueToLongString(GlutamineStates enumValue) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:220: warning: Member enumValueToString(LysineStates enumValue) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:226: warning: Member enumValueToLongString(LysineStates enumValue) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:241: warning: Member enumValueToString(ArginineStates enumValue) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:248: warning: Member enumValueToLongString(ArginineStates enumValue) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:257: warning: Member select_res(int resnr, const char *title, gmx::ArrayRef< const RtpRename > rr) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:279: warning: Member get_asptp(int resnr, gmx::ArrayRef< const RtpRename > rr) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:284: warning: Member get_glutp(int resnr, gmx::ArrayRef< const RtpRename > rr) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:289: warning: Member get_glntp(int resnr, gmx::ArrayRef< const RtpRename > rr) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:294: warning: Member get_lystp(int resnr, gmx::ArrayRef< const RtpRename > rr) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:299: warning: Member get_argtp(int resnr, gmx::ArrayRef< const RtpRename > rr) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:304: warning: Member get_histp(int resnr, gmx::ArrayRef< const RtpRename > rr) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:309: warning: Member read_rtprename(const char *fname, FILE *fp, std::vector< RtpRename > *rtprename) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:367: warning: Member search_resrename(gmx::ArrayRef< const RtpRename > rr, const char *name, bool bStart, bool bEnd, bool bCompareFFRTPname) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:413: warning: Member rename_resrtp(t_atoms *pdba, int nterpairs, gmx::ArrayRef< const int > r_start, gmx::ArrayRef< const int > r_end, gmx::ArrayRef< const RtpRename > rr, t_symtab *symtab, bool bVerbose, const gmx::MDLogger &logger) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:471: warning: Member pdbres_to_gmxrtp(t_atoms *pdba) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:484: warning: Member rename_pdbres(t_atoms *pdba, const char *oldnm, const char *newnm, bool bFullCompare, t_symtab *symtab) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:579: warning: Member check_occupancy(t_atoms *atoms, const char *filename, bool bVerbose, const gmx::MDLogger &logger) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:642: warning: Member write_posres(const char *fn, t_atoms *pdba, real fc) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:671: warning: Member read_pdball(const char *inf, bool bOutput, const char *outf, char **title, t_atoms *atoms, rvec **x, PbcType *pbcType, matrix box, bool bRemoveH, t_symtab *symtab, const ResidueTypeMap &residueTypeMap, const char *watres, AtomProperties *aps, bool bVerbose) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:745: warning: Member process_chain(const gmx::MDLogger &logger, t_atoms *pdba, gmx::ArrayRef< gmx::RVec > x, bool bTrpU, bool bPheU, bool bTyrU, bool bLysMan, bool bAspMan, bool bGluMan, bool bHisMan, bool bArgMan, bool bGlnMan, real angle, real distance, t_symtab *symtab, gmx::ArrayRef< const RtpRename > rr) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:835: warning: Member pdbicomp(const t_pdbindex &a, const t_pdbindex &b) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:853: warning: Member sort_pdbatoms(gmx::ArrayRef< const PreprocessResidue > restp_chain, int natoms, t_atoms **pdbaptr, t_atoms **newPdbAtoms, std::vector< gmx::RVec > *x) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:939: warning: Member remove_duplicate_atoms(t_atoms *pdba, gmx::ArrayRef< gmx::RVec > x, bool bVerbose, const gmx::MDLogger &logger) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:1011: warning: Member checkResidueTypeSanity(t_atoms *pdba, int r0, int r1, const ResidueTypeMap &residueTypeMap) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:1085: warning: Member find_nc_ter(t_atoms *pdba, int r0, int r1, int *r_start, int *r_end, const ResidueTypeMap &residueTypeMap, const gmx::MDLogger &logger) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:1320: warning: Member modify_chain_numbers(t_atoms *pdba, ChainSeparationType chainSeparation, const gmx::MDLogger &logger) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:1444: warning: Member checkChainCyclicity(t_atoms *pdba, rvec *pdbx, int start_ter, int end_ter, gmx::ArrayRef< const PreprocessResidue > rtpFFDB, gmx::ArrayRef< const RtpRename > rr, real long_bond_dist_, real short_bond_dist_) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:1309: warning: Member c_chainSeparationTypeNames (variable) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:1312: warning: Member c_chainSeparationTypeNotificationMessages (variable) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:1569: warning: Member c_vsitesTypeNames (variable) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:1585: warning: Member c_waterTypeNames (variable) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/pdb2gmx.cpp:1596: warning: Member c_mergeTypeNames (variable) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_calculate_splines_sycl.h:74: warning: Member assertIsFinite(Float3 gmx_unused arg) (function) of namespace anonymous_namespace{pme_gpu_calculate_splines_sycl.h} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_gpu_calculate_splines_sycl.h:82: warning: Member assertIsFinite(T gmx_unused arg) (function) of namespace anonymous_namespace{pme_gpu_calculate_splines_sycl.h} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/state.cpp:95: warning: Member c_currentVersion (variable) of namespace anonymous_namespace{state.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/state.cpp:200: warning: Member c_dfHistoryCurrentVersion (variable) of namespace anonymous_namespace{state.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/h5md.h:55: warning: Member hid_t (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/h5md.h:57: warning: Member herr_t (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:875: warning: Member mode (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:435: warning: Member GpuPairlistByLocality (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:77: warning: Member FCiFloat3 (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/optionflags.h:107: warning: explicit link request to 'OptionFlag' could not be resolved /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/selection/selectionenums.h:82: warning: explicit link request to 'SelectionFlag' could not be resolved /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/oclraii.h:131: warning: Member ClCommandQueue (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/oclraii.h:132: warning: Member ClProgram (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/oclraii.h:133: warning: Member ClKernel (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/h5md.h:59: warning: Member H5mdFileMode (enumeration) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/gpuhaloexchange_impl_gpu_sycl.cpp:63: warning: Member packSendBufKernel(Float3 *__restrict__ gm_dataPacked, const Float3 *__restrict__ gm_data, const int *__restrict__ gm_map, int mapSize, Float3 coordinateShift) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/gpuhaloexchange_impl_gpu_sycl.cpp:119: warning: Member launchPackSendBufKernel(const DeviceStream &deviceStream, int xSendSize, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/gpuhaloexchange_impl_gpu_sycl.cpp:134: warning: Member launchUnpackRecvBufKernel(const DeviceStream &deviceStream, int fRecvSize, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_cufftmp.cpp:102: warning: Member handleCufftError(cufftResult_t status, const char *msg) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_sycl_vkfft.cpp:258: warning: Member launchVkFft(const DeviceBuffer< float > &realGrid, const DeviceBuffer< float > &complexGrid, NativeQueue queue, gmx_fft_direction fftDirection, VkFFTApplication *application, VkFFTLaunchParams *launchParams) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:94: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:99: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:120: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:125: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/h5md_low_level_util.h:63: warning: Member throwUponH5mdError(const bool errorExists, const std::string &message) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/massrepartitioning.cpp:57: warning: Member smallestAtomMass(const gmx_mtop_t &mtop) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/simd_support.cpp:70: warning: Member simdString(SimdType s) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/simd_support.cpp:199: warning: Member simdCompiled() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces_gpu_impl_gpu.cpp:67: warning: Member chooseSubGroupSizeForDevice(const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:878: warning: Member bondedKernel(sycl::handler &cgh, const BondedGpuKernelParameters &kernelParams, const DeviceBuffer< t_iatom > gm_iatoms_[numFTypesOnGpu], float *__restrict__ gm_vTot, const t_iparams *__restrict__ gm_forceParams_, const sycl::float4 *__restrict__ gm_xq_, Float3 *__restrict__ gm_f_, Float3 *__restrict__ gm_fShift_) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:1498: warning: Member do_force(FILE *log, const t_commrec *cr, const gmx_multisim_t *ms, const t_inputrec &inputrec, const MDModulesNotifiers &mdModulesNotifiers, Awh *awh, gmx_enfrot *enforcedRotation, ImdSession *imdSession, pull_t *pull_work, int64_t step, t_nrnb *nrnb, gmx_wallcycle *wcycle, const gmx_localtop_t *top, const matrix box, ArrayRefWithPadding< RVec > coordinates, ArrayRef< RVec > velocities, const history_t *hist, ForceBuffersView *force, tensor vir_force, const t_mdatoms *mdatoms, gmx_enerdata_t *enerd, ArrayRef< const real > lambda, t_forcerec *fr, const MdrunScheduleWorkload &runScheduleWork, VirtualSitesHandler *vsite, rvec mu_tot, double t, gmx_edsam *ed, CpuPpLongRangeNonbondeds *longRangeNonbondeds, const DDBalanceRegionHandler &ddBalanceRegionHandler) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/leapfrog_gpu_internal_sycl.cpp:170: warning: unable to resolve reference to 'NumTempScaleValues' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/lincs_gpu_internal_sycl.cpp:452: warning: Member launchLincsKernel(const DeviceStream &deviceStream, const int numConstraintsThreads, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:163: warning: Member sum_forces(ArrayRef< RVec > f, ArrayRef< const RVec > forceToAdd) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:176: warning: Member calc_virial(int start, int homenr, const rvec x[], const ForceWithShiftForces &forceWithShiftForces, tensor vir_part, const matrix box, t_nrnb *nrnb, const t_forcerec *fr, PbcType pbcType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:205: warning: Member pull_potential_wrapper(const t_commrec *cr, const t_inputrec &ir, const matrix box, ArrayRef< const RVec > x, const t_mdatoms *mdatoms, gmx_enerdata_t *enerd, pull_t *pull_work, const real *lambda, double t, gmx_wallcycle *wcycle) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:238: warning: Member pme_receive_force_ener(t_forcerec *fr, const t_commrec *cr, ForceWithVirial *forceWithVirial, gmx_enerdata_t *enerd, bool useGpuPmePpComms, bool receivePmeForceToGpu, gmx_wallcycle *wcycle) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:280: warning: Member print_large_forces(FILE *fp, const t_mdatoms *md, const t_commrec *cr, int64_t step, real forceTolerance, ArrayRef< const RVec > x, ArrayRef< const RVec > f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:429: warning: Member do_nb_verlet(t_forcerec *fr, const interaction_const_t *ic, gmx_enerdata_t *enerd, const StepWorkload &stepWork, const InteractionLocality ilocality, const int clearF, const int64_t step, t_nrnb *nrnb, gmx_wallcycle *wcycle) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:476: warning: Member clearRVecs(ArrayRef< RVec > v, const bool useOpenmpThreading) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:942: warning: Member launchGpuEndOfStepTasks(nonbonded_verlet_t *nbv, ListedForcesGpu *listedForcesGpu, gmx_pme_t *pmedata, gmx_enerdata_t *enerd, const MdrunScheduleWorkload &runScheduleWork, int64_t step, gmx_wallcycle *wcycle) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:1108: warning: Member reduceAndUpdateMuTot(DipoleData *dipoleData, const t_commrec *cr, const bool haveFreeEnergy, ArrayRef< const real > lambda, rvec muTotal, const DDBalanceRegionHandler &ddBalanceRegionHandler) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/propagator.cpp:759: warning: Member hasStartVelocityScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/propagator.cpp:768: warning: Member hasEndVelocityScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/propagator.cpp:775: warning: Member hasPositionScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/propagator.cpp:781: warning: Member hasParrinelloRahmanScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/propagator.cpp:907: warning: Member getConnection(Propagator< integrationStage > *propagator, const PropagatorTag &propagatorTag) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/pullelement.cpp:125: warning: Member doCheckpointData(CheckpointData< operation > *checkpointData, ArrayRef< double > previousStepCom) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:149: warning: Member copy_int_to_nbat_int(const int *a, int na, int na_round, const int *in, int fill, int *innb) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:289: warning: Member copyRVecToNbatXYZReal(int numAtoms, const rvec *x, real *xnb, int a0) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:330: warning: Member set_lj_parameter_data(nbnxn_atomdata_t::Params *params, gmx_bool bSIMD) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:472: warning: Member nbnxn_atomdata_params_init(const MDLogger &mdlog, nbnxn_atomdata_t::Params *params, const NbnxmKernelType kernelType, const std::optional< LJCombinationRule > &ljCombinationRule, const LJCombinationRule pmeLJCombinationRule, ArrayRef< const real > nbfp, const bool addFillerAtomType, const int numEnergyGroups) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:749: warning: Member copy_lj_to_nbat_lj_comb(ArrayRef< const real > ljparam_type, const int *type, int na, real *ljparam_at) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:766: warning: Member nbnxn_atomdata_set_atomtypes(nbnxn_atomdata_t::Params *params, const GridSet &gridSet, ArrayRef< const int > atomTypes) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:793: warning: Member nbnxn_atomdata_set_ljcombparams(nbnxn_atomdata_t::Params *params, const int XFormat, const GridSet &gridSet) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:838: warning: Member nbnxn_atomdata_set_charges(nbnxn_atomdata_t *nbat, const GridSet &gridSet, ArrayRef< const real > charges) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:896: warning: Member nbnxn_atomdata_mask_fep(nbnxn_atomdata_t *nbat, const GridSet &gridSet) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:938: warning: Member nbnxn_atomdata_set_energygroups(const GridSet &gridSet, ArrayRef< const int32_t > atomInfo, EnergyGroupsPerCluster *energyGroupsPerCluster) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:998: warning: Member getGridRange(const GridSet &gridSet, const AtomLocality locality) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:1028: warning: Member copyXToNbatXForGridPart(const Grid &grid, const Range< int > &columnRange, const rvec *coordinates, nbnxn_atomdata_t *nbat) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:1061: warning: Member copyXToNbatXForGridPartIndexed(const Grid &grid, const Range< int > &columnRange, ArrayRef< const int > atomIndices, const rvec *coordinates, nbnxn_atomdata_t *nbat) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:1139: warning: Member nbnxn_atomdata_clear_reals(ArrayRef< real > dest, int i0, int i1) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:1147: warning: Member nbnxn_atomdata_reduce_reals(real *gmx_restrict dest, gmx_bool bDestSet, const real **gmx_restrict src, int nsrc, int i0, int i1) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:1179: warning: Member nbnxn_atomdata_reduce_reals_simd(real gmx_unused *gmx_restrict dest, gmx_bool gmx_unused bDestSet, const gmx_unused real **gmx_restrict src, int gmx_unused nsrc, int gmx_unused i0, int gmx_unused i1) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:1223: warning: Member addNbatFXYZToFPart(const nbnxn_atomdata_output_t &out, const int a0, const int a1, const int *cellIndices, ArrayRef< RVec > forces) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.cpp:1363: warning: Member getAtomRange(const AtomLocality locality, const GridSet &gridSet) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/grid.cpp:151: warning: Member getMaxNumCells(const Grid::Geometry &geometry, const int numAtoms, const int numColumns) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/gridset.cpp:171: warning: Member getGridOffset(ArrayRef< const Grid > grids, int gridIndex) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:1320: warning: Member launchNbnxmKernelHelper(NbnxmGpu *nb, const StepWorkload &stepWork, InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:61: warning: Member launchNbnxmKernelHelper< false, false, false >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:62: warning: Member launchNbnxmKernelHelper< false, false, true >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:63: warning: Member launchNbnxmKernelHelper< false, true, true >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:64: warning: Member launchNbnxmKernelHelper< false, true, false >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:66: warning: Member launchNbnxmKernelHelper< true, false, false >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:67: warning: Member launchNbnxmKernelHelper< true, false, true >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:68: warning: Member launchNbnxmKernelHelper< true, true, true >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel.cpp:69: warning: Member launchNbnxmKernelHelper< true, true, false >(NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_body.h:119: warning: Member fetchNbfpC6C12(const float2 *nbfpComb, int type) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_utils.h:85: warning: Member nb_any_internal(int predicate, int widx) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_utils.h:108: warning: Member numberOfKernelBlocksSanityCheck(int numSci, const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_utils.h:125: warning: Member requiredSharedMemorySize() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kerneldispatch.cpp:375: warning: Member accountFlops(t_nrnb *nrnb, const PairlistSet &pairlistSet, const nonbonded_verlet_t &nbv, const interaction_const_t &ic, const gmx::StepWorkload &stepWork) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_prune.cpp:148: warning: Member nbnxmRefPruneKernel< NbnxmKernelType::Cpu4x4_PlainC >(NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, ArrayRef< const RVec > shiftvec, real rlistInner) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_prune.cpp:153: warning: Member nbnxmRefPruneKernel< NbnxmKernelType::Cpu1x1_PlainC >(NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, ArrayRef< const RVec > shiftvec, real rlistInner) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:62: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:74: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:86: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:98: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:110: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:122: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:134: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:146: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:158: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:170: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:182: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:194: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:206: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:218: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:230: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:242: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:254: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:266: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:278: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:290: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:302: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:314: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:326: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:338: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:350: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:362: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:374: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:386: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:398: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:410: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:423: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:435: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:447: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:459: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:471: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:483: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:495: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:507: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:519: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:531: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:543: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:555: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:567: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:579: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:591: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:603: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:615: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:627: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:639: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:651: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:663: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:675: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:687: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:699: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:711: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:723: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:735: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:747: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:759: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:771: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:784: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:796: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:808: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:820: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:832: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:844: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:856: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:868: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:880: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:892: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:904: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:916: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:928: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:940: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:952: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:964: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:976: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:988: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1000: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1012: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1024: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1036: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1048: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1060: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1072: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1084: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1096: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1108: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1120: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1132: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:62: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:74: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:86: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:98: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:110: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:122: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:134: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:146: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:158: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:170: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:182: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:194: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:206: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:218: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:230: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:242: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:254: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:266: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:278: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:290: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:302: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:314: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:326: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:338: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:350: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:362: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:374: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:386: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:398: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:410: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:423: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:435: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:447: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:459: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:471: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:483: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:495: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:507: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:519: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:531: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:543: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:555: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:567: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:579: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:591: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:603: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:615: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:627: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:639: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:651: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:663: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:675: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:687: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:699: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:711: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:723: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:735: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:747: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:759: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:771: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:784: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:796: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:808: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:820: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:832: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:844: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:856: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:868: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:880: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:892: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:904: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:916: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:928: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:940: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:952: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:964: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:976: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:988: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1000: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1012: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1024: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1036: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1048: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1060: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1072: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1084: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1096: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1108: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1120: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1132: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:122: warning: Member isGpuKernelType(const NbnxmKernelType kernelType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_setup.cpp:261: warning: Member nbnxmKernelTypeToName(NbnxmKernelType kernelType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:149: warning: Member isGpuSpecificPairlist(const PairlistType pairlistType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:269: warning: Member sc_gpuPairlistHasSplitJCluster(const PairlistType pairlistType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_buffer_ops.cpp:65: warning: Member nbnxn_gpu_x_to_nbat_x(const Grid &grid, NbnxmGpu *nb, DeviceBuffer< RVec > d_x, GpuEventSynchronizer *xReadyOnDevice, const AtomLocality locality, int gridId, int numColumnsMax, bool mustInsertNonLocalDependency) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:95: warning: Member init_ewald_coulomb_force_table(const EwaldCorrectionTables &tables, NBParamGpu *nbp, const DeviceContext &deviceContext, const DeviceStream &deviceStream) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:114: warning: Member useTabulatedEwaldByDefault(const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:148: warning: Member nbnxn_gpu_pick_ewald_kernel_type(const interaction_const_t &ic, const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:198: warning: Member set_cutoff_parameters(NBParamGpu *nbp, const interaction_const_t &ic, const PairlistParams &listParams) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:248: warning: Member init_timings(gmx_wallclock_gpu_nbnxn_t *t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:297: warning: Member nbnxmGpuPickVdwKernelType(const interaction_const_t &ic, LJCombinationRule ljCombinationRule) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:351: warning: Member nbnxmGpuPickElectrostaticsKernelType(const interaction_const_t &ic, const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:437: warning: Member initializeGpuLists(bool localAndNonLocal) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:448: warning: Member gpu_init(const DeviceStreamManager &deviceStreamManager, const interaction_const_t *ic, const PairlistParams &listParams, const nbnxn_atomdata_t *nbat, const bool bLocalAndNonlocal) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:512: warning: Member gpu_pme_loadbal_update_param(nonbonded_verlet_t *nbv, const interaction_const_t &ic) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:530: warning: Member gpu_upload_shiftvec(NbnxmGpu *nb, const nbnxn_atomdata_t *nbatom) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:691: warning: Member gpu_init_atomdata(NbnxmGpu *nb, const nbnxn_atomdata_t *nbat) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:794: warning: Member gpu_clear_outputs(NbnxmGpu *nb, bool computeVirial) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:825: warning: Member gpu_is_kernel_ewald_analytical(const NbnxmGpu *nb) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:831: warning: Member setupGpuShortRangeWorkLow(NbnxmGpu *nb, const ListedForcesGpu *listedForcesGpu, const InteractionLocality iLocality) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:844: warning: Member haveGpuShortRangeWork(const NbnxmGpu *nb, const InteractionLocality interactionLocality) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:984: warning: Member nbnxnInsertNonlocalGpuDependency(NbnxmGpu *nb, const InteractionLocality interactionLocality) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:1079: warning: Member nbnxn_gpu_init_x_to_nbat_x(const GridSet &gridSet, NbnxmGpu *gpu_nbv) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:1261: warning: Member gpuGetNBAtomData(NbnxmGpu *nb) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:1267: warning: Member gpu_get_f(NbnxmGpu *nb) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:90: warning: Member constexpr(doCalcEnergies) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:104: warning: Member c_useSimdGpuClusterPairDistance(const PairlistType layoutType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:121: warning: Member sizeNeededForBufferFlags(const int numAtoms) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:127: warning: Member resizeAndZeroBufferFlags(std::vector< gmx_bitmask_t > *flags, const int numAtoms) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:142: warning: Member listRangeForBoundingBoxToGridCell(real rlist, const GridDimensions &gridDims) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:154: warning: Member listRangeForGridCellToGridCell(real rlist, const GridDimensions &iGridDims, const GridDimensions &jGridDims) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:166: warning: Member get_cell_range(real b0, real b1, const GridDimensions &jGridDims, real d2, real rlist, int *cf, int *cl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:194: warning: Member clusterpairInRangePlainC(const NbnxmPairlistGpuWork &work, const int si, const int csj, const int jCoordStride, const real *x_j, const real rlist2) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:346: warning: Member clusterpairInRange(const NbnxmPairlistGpuWork &work, const int si, const int csj, const int jCoordStride, const real *x_j, const real rlist2) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:414: warning: Member createGpuPairlists(int numLists) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:494: warning: Member print_nblist_statistics(FILE *fp, const NbnxnPairlistCpu &nbl, const GridSet &gridSet, const real rl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:552: warning: Member print_nblist_statistics(FILE *fp, const NbnxnPairlistGpu &nbl, const GridSet &gridSet, const real rl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:633: warning: Member get_exclusion_mask(NbnxnPairlistGpu *nbl, int cjPacked, int warp) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:656: warning: Member setSelfAndNewtonExclusionsGpu(NbnxnPairlistGpu *nbl, const int cjPackedIndex, const int jOffsetInGroup, const int iClusterInCell) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:696: warning: Member makeClusterListSimple(const Grid &jGrid, NbnxnPairlistCpu *nbl, int icluster, int jclusterFirst, int jclusterLast, bool excludeSubDiagonal, const real *gmx_restrict x_j, real rlist2, float rbb2, int *gmx_restrict numDistanceChecks) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:817: warning: Member make_cluster_list_supersub(const Grid &iGrid, const Grid &jGrid, NbnxnPairlistGpu *nbl, const int sci, const int scj, const bool excludeSubDiagonal, const int stride, const real *x, const real rlist2, const float rbb2, int *numDistanceChecks) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:969: warning: Member numContiguousJClusters(const int cjIndexStart, const int cjIndexEnd, const JClusterListType &cjList) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1024: warning: Member findJClusterInJList(int jCluster, const JListRanges &ranges, const JClusterListType &cjList) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1065: warning: Member setExclusionsForIEntry(const GridSet &gridSet, NbnxnPairlistCpu *nbl, bool diagRemoved, int na_cj_2log, const ListOfLists< int > &exclusions) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1135: warning: Member getCoordinate(const nbnxn_atomdata_t &nbat, const int a) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1260: warning: Member make_fep_list(ArrayRef< const int > atomIndices, const nbnxn_atomdata_t *nbat, NbnxnPairlistCpu *nbl, bool bDiagRemoved, const real shx, const real shy, const real shz, const real gmx_unused rlist_fep2, const Grid &iGrid, const Grid &jGrid, t_nblist *nlist) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1438: warning: Member cj_mod_cjPacked(int cj) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1445: warning: Member cj_to_cjPacked(int cj) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1452: warning: Member a_mod_wj(int a) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1459: warning: Member make_fep_list(ArrayRef< const int > atomIndices, const nbnxn_atomdata_t *nbat, NbnxnPairlistGpu *nbl, bool bDiagRemoved, real shx, real shy, real shz, real rlist_fep2, const Grid &iGrid, const Grid &jGrid, t_nblist *nlist) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1606: warning: Member setExclusionsForIEntry(const GridSet &gridSet, NbnxnPairlistGpu *nbl, bool diagRemoved, int gmx_unused na_cj_2log, const ListOfLists< int > &exclusions) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1710: warning: Member addNewIEntry(NbnxnPairlistCpu *nbl, int ci, int shift, int flags) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1724: warning: Member addNewIEntry(NbnxnPairlistGpu *nbl, int sci, int shift, int gmx_unused flags) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1738: warning: Member sort_cj_excl(nbnxn_cj_t *cj, int ncj, NbnxmPairlistCpuWork *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1770: warning: Member closeIEntry(NbnxnPairlistCpu *nbl, int gmx_unused sp_max_av, bool gmx_unused progBal, float gmx_unused nsp_tot_est, int gmx_unused thread, int gmx_unused nthread) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1815: warning: Member split_sci_entry(NbnxnPairlistGpu *nbl, int nsp_target_av, bool progBal, float nsp_tot_est, int thread, int nthread) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1897: warning: Member closeIEntry(NbnxnPairlistGpu *nbl, int nsp_max_av, bool progBal, float nsp_tot_est, int thread, int nthread) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1927: warning: Member sync_work(NbnxnPairlistCpu gmx_unused *nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1933: warning: Member sync_work(NbnxnPairlistGpu *nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1939: warning: Member clear_pairlist(NbnxnPairlistCpu *nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1952: warning: Member clear_pairlist(NbnxnPairlistGpu *nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1961: warning: Member set_icell_bb_simple(ArrayRef< const BoundingBox > bb, int ci, const RVec &shift, BoundingBox *bb_ci) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1973: warning: Member set_icell_bb(const Grid &iGrid, int ci, const RVec &shift, NbnxmPairlistCpuWork *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2006: warning: Member set_icell_bb_supersub(ArrayRef< const BoundingBox > bb, int ci, const RVec &shift, BoundingBox *bb_ci) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2016: warning: Member set_icell_bb(const Grid &iGrid, int ci, const RVec &shift, NbnxmPairlistGpuWork *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2029: warning: Member icellSetXSimple(int ci, const RVec &shift, int stride, const real *x, NbnxmPairlistCpuWork::IClusterData *iClusterData) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2052: warning: Member icell_set_x(int ci, const RVec &shift, int stride, const real *x, const ClusterDistanceKernelType kernelType, NbnxmPairlistCpuWork *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2085: warning: Member icell_set_x(int ci, const RVec &shift, int stride, const real *x, ClusterDistanceKernelType, NbnxmPairlistGpuWork *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2129: warning: Member minimum_subgrid_size_xy(const Grid &grid) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2145: warning: Member effective_buffer_1x1_vs_MxN(const Grid &iGrid, const Grid &jGrid) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2171: warning: Member nonlocal_vol2(const gmx::DomdecZones &zones, const rvec ls, real r) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2214: warning: Member get_nsubpair_target(const GridSet &gridSet, const InteractionLocality iloc, const real rlist, const int min_ci_balanced, int *nsubpair_target, float *nsubpair_tot_est) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2313: warning: Member print_nblist_ci_cj(FILE *fp, const NbnxnPairlistCpu &nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2328: warning: Member print_nblist_sci_cj(FILE *fp, const NbnxnPairlistGpu &nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2364: warning: Member combine_nblists(ArrayRef< const NbnxnPairlistGpu > nbls, NbnxnPairlistGpu *nblc) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2438: warning: Member balance_fep_lists(ArrayRef< std::unique_ptr< t_nblist > > fepLists, ArrayRef< PairsearchWork > work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2526: warning: Member next_ci(const Grid &grid, int nth, int ci_block, int *ci_x, int *ci_y, int *ci_b, int *ci) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2559: warning: Member boundingbox_only_distance2(const GridDimensions &iGridDims, const GridDimensions &jGridDims, real rlist, bool simple, const PairlistType layoutType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2597: warning: Member get_ci_block_size(const Grid &iGrid, const bool haveMultipleDomains, const int numLists) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2654: warning: Member getBufferFlagShift(int numAtomsPerCluster) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2665: warning: Member makeClusterListWrapper(NbnxnPairlistCpu *nbl, const Grid gmx_unused &iGrid, const int ci, const Grid &jGrid, const int firstCell, const int lastCell, const bool excludeSubDiagonal, const nbnxn_atomdata_t *nbat, const real rlist2, const real rbb2, const ClusterDistanceKernelType kernelType, int *numDistanceChecks) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2704: warning: Member makeClusterListWrapper(NbnxnPairlistGpu *nbl, const Grid &gmx_unused iGrid, const int ci, const Grid &jGrid, const int firstCell, const int lastCell, const bool excludeSubDiagonal, const nbnxn_atomdata_t *nbat, const real rlist2, const real rbb2, ClusterDistanceKernelType gmx_unused kernelType, int *numDistanceChecks) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2724: warning: Member getNumSimpleJClustersInList(const NbnxnPairlistCpu &nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2729: warning: Member getNumSimpleJClustersInList(const gmx_unused NbnxnPairlistGpu &nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2734: warning: Member incrementNumSimpleJClustersInList(NbnxnPairlistCpu *nbl, int ncj_old_j) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2740: warning: Member incrementNumSimpleJClustersInList(NbnxnPairlistGpu gmx_unused *nbl, int gmx_unused ncj_old_j) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2744: warning: Member checkListSizeConsistency(const NbnxnPairlistCpu &nbl, const bool haveFreeEnergy) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2752: warning: Member checkListSizeConsistency(const NbnxnPairlistGpu gmx_unused &nbl, bool gmx_unused haveFreeEnergy) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2758: warning: Member setBufferFlags(const NbnxnPairlistCpu &nbl, const int ncj_old_j, const int gridj_flag_shift, gmx_bitmask_t *gridj_flag, const int th) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2775: warning: Member setBufferFlags(const NbnxnPairlistGpu gmx_unused &nbl, int gmx_unused ncj_old_j, int gmx_unused gridj_flag_shift, gmx_bitmask_t gmx_unused *gridj_flag, int gmx_unused th) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:2786: warning: Member nbnxn_make_pairlist_part(const GridSet &gridSet, const Grid &iGrid, const Grid &jGrid, PairsearchWork *work, const nbnxn_atomdata_t *nbat, const ListOfLists< int > &exclusions, real rlist, const PairlistType pairlistType, int ci_block, bool bFBufferFlag, int nsubpair_max, bool progBal, float nsubpair_tot_est, int th, int nth, T *nbl, t_nblist *nbl_fep) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:3304: warning: Member reduce_buffer_flags(ArrayRef< PairsearchWork > searchWork, int nsrc, ArrayRef< gmx_bitmask_t > dest) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:3318: warning: Member print_reduction_cost(ArrayRef< const gmx_bitmask_t > flags, int nout) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:3372: warning: Member copySelectedListRange(const nbnxn_ci_t *gmx_restrict srcCi, const NbnxnPairlistCpu *gmx_restrict src, NbnxnPairlistCpu *gmx_restrict dest, gmx_bitmask_t *flag, int iFlagShift, int jFlagShift, int t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:3408: warning: Member countClusterpairs(ArrayRef< const NbnxnPairlistCpu > pairlists) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:3430: warning: Member rebalanceSimpleLists(ArrayRef< const NbnxnPairlistCpu > srcSet, ArrayRef< NbnxnPairlistCpu > destSet, ArrayRef< PairsearchWork > searchWork) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:3505: warning: Member checkRebalanceSimpleLists(ArrayRef< const NbnxnPairlistCpu > lists) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:3539: warning: Member sort_sci(NbnxnPairlistGpu *nbl) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:3594: warning: Member getIZoneRange(const GridSet::DomainSetup &domainSetup, const InteractionLocality locality) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:3614: warning: Member getJZoneRange(const gmx::DomdecZones *ddZones, const InteractionLocality locality, const int iZone) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:3636: warning: Member getGridList(ArrayRef< const Grid > grids, const Range< int > &ddZoneRange) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:73: warning: Member sc_iClusterSizeSimd() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:82: warning: Member sc_jClusterSizeSimd() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:252: warning: Member setICellCoordinatesSimd4xM(int gmx_unused ci, const RVec gmx_unused &shift, int gmx_unused stride, const real gmx_unused *x, NbnxmPairlistCpuWork gmx_unused *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:265: warning: Member setICellCoordinatesSimd2xMM(int gmx_unused ci, const RVec gmx_unused &shift, int gmx_unused stride, const real gmx_unused *x, NbnxmPairlistCpuWork gmx_unused *work) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:504: warning: Member makeClusterListSimd4xM(const Grid gmx_unused &jGrid, NbnxnPairlistCpu gmx_unused *nbl, int gmx_unused icluster, int gmx_unused firstCell, int gmx_unused lastCell, bool gmx_unused excludeSubDiagonal, const real gmx_unused *gmx_restrict x_j, real gmx_unused rlist2, float gmx_unused rbb2, int gmx_unused *gmx_restrict numDistanceChecks) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_simd_kernel.cpp:523: warning: Member makeClusterListSimd2xMM(const Grid gmx_unused &jGrid, NbnxnPairlistCpu gmx_unused *nbl, int gmx_unused icluster, int gmx_unused firstCell, int gmx_unused lastCell, bool gmx_unused excludeSubDiagonal, const real gmx_unused *gmx_restrict x_j, real gmx_unused rlist2, float gmx_unused rbb2, int gmx_unused *gmx_restrict numDistanceChecks) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl.cpp:256: warning: Member launchSciSortOnGpu(GpuPairlist *plist, const int maxWorkGroupSize, const DeviceStream &deviceStream) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl.cpp:228: warning: Member launchPrefixSumKernel(sycl::queue &q, GpuPairlistSorting *sorting) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl.cpp:241: warning: Member launchBucketSortKernel(sycl::queue &q, GpuPairlist *plist) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel.cpp:53: warning: Member getNbnxmSubGroupSize(const DeviceInformation &deviceInfo, PairlistType layoutType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel.cpp:104: warning: Member launchNbnxmKernel(NbnxmGpu *nb, const gmx::StepWorkload &stepWork, const InteractionLocality iloc, bool doPrune) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_utils.h:58: warning: Member sc_superClInteractionMask(const PairlistType layoutType) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/selectioncollection.cpp:978: warning: Member swap(SelectionCollection &lhs, SelectionCollection &rhs) noexcept (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/decidegpuusage.cpp:175: warning: Member decideWhetherToUseGpusForPmeFft(const TaskTarget pmeFftTarget) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/decidegpuusage.cpp:182: warning: Member canUseGpusForPme(const bool useGpuForNonbonded, const TaskTarget pmeTarget, const TaskTarget pmeFftTarget, const t_inputrec &inputrec, std::string *errorMessage) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/stringutil.cpp:132: warning: Member formatString(gmx_fmtstr const char *fmt,...) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulationinput.h:120: warning: Member globalSimulationState(const SimulationInput &) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulationinput.h:121: warning: Member applyGlobalInputRecord(const SimulationInput &, t_inputrec *) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulationinput.h:122: warning: Member applyGlobalTopology(const SimulationInput &, gmx_mtop_t *) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:200: warning: Member toString(bool t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:204: warning: Member toString(int t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:208: warning: Member toString(int64_t t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:212: warning: Member toString(float t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:216: warning: Member toString(double t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:220: warning: Member toString(unsigned char t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/strconvert.h:224: warning: Member toString(std::string t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/vec.h:625: warning: Member norm2(T *v) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/tests/colvarsoptions.cpp:87: warning: Member colvarsConfig (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/requirements.cpp:59: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/requirements.cpp:63: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:161: warning: Member c_disableAlternatingWait (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/nosehooverchains.cpp:67: warning: Member nhcUsageNames (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/gpu_types_common.h:88: warning: Member c_sciSortingItemsPerThread (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/gpu_types_common.h:463: warning: Member elecEwald (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/gpu_types_common.h:466: warning: Member elecEwaldTab (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/gpu_types_common.h:469: warning: Member ljEwald (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_data_mgmt.cpp:76: warning: Member gpu_min_ci_balanced_factor (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_body.h:574: warning: Member nbparam (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_body.h:574: warning: Member plist (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_utils.h:70: warning: Member c_subWarp (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_kernel_utils.h:82: warning: Member c_fbufStride (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp:59: warning: Member refPairlistLayoutType (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp:61: warning: Member c_clSize (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:82: warning: unable to resolve reference to 'ElecType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:106: warning: unable to resolve reference to 'VdwType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_geometry.cpp:49: warning: Member c_nbnxnRlistIncreaseOutsideFactor (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:56: warning: Member epsilon (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:59: warning: Member sigma6 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:60: warning: Member c6 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:61: warning: Member c12 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:63: warning: Member return (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:69: warning: Member repulsionShift (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:70: warning: Member rVdwSwitch (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:73: warning: Member rInv (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:74: warning: Member r2 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:75: warning: Member fInvR (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:76: warning: Member eLJ (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:80: warning: Member dispShiftV3 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:81: warning: Member repuShiftV2 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:82: warning: Member repuShiftV3 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:84: warning: Member r (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:85: warning: Member rSwitch (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_kernel_utils.h:104: warning: Member typeI (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:119: warning: Member c_pbcShiftBackward (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.cpp:1224: warning: Member max_nrj_fep (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:55: warning: Member c_centralShiftIndex (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:56: warning: Member c_numShiftVectors (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment/decidegpuusage.cpp:126: warning: Member c_gpuBuildSyclWithoutGpuFft (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:83: warning: Member c_angstrom (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:84: warning: Member c_kilo (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:85: warning: Member c_nano (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:86: warning: Member c_pico (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:87: warning: Member c_nm2A (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:88: warning: Member c_cal2Joule (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:89: warning: Member c_electronCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:91: warning: Member c_amu (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:92: warning: Member c_boltzmann (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:93: warning: Member c_avogadro (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:94: warning: Member c_universalGasConstant (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:95: warning: Member c_boltz (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:96: warning: Member c_faraday (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:97: warning: Member c_planck1 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:98: warning: Member c_planck (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:100: warning: Member c_epsilon0Si (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:102: warning: Member c_epsilon0 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:105: warning: Member c_speedOfLight (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:107: warning: Member c_rydberg (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:109: warning: Member c_one4PiEps0 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:114: warning: Member c_barMdunits (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:115: warning: Member c_presfac (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:120: warning: Member c_debye2Enm (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:121: warning: Member c_enm2Debye (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:125: warning: Member c_fieldfac (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:128: warning: Member c_hartree2Kj (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:129: warning: Member c_bohr2Nm (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:130: warning: Member c_hartreeBohr2Md (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:132: warning: Member c_rad2Deg (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/math/units.h:133: warning: Member c_deg2Rad (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:787: warning: Member CompileTimeStringJoin_v (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:64: warning: Member sc_atomInfo_HasPerturbedCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:65: warning: Member sc_atomInfo_Exclusion (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:66: warning: Member sc_atomInfo_Constraint (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:67: warning: Member sc_atomInfo_Settle (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:68: warning: Member sc_atomInfo_BondCommunication (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:69: warning: Member sc_atomInfo_HasVdw (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:70: warning: Member sc_atomInfo_HasCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/atominfo.h:71: warning: Member sc_atomInfo_IsFillerParticle (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:53: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:54: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:55: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:56: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:57: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJ_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:58: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:59: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:60: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:61: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:62: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJ_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:63: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:64: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:65: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:66: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:68: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:69: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:70: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:71: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:72: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:73: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:74: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:75: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:76: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:77: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:78: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:79: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:80: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:81: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:82: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:84: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:85: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:86: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:87: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:88: warning: Member nbnxn_kernel_1x1_ElecRF_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:89: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:90: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:91: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:92: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:93: warning: Member nbnxn_kernel_1x1_ElecQSTab_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:94: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:95: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:96: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:97: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_1x1.h:98: warning: Member nbnxn_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:54: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:55: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:56: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:57: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:58: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJ_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:59: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:60: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:61: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:62: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:63: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJ_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:64: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJFsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:65: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJPsw_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:66: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombGeom_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:67: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombLB_F_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:69: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:70: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:71: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:72: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:73: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:74: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:75: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:76: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:77: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:78: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:79: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJ_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:80: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJFsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:81: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJPsw_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:82: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:83: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombLB_VF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:85: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:86: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:87: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:88: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:89: warning: Member nbnxn_kernel_4x4_ElecRF_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:90: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:91: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:92: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:93: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:94: warning: Member nbnxn_kernel_4x4_ElecQSTab_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:95: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJ_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:96: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJFsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:97: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJPsw_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:98: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.h:99: warning: Member nbnxn_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombLB_VgrpF_ref (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:44: warning: Member c_dBoxY (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:45: warning: Member c_dBoxX (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:295: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:340: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:398: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:374: warning: Member c_simdBestPairAlignment (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:652: warning: Member Simd4NFloat (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:698: warning: Member Simd4NDouble (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:741: warning: Member Simd4NReal (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:512: warning: Member load(const std::enable_if_t< std::is_arithmetic_v< T >, T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:518: warning: Member load(const AlignedArray< internal::SimdTraitsT< T >, N > &m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:536: warning: Member loadU(const std::enable_if_t< std::is_arithmetic_v< T >, T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:542: warning: Member loadU(const AlignedArray< internal::SimdTraitsT< T >, N > &m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:623: warning: Member load(const internal::Simd4TraitsT< T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:628: warning: Member loadU(const internal::Simd4TraitsT< T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:657: warning: Member loadUNDuplicate4(const float *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:661: warning: Member load4DuplicateN(const float *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:665: warning: Member loadU4NOffset(const float *f, int) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:703: warning: Member loadUNDuplicate4(const double *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:707: warning: Member load4DuplicateN(const double *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:711: warning: Member loadU4NOffset(const double *f, int) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:398: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:295: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:305: warning: unable to resolve reference to 'SimdIBool' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:340: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:352: warning: unable to resolve reference to 'SimdBool' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:353: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:353: warning: unable to resolve reference to 'SimdIBool' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:354: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:356: warning: unable to resolve reference to 'cvtB2IB' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:356: warning: unable to resolve reference to 'cvtIB2B' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/sim_util.cpp:593: warning: argument 'wcycle' from the argument list of gmx::computeSpecialForces has multiple @param documentation sections /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/correlationhistory.h:61: warning: unable to resolve reference to 'updateCorrelationGridHistory' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:99: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:100: warning: @copydetails or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:94: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:95: warning: @copydetails or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:125: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:126: warning: @copydetails or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:120: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/checkpoint.h:121: warning: @copydetails or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/requirements.cpp:63: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/requirements.cpp:59: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/options/basicoptionstorage.h:73: warning: Member formatSingleValue(const bool &value) const override (function) of class gmx::BooleanOptionStorage is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/options/optionstoragetemplate.h:321: warning: Member normalizeValues(const std::vector< Any > &values) const override (function) of class OptionStorageTemplateSimple< bool > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/booltype.h:72: warning: Member value_ (variable) of struct gmx::BoolType is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_force_sender_gpu_impl.h:74: warning: Member flag (variable) of struct gmx::CacheLineAlignedFlag is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_tuning.cpp:446: warning: Member mtop (variable) of struct gmx::CalcVerletBufferParameters is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_tuning.cpp:447: warning: Member effectiveAtomDensity (variable) of struct gmx::CalcVerletBufferParameters is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_tuning.cpp:448: warning: Member inputrec (variable) of struct gmx::CalcVerletBufferParameters is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_tuning.cpp:449: warning: Member pressureTolerance (variable) of struct gmx::CalcVerletBufferParameters is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_tuning.cpp:450: warning: Member listSetup (variable) of struct gmx::CalcVerletBufferParameters is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_tuning.cpp:451: warning: Member useGpuList (variable) of struct gmx::CalcVerletBufferParameters is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist_tuning.cpp:452: warning: Member mtsFactor (variable) of struct gmx::CalcVerletBufferParameters is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/clfftinitializer.h:96: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(ClfftInitializer) (function) of class gmx::ClfftInitializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/colvarproxygromacs.h:85: warning: Member gmxPbc_ (variable) of class gmx::ColvarProxyGromacs is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/colvarproxygromacs.h:88: warning: Member logger_ (variable) of class gmx::ColvarProxyGromacs is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/colvarproxygromacs.h:95: warning: Member rng_ (variable) of class gmx::ColvarProxyGromacs is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/colvarproxygromacs.h:96: warning: Member normalDistribution_ (variable) of class gmx::ColvarProxyGromacs is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/colvarproxygromacs.h:85: warning: Member gmxPbc_ (variable) of class gmx::ColvarProxyGromacs is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/colvarproxygromacs.h:88: warning: Member logger_ (variable) of class gmx::ColvarProxyGromacs is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/colvarproxygromacs.h:95: warning: Member rng_ (variable) of class gmx::ColvarProxyGromacs is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/colvarproxygromacs.h:96: warning: Member normalDistribution_ (variable) of class gmx::ColvarProxyGromacs is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/colvarproxygromacs.h:85: warning: Member gmxPbc_ (variable) of class gmx::ColvarProxyGromacs is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/colvarproxygromacs.h:88: warning: Member logger_ (variable) of class gmx::ColvarProxyGromacs is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/colvarproxygromacs.h:95: warning: Member rng_ (variable) of class gmx::ColvarProxyGromacs is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/colvars/colvarproxygromacs.h:96: warning: Member normalDistribution_ (variable) of class gmx::ColvarProxyGromacs is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:765: warning: Member impl() noexcept (function) of struct gmx::CompileTimeStringJoin is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:781: warning: Member stringArray (variable) of struct gmx::CompileTimeStringJoin is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:783: warning: Member value (variable) of struct gmx::CompileTimeStringJoin is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/scattering-debye.h:104: warning: Member getIntensity(size_t qi) (function) of class gmx::ComputeDebyeScattering is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/computeglobalselement.cpp:392: warning: Member getElementPointerImpl(LegacySimulatorData *legacySimulatorData, ModularSimulatorAlgorithmBuilderHelper *builderHelper, StatePropagatorData *statePropagatorData, EnergyData *energyData, FreeEnergyPerturbationData *freeEnergyPerturbationData, GlobalCommunicationHelper *globalCommunicationHelper, ObservablesReducer *observablesReducer) (function) of class gmx::ComputeGlobalsElement is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/computeglobalselement.cpp:426: warning: Member getElementPointerImpl(LegacySimulatorData *simulator, ModularSimulatorAlgorithmBuilderHelper *builderHelper, StatePropagatorData *statePropagatorData, EnergyData *energyData, FreeEnergyPerturbationData *freeEnergyPerturbationData, GlobalCommunicationHelper *globalCommunicationHelper, ObservablesReducer *observablesReducer) (function) of class gmx::ComputeGlobalsElement is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/mdmodulesnotifiers.h:173: warning: Member coordinates_ (variable) of struct gmx::CoordinatesAndBoxPreprocessed is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/mdmodulesnotifiers.h:174: warning: Member box_ (variable) of struct gmx::CoordinatesAndBoxPreprocessed is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/mdmodulesnotifiers.h:175: warning: Member pbc_ (variable) of struct gmx::CoordinatesAndBoxPreprocessed is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/coordstate.h:86: warning: found documented return type for gmx::CoordState::sampleUmbrellaGridpoint that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_coulomb_functions.h:134: warning: Member CoulombCalculator(const interaction_const_t &ic) (function) of class gmx::CoulombCalculator< KernelCoulombType::EwaldAnalytical > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_coulomb_functions.h:145: warning: Member force(const std::array< SimdReal, nR > &rSquaredV, const std::array< SimdReal, nR > gmx_unused &dummyRInvV, const std::array< SimdReal, nR > &rInvExclV, const std::array< SimdBool, nR > &withinCutoffV) (function) of class gmx::CoulombCalculator< KernelCoulombType::EwaldAnalytical > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_coulomb_functions.h:194: warning: Member CoulombCalculator(const interaction_const_t &ic) (function) of class gmx::CoulombCalculator< KernelCoulombType::EwaldTabulated > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_coulomb_functions.h:83: warning: Member CoulombCalculator(const interaction_const_t &ic) (function) of class gmx::CoulombCalculator< KernelCoulombType::RF > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_diagonal_masker.h:106: warning: Member DiagonalMasker(const nbnxn_atomdata_t::SimdMasks &simdMasks) (function) of class gmx::DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeEqualsISize > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_diagonal_masker.h:132: warning: Member DiagonalMasker(const nbnxn_atomdata_t::SimdMasks &simdMasks) (function) of class gmx::DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeIsDoubleISize > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_diagonal_masker.h:165: warning: Member DiagonalMasker(const nbnxn_atomdata_t::SimdMasks &simdMasks) (function) of class gmx::DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeIsHalfISize > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec_zones.h:104: warning: Member DomdecZones(ArrayRef< const int > ddDims) (function) of class gmx::DomdecZones is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/options/basicoptionstorage.h:134: warning: Member formatSingleValue(const double &value) const override (function) of class gmx::DoubleOptionStorage is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/options/optionstoragetemplate.h:321: warning: Member normalizeValues(const std::vector< Any > &values) const override (function) of class OptionStorageTemplateSimple< double > is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/enumerationhelpers.h:333: warning: Member value (variable) of class gmx::EnumClassSuitsEnumerationArray is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/enumerationhelpers.h:250: warning: Member const_iterator (typedef) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/enumerationhelpers.h:251: warning: Member reverse_iterator (typedef) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/enumerationhelpers.h:252: warning: Member const_reverse_iterator (typedef) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/enumerationhelpers.h:274: warning: Member const_pointer (typedef) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/enumerationhelpers.h:229: warning: Member operator[](const std::size_t arrayIndex) const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/enumerationhelpers.h:235: warning: Member operator[](const EnumType enumIndex) (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/enumerationhelpers.h:240: warning: Member operator[](const EnumType enumIndex) const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/enumerationhelpers.h:258: warning: Member end() (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/enumerationhelpers.h:259: warning: Member begin() const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/enumerationhelpers.h:260: warning: Member end() const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/enumerationhelpers.h:266: warning: Member rend() (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/enumerationhelpers.h:267: warning: Member rbegin() const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/enumerationhelpers.h:268: warning: Member rend() const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/enumerationhelpers.h:181: warning: Member end() const (function) of class gmx::EnumerationWrapper is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/options/basicoptionstorage.h:236: warning: Member formatSingleValue(const int &value) const override (function) of class gmx::EnumOptionStorage is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/options/optionstoragetemplate.h:321: warning: Member normalizeValues(const std::vector< Any > &values) const override (function) of class OptionStorageTemplateSimple< int > is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/stringutil.h:441: warning: Member operator()(const std::string &lhs, const std::string &rhs) const (function) of class gmx::EqualCaseInsensitive is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:87: warning: Member IExceptionInfo(const IExceptionInfo &)=default (function) of class gmx::internal::IExceptionInfo is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:88: warning: Member IExceptionInfo(IExceptionInfo &&) noexcept=default (function) of class gmx::internal::IExceptionInfo is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:89: warning: Member operator=(const IExceptionInfo &)=default (function) of class gmx::internal::IExceptionInfo is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:90: warning: Member operator=(IExceptionInfo &&) noexcept=default (function) of class gmx::internal::IExceptionInfo is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:126: warning: Member doUShortArray(unsigned short *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:133: warning: Member doIntArray(int *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:140: warning: Member doInt32Array(int32_t *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:147: warning: Member doInt64Array(int64_t *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:154: warning: Member doFloatArray(float *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:161: warning: Member doDoubleArray(double *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:168: warning: Member doRealArray(real *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:175: warning: Member doIvecArray(ivec *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/options/filenameoptionstorage.h:74: warning: Member formatSingleValue(const std::string &value) const override (function) of class gmx::FileNameOptionStorage is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/options/optionstoragetemplate.h:321: warning: Member normalizeValues(const std::vector< Any > &values) const override (function) of class OptionStorageTemplateSimple< std::string > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/options/basicoptionstorage.h:162: warning: Member formatSingleValue(const float &value) const override (function) of class gmx::FloatOptionStorage is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/options/optionstoragetemplate.h:321: warning: Member normalizeValues(const std::vector< Any > &values) const override (function) of class OptionStorageTemplateSimple< float > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/iforceprovider.h:112: warning: Member homenr_ (variable) of class gmx::ForceProviderInput is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/iforceprovider.h:113: warning: Member chargeA_ (variable) of class gmx::ForceProviderInput is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/iforceprovider.h:114: warning: Member massT_ (variable) of class gmx::ForceProviderInput is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec_zones.h:80: warning: Member x0 (variable) of struct gmx::gmx_domdec_zone_size_t is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec_zones.h:82: warning: Member x1 (variable) of struct gmx::gmx_domdec_zone_size_t is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec_zones.h:84: warning: Member bb_x0 (variable) of struct gmx::gmx_domdec_zone_size_t is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domdec_zones.h:86: warning: Member bb_x1 (variable) of struct gmx::gmx_domdec_zone_size_t is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_hip_rocfft.cpp:180: warning: Member complexGrid_ (variable) of class gmx::Gpu3dFft::ImplHipRocfft::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_hip_rocfft.cpp:181: warning: Member pmeStream_ (variable) of class gmx::Gpu3dFft::ImplHipRocfft::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_hip_vkfft.cpp:105: warning: Member configuration_ (variable) of class gmx::Gpu3dFft::ImplHipVkFft::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_hip_vkfft.cpp:106: warning: Member application_ (variable) of class gmx::Gpu3dFft::ImplHipVkFft::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_hip_vkfft.cpp:107: warning: Member bufferSize_ (variable) of class gmx::Gpu3dFft::ImplHipVkFft::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_hip_vkfft.cpp:108: warning: Member inputBufferSize_ (variable) of class gmx::Gpu3dFft::ImplHipVkFft::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_hip_vkfft.cpp:109: warning: Member deviceStream_ (variable) of class gmx::Gpu3dFft::ImplHipVkFft::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_hip_vkfft.cpp:111: warning: Member realGrid_ (variable) of class gmx::Gpu3dFft::ImplHipVkFft::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_ocl_vkfft.cpp:106: warning: Member configuration_ (variable) of class gmx::Gpu3dFft::ImplOclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_ocl_vkfft.cpp:107: warning: Member application_ (variable) of class gmx::Gpu3dFft::ImplOclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_ocl_vkfft.cpp:108: warning: Member launchParams_ (variable) of class gmx::Gpu3dFft::ImplOclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_ocl_vkfft.cpp:109: warning: Member bufferSize_ (variable) of class gmx::Gpu3dFft::ImplOclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_ocl_vkfft.cpp:110: warning: Member inputBufferSize_ (variable) of class gmx::Gpu3dFft::ImplOclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_ocl_vkfft.cpp:111: warning: Member context_ (variable) of class gmx::Gpu3dFft::ImplOclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_ocl_vkfft.cpp:112: warning: Member device_ (variable) of class gmx::Gpu3dFft::ImplOclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_ocl_vkfft.cpp:113: warning: Member commandQueue_ (variable) of class gmx::Gpu3dFft::ImplOclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_ocl_vkfft.cpp:115: warning: Member realGrid_ (variable) of class gmx::Gpu3dFft::ImplOclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_sycl_rocfft.cpp:240: warning: Member complexGrid_ (variable) of class gmx::Gpu3dFft::ImplSyclRocfft::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_sycl_vkfft.cpp:124: warning: Member configuration_ (variable) of class gmx::Gpu3dFft::ImplSyclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_sycl_vkfft.cpp:125: warning: Member application_ (variable) of class gmx::Gpu3dFft::ImplSyclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_sycl_vkfft.cpp:126: warning: Member launchParams_ (variable) of class gmx::Gpu3dFft::ImplSyclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_sycl_vkfft.cpp:127: warning: Member bufferSize_ (variable) of class gmx::Gpu3dFft::ImplSyclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_sycl_vkfft.cpp:128: warning: Member inputBufferSize_ (variable) of class gmx::Gpu3dFft::ImplSyclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_sycl_vkfft.cpp:129: warning: Member queue_device_ (variable) of class gmx::Gpu3dFft::ImplSyclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/gpu_3dfft_sycl_vkfft.cpp:131: warning: Member realGrid_ (variable) of class gmx::Gpu3dFft::ImplSyclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/gpuforcereduction.h:125: warning: Member registerForcesReadyNvshmemFlags(DeviceBuffer< uint64_t > syncObj) (function) of class gmx::GpuForceReduction is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/gpuhaloexchange.h:105: warning: Member GpuHaloExchange(GpuHaloExchange &&source) noexcept (function) of class gmx::GpuHaloExchange is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/gpuhaloexchange.h:106: warning: Member operator=(GpuHaloExchange &&source) noexcept (function) of class gmx::GpuHaloExchange is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/gridset.h:137: warning: Member setNonLocalGrid(const int gridIndex, const int ddZone, const GridDimensions &gridDimensions, ArrayRef< const std::pair< int, int > > columns, ArrayRef< const int32_t > atomInfo, ArrayRef< const RVec > x, nbnxn_atomdata_t *nbat) (function) of class gmx::GridSet is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/haloexchange.h:93: warning: Member HaloExchange(PbcType pbcType) (function) of class gmx::HaloExchange is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/nnpotmodel.h:76: warning: Member prepareAtomNumbers(std::vector< int > &)=0 (function) of class gmx::INNPotModel is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/nnpotmodel.h:77: warning: Member prepareBox(matrix &)=0 (function) of class gmx::INNPotModel is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/nnpotmodel.h:78: warning: Member preparePbcType(PbcType &)=0 (function) of class gmx::INNPotModel is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/options/basicoptionstorage.h:115: warning: Member formatSingleValue(const int64_t &value) const override (function) of class gmx::Int64OptionStorage is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/options/optionstoragetemplate.h:321: warning: Member normalizeValues(const std::vector< Any > &values) const override (function) of class OptionStorageTemplateSimple< int64_t > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/options/basicoptionstorage.h:95: warning: Member formatSingleValue(const int &value) const override (function) of class gmx::IntegerOptionStorage is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/options/optionstoragetemplate.h:321: warning: Member normalizeValues(const std::vector< Any > &values) const override (function) of class OptionStorageTemplateSimple< int > is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:86: warning: Member doUChar(unsigned char *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:87: warning: Member doChar(char *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:88: warning: Member doUShort(unsigned short *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:89: warning: Member doInt(int *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:90: warning: Member doInt32(int32_t *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:91: warning: Member doInt64(int64_t *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:92: warning: Member doFloat(float *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:93: warning: Member doDouble(double *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:94: warning: Member doReal(real *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:95: warning: Member doIvec(ivec *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:96: warning: Member doRvec(rvec *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:97: warning: Member doString(std::string *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:98: warning: Member doOpaque(char *data, std::size_t size)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:112: warning: Member doCharArray(char *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:119: warning: Member doUCharArray(unsigned char *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:126: warning: Member doUShortArray(unsigned short *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:133: warning: Member doIntArray(int *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:140: warning: Member doInt32Array(int32_t *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:147: warning: Member doInt64Array(int64_t *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:154: warning: Member doFloatArray(float *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:161: warning: Member doDoubleArray(double *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:168: warning: Member doRealArray(real *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:175: warning: Member doIvecArray(ivec *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/iserializer.h:182: warning: Member doRvecArray(rvec *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/checkpointdata.h:146: warning: Member value (variable) of struct gmx::IsSerializableEnum is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/checkpointdata.h:133: warning: Member value (variable) of struct gmx::IsSerializableType is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/legacymdrunoptions.h:155: warning: Member ddrank_opt_choices[static_cast< int >(DdRankOrder::Count)+1] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/legacymdrunoptions.h:160: warning: Member dddlb_opt_choices[static_cast< int >(DlbOption::Count)+1] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/legacymdrunoptions.h:165: warning: Member thread_aff_opt_choices[static_cast< int >(ThreadAffinity::Count)+1] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/legacymdrunoptions.h:170: warning: Member nbpu_opt_choices[5] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/legacymdrunoptions.h:171: warning: Member pme_opt_choices[5] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/legacymdrunoptions.h:172: warning: Member pme_fft_opt_choices[5] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/legacymdrunoptions.h:173: warning: Member bonded_opt_choices[5] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/legacymdrunoptions.h:174: warning: Member update_opt_choices[5] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/legacymdrunoptions.h:175: warning: Member devicesSelectedByUser (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/legacymdrunoptions.h:176: warning: Member userGpuTaskAssignment (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/legacymdrunoptions.h:179: warning: Member imdOptions (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/legacymdrunoptions.h:181: warning: Member pa[48] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_lennardjones_functions.h:328: warning: Member LennardJonesCalculator(const interaction_const_t &ic) (function) of class gmx::LennardJonesCalculator< calculateEnergies, InteractionModifiers::ForceSwitch > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_lennardjones_functions.h:488: warning: Member LennardJonesCalculator(const interaction_const_t &ic) (function) of class gmx::LennardJonesCalculator< calculateEnergies, InteractionModifiers::PotSwitch > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_lennardjones_functions.h:175: warning: Member LennardJonesCalculator(const interaction_const_t gmx_unused &ic) (function) of class gmx::LennardJonesCalculator< false, InteractionModifiers::PotShift > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_lennardjones_functions.h:205: warning: Member forceSigmaEpsilon(const std::array< SimdReal, inputSize > &rInvV, const std::array< SimdBool, interactSize > &interactV, SimdBool *withinCutoffV, const std::array< SimdReal, nR > &sigmaV, const std::array< SimdReal, nR > &epsilonV, SimdReal sixth, SimdReal twelfth, std::array< SimdReal, nR > &frLJV, std::array< SimdReal, vljvSize > &vLJV) (function) of class gmx::LennardJonesCalculator< false, InteractionModifiers::PotShift > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_lennardjones_functions.h:227: warning: Member LennardJonesCalculator(const interaction_const_t &ic) (function) of class gmx::LennardJonesCalculator< true, InteractionModifiers::PotShift > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_lennardjones_functions.h:266: warning: Member forceSigmaEpsilon(const std::array< SimdReal, inputSize > &rInvV, const std::array< SimdBool, interactSize > &interactV, SimdBool *withinCutoffV, const std::array< SimdReal, nR > &sigmaV, const std::array< SimdReal, nR > &epsilonV, SimdReal sixth, SimdReal twelfth, std::array< SimdReal, nR > &frLJV, std::array< SimdReal, vljvSize > &vLJV) (function) of class gmx::LennardJonesCalculator< true, InteractionModifiers::PotShift > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/lincs.cpp:226: warning: Member tmpncc (variable) of class gmx::Lincs is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/lincs.cpp:227: warning: Member tmp1 (variable) of class gmx::Lincs is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/lincs.cpp:228: warning: Member tmp2 (variable) of class gmx::Lincs is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/lincs.cpp:229: warning: Member tmp3 (variable) of class gmx::Lincs is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/lincs.cpp:230: warning: Member tmp4 (variable) of class gmx::Lincs is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/mdgraph_gpu_impl.h:146: warning: Member Graph (typedef) of class gmx::MdGpuGraph::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/mdgraph_gpu_impl.h:147: warning: Member GraphInstance (typedef) of class gmx::MdGpuGraph::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrunutility/mdmodulesnotifiers.h:91: warning: Member MDModulesAtomsRedistributedSignal(const matrix box, gmx::ArrayRef< const RVec > x) (function) of struct gmx::MDModulesAtomsRedistributedSignal is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/runner.h:148: warning: Member operator=(Mdrunner &&handle) noexcept (function) of class gmx::Mdrunner is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/runner.h:394: warning: Member operator=(MdrunnerBuilder &&builder) noexcept (function) of class gmx::MdrunnerBuilder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/message_string_collector.h:67: warning: Member MessageStringCollector(MessageStringCollector &&) noexcept (function) of class gmx::MessageStringCollector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/include/gromacs/utility/message_string_collector.h:68: warning: Member operator=(MessageStringCollector &&) noexcept (function) of class gmx::MessageStringCollector is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/opencl/nbnxm_ocl_types.h:149: warning: Member kernel_noener_noprune_ptr[c_numElecTypes][c_numVdwTypes] (variable) of struct gmx::NbnxmGpu is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/opencl/nbnxm_ocl_types.h:150: warning: Member kernel_ener_noprune_ptr[c_numElecTypes][c_numVdwTypes] (variable) of struct gmx::NbnxmGpu is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/opencl/nbnxm_ocl_types.h:151: warning: Member kernel_noener_prune_ptr[c_numElecTypes][c_numVdwTypes] (variable) of struct gmx::NbnxmGpu is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/opencl/nbnxm_ocl_types.h:152: warning: Member kernel_ener_prune_ptr[c_numElecTypes][c_numVdwTypes] (variable) of struct gmx::NbnxmGpu is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/opencl/nbnxm_ocl_types.h:162: warning: Member kernel_memset_f (variable) of struct gmx::NbnxmGpu is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/opencl/nbnxm_ocl_types.h:163: warning: Member kernel_memset_f2 (variable) of struct gmx::NbnxmGpu is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/opencl/nbnxm_ocl_types.h:164: warning: Member kernel_memset_f3 (variable) of struct gmx::NbnxmGpu is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlistwork.h:62: warning: Member NbnxmPairlistCpuWork(const int iClusterSize) (function) of struct gmx::NbnxmPairlistCpuWork is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlistwork.h:67: warning: Member IClusterData(const int iClusterSize) (function) of struct gmx::NbnxmPairlistCpuWork::IClusterData is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.h:184: warning: Member nbnxn_atomdata_t(PinningPolicy pinningPolicy) (function) of struct gmx::nbnxn_atomdata_t is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/atomdata.h:224: warning: Member SimdMasks(NbnxmKernelType kernelType) (function) of struct gmx::nbnxn_atomdata_t::SimdMasks is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.h:286: warning: Member NbnxnPairlistCpu(int iClusterSize) (function) of struct gmx::NbnxnPairlistCpu is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/nnpotforceprovider.h:65: warning: Member NNPotForceProvider(const NNPotParameters &, const MDLogger *logger) (function) of class gmx::NNPotForceProvider is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/nnpotoptions.h:108: warning: Member modelNeedsInput(const std::string &input) const (function) of struct gmx::NNPotParameters is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/nnpotoptions.h:103: warning: Member numAtoms_ (variable) of struct gmx::NNPotParameters is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm.h:406: warning: Member setupFepThreadedForceBuffer(int numAtomsForce) (function) of struct gmx::nonbonded_verlet_t is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm.h:417: warning: Member localGrid() const (function) of struct gmx::nonbonded_verlet_t is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm.h:419: warning: Member setNonLocalGrid(int gridIndex, int ddZone, const GridDimensions &gridDimensions, ArrayRef< const std::pair< int, int > > columns, ArrayRef< const int32_t > atomInfo, ArrayRef< const RVec > x) (function) of struct gmx::nonbonded_verlet_t is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairlist.h:237: warning: Member PackedJClusterList(const PinningPolicy pinningPolicy) (function) of class gmx::PackedJClusterList is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:218: warning: Member allocator_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:219: warning: Member size_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:220: warning: Member reference (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:221: warning: Member const_reference (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:222: warning: Member storage_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:223: warning: Member pointer (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:224: warning: Member const_pointer (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:225: warning: Member iterator (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:226: warning: Member const_iterator (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:227: warning: Member difference_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:351: warning: Member data() const noexcept (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:353: warning: Member begin() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:354: warning: Member end() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:356: warning: Member cbegin() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:357: warning: Member cend() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:359: warning: Member begin() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:360: warning: Member end() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:362: warning: Member cbegin() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/include/gromacs/math/paddedvector.h:363: warning: Member cend() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/pairsearch.h:216: warning: Member setNonLocalGrid(int gridIndex, int zone, const GridDimensions &gridDimensions, ArrayRef< const std::pair< int, int > > columns, ArrayRef< const int32_t > atomInfo, ArrayRef< const RVec > x, nbnxn_atomdata_t *nbat) (function) of class gmx::PairSearch is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_force_sender_gpu.h:112: warning: Member waitForEvents() (function) of class gmx::PmeForceSenderGpu is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/pme_force_sender_gpu_impl.h:138: warning: Member waitForEvents() (function) of class gmx::PmeForceSenderGpu::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/qmmm/qmmmforceprovider.h:69: warning: Member QMMMForceProvider(const QMMMParameters ¶meters, const LocalAtomSet &localQMAtomSet, const LocalAtomSet &localMMAtomSet, PbcType pbcType, const MDLogger &logger) (function) of class gmx::QMMMForceProvider is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/qmmm/qmmmtypes.h:142: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(QMMMParameters) (function) of struct gmx::QMMMParameters is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/range.h:75: warning: Member iterator_category (typedef) of struct gmx::Range::iterator is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/range.h:76: warning: Member difference_type (typedef) of struct gmx::Range::iterator is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/range.h:77: warning: Member value_type (typedef) of struct gmx::Range::iterator is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/range.h:78: warning: Member pointer (typedef) of struct gmx::Range::iterator is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/range.h:79: warning: Member reference (typedef) of struct gmx::Range::iterator is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/restraint/manager.h:90: warning: Member operator=(const RestraintManager &)=default (function) of class gmx::RestraintManager is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/restraint/manager.h:91: warning: Member RestraintManager(RestraintManager &&) noexcept=default (function) of class gmx::RestraintManager is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/restraint/manager.h:92: warning: Member operator=(RestraintManager &&) noexcept=default (function) of class gmx::RestraintManager is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/restraint/restraintmdmodule_impl.h:287: warning: Member operator=(RestraintMDModuleImpl &&) noexcept=default (function) of class gmx::RestraintMDModuleImpl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/scattering-debye.h:104: warning: Member getIntensity(size_t qi) (function) of class gmx::ComputeDebyeScattering is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/scattering-debye.h:104: warning: Member getIntensity(size_t qi) (function) of class gmx::ComputeDebyeScattering is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/update_constrain_gpu_internal.h:63: warning: Member ScalingMatrix(const Matrix3x3 &m) (function) of struct gmx::ScalingMatrix is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/update_constrain_gpu_internal.h:67: warning: Member xx (variable) of struct gmx::ScalingMatrix is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/update_constrain_gpu_internal.h:67: warning: Member zz (variable) of struct gmx::ScalingMatrix is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/update_constrain_gpu_internal.h:67: warning: Member yx (variable) of struct gmx::ScalingMatrix is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/update_constrain_gpu_internal.h:67: warning: Member zx (variable) of struct gmx::ScalingMatrix is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/update_constrain_gpu_internal.h:67: warning: Member zy (variable) of struct gmx::ScalingMatrix is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/selection/selectioncollection.h:145: warning: Member SelectionCollection(const SelectionCollection &rhs) (function) of class gmx::SelectionCollection is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/selection/selectioncollection.h:146: warning: Member operator=(SelectionCollection rhs) (function) of class gmx::SelectionCollection is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/selection/selectioncollection.h:147: warning: Member swap(SelectionCollection &rhs) noexcept (function) of class gmx::SelectionCollection is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/evaluate.cpp:415: warning: found documented return type for gmx::SelectionEvaluator::evaluate that does not return anything /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulationinputhandle.h:139: warning: Member SimulationInputHandle(const SimulationInputHandle &source) (function) of class gmx::SimulationInputHandle is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulationinputhandle.h:140: warning: Member SimulationInputHandle(SimulationInputHandle &&) noexcept=default (function) of class gmx::SimulationInputHandle is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulationinputhandle.h:142: warning: Member operator=(const SimulationInputHandle &rhs) (function) of class gmx::SimulationInputHandle is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulationinputhandle.h:143: warning: Member operator=(SimulationInputHandle &&) noexcept=default (function) of class gmx::SimulationInputHandle is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.h:356: warning: Member add(MembedHolder &&membedHolder) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.h:358: warning: Member add(std::unique_ptr< StopHandlerBuilder > stopHandlerBuilder) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.h:360: warning: Member add(SimulatorStateData &&simulatorStateData) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.h:365: warning: Member add(SimulatorConfig &&simulatorConfig) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.h:372: warning: Member add(SimulatorEnv &&simulatorEnv) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.h:377: warning: Member add(Profiling &&profiling) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.h:379: warning: Member add(ConstraintsParam &&constraintsParam) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.h:384: warning: Member add(LegacyInput &&legacyInput) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.h:389: warning: Member add(ReplicaExchangeParameters &&replicaExchangeParameters) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.h:391: warning: Member add(InteractiveMD &&interactiveMd) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.h:396: warning: Member add(SimulatorModules &&simulatorModules) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.h:401: warning: Member add(CenterOfMassPulling &¢erOfMassPulling) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.h:406: warning: Member add(IonSwapping &&ionSwapping) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.h:411: warning: Member add(TopologyData &&topologyData) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/simulatorbuilder.h:416: warning: Member add(BoxDeformationHandle &&boxDeformation) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/options/basicoptionstorage.h:191: warning: Member formatSingleValue(const std::string &value) const override (function) of class gmx::StringOptionStorage is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/options/optionstoragetemplate.h:321: warning: Member normalizeValues(const std::vector< Any > &values) const override (function) of class OptionStorageTemplateSimple< std::string > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdrun/tpi.cpp:177: warning: Member TestParticleInsertion(const t_inputrec &inputRec, const gmx_mtop_t &topGlobal, const gmx_localtop_t &top, const t_mdatoms &mdatoms, const MDModulesNotifiers &mdModulesNotifiers, t_forcerec *forceRec, gmx_enerdata_t *enerd, const Range< int > &testAtomsRange, ArrayRef< const RVec > xMoleculeToInsert, real beta, real rfExclusionEnergy, real referenceVolume, int numTasks, int taskIndex) (function) of class gmx::TestParticleInsertion is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/threaded_force_buffer.h:120: warning: Member processMask() (function) of class gmx::ThreadForceBuffer is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/torchmodel.h:91: warning: Member prepareAtomNumbers(std::vector< int > &atomTypes) override (function) of class gmx::TorchModel is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/torchmodel.h:92: warning: Member prepareBox(matrix &box) override (function) of class gmx::TorchModel is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/nnpot/torchmodel.h:93: warning: Member preparePbcType(PbcType &pbcType) override (function) of class gmx::TorchModel is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/update.cpp:131: warning: Member update_coords(const t_inputrec &inputRecord, int64_t step, int homenr, bool havePartiallyFrozenAtoms, gmx::ArrayRef< const ParticleType > ptype, gmx::ArrayRef< const real > invMass, gmx::ArrayRef< const gmx::RVec > invMassPerDim, t_state *state, const gmx::ArrayRefWithPadding< const gmx::RVec > &f, t_fcdata *fcdata, const gmx_ekindata_t *ekind, const Matrix3x3 &parrinelloRahmanM, int UpdatePart, const t_commrec *cr, bool haveConstraints) (function) of class Update::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/update.cpp:147: warning: Member finish_update(const t_inputrec &inputRecord, bool havePartiallyFrozenAtoms, int homenr, gmx::ArrayRef< const unsigned short > cFREEZE, t_state *state, gmx_wallcycle *wcycle, bool haveConstraints) (function) of class Update::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/update.cpp:155: warning: Member update_sd_second_half(const t_inputrec &inputRecord, int64_t step, real *dvdlambda, int homenr, gmx::ArrayRef< const ParticleType > ptype, gmx::ArrayRef< const real > invMass, t_state *state, const t_commrec *cr, t_nrnb *nrnb, gmx_wallcycle *wcycle, gmx::Constraints *constr, bool do_log, bool do_ene) (function) of class Update::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/update.cpp:169: warning: Member update_for_constraint_virial(const t_inputrec &inputRecord, int homenr, bool havePartiallyFrozenAtoms, gmx::ArrayRef< const real > invmass, gmx::ArrayRef< const gmx::RVec > invMassPerDim, const t_state &state, const gmx::ArrayRefWithPadding< const gmx::RVec > &f, const gmx_ekindata_t &ekind) (function) of class Update::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/update.cpp:178: warning: Member update_temperature_constants(const t_inputrec &inputRecord, const gmx_ekindata_t &ekind) (function) of class Update::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/update.cpp:180: warning: Member getAndersenRandomizeGroup() const (function) of class Update::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/update.cpp:182: warning: Member getBoltzmanFactor() const (function) of class Update::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/update.cpp:184: warning: Member xp() (function) of class Update::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/update.cpp:186: warning: Member deform() const (function) of class Update::Impl is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/updategroups.h:113: warning: Member useUpdateGroups() const (function) of class gmx::UpdateGroups is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/updategroups.h:114: warning: Member maxUpdateGroupRadius() const (function) of class gmx::UpdateGroups is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/updategroups.h:115: warning: Member updateGroupingPerMoleculeType() const (function) of class gmx::UpdateGroups is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/checkpointdata.h:421: warning: Member empty() const (function) of class gmx::WriteCheckpointDataHolder is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/hbond.cpp:185: warning: Member c_maxHydrogensWithOxygen (variable) of namespace gmx::analysismodules::anonymous_namespace{hbond.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/hbond.cpp:187: warning: Member c_maxHydrogensWithNitrogen (variable) of namespace gmx::analysismodules::anonymous_namespace{hbond.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/hbond.cpp:189: warning: Member c_maxHydrogenBonds (variable) of namespace gmx::analysismodules::anonymous_namespace{hbond.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/hbond.cpp:135: warning: Member HbondStorageFrame(int frnr, std::vector< HBond > data) (function) of struct gmx::analysismodules::anonymous_namespace{hbond.cpp}::HbondStorageFrame is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/msd.cpp:294: warning: Member MsdCoordinateManager(const int numAtoms, ArrayRef< const MoleculeData > molecules, ArrayRef< const int > moleculeIndexMapping) (function) of class gmx::analysismodules::anonymous_namespace{msd.cpp}::MsdCoordinateManager is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/msd.cpp:124: warning: Member MsdColumnProxy(std::vector< double > *column) (function) of class gmx::analysismodules::anonymous_namespace{msd.cpp}::MsdData::MsdColumnProxy is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/msd.cpp:126: warning: Member push_back(double value) (function) of class gmx::analysismodules::anonymous_namespace{msd.cpp}::MsdData::MsdColumnProxy is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/modules/msd.cpp:380: warning: Member MsdGroupData(const Selection &inputSel, ArrayRef< const MoleculeData > molecules, ArrayRef< const int > moleculeAtomMapping) (function) of struct gmx::analysismodules::anonymous_namespace{msd.cpp}::MsdGroupData is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/awh_history.cpp:71: warning: Member doCheckpoint(CheckpointData< operation > checkpointData, AwhPointStateHistory *awhPointStateHistory) (function) of namespace gmx::anonymous_namespace{awh_history.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/awh_history.cpp:88: warning: Member doCheckpoint(CheckpointData< operation > checkpointData, AwhBiasStateHistory *awhBiasStateHistory) (function) of namespace gmx::anonymous_namespace{awh_history.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/awh_history.cpp:102: warning: Member doCheckpoint(CheckpointData< operation > checkpointData, CorrelationBlockDataHistory *correlationBlockDataHistory) (function) of namespace gmx::anonymous_namespace{awh_history.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/awh_history.cpp:123: warning: Member doCheckpoint(CheckpointData< operation > checkpointData, CorrelationGridHistory *correlationGridHistory) (function) of namespace gmx::anonymous_namespace{awh_history.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/awh_history.cpp:144: warning: Member doCheckpointData(CheckpointData< operation > checkpointData, AwhBiasHistory *awhBiasHistory) (function) of namespace gmx::anonymous_namespace{awh_history.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/awh_history.cpp:68: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{awh_history.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/domainpaircomm.cpp:242: warning: Member filterBondComm (variable) of struct gmx::anonymous_namespace{domainpaircomm.cpp}::DistanceCalculationInfo is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/electricfield.cpp:186: warning: @copybrief or @copydoc target 'IForceProvider::calculateForces()' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/electricfield.cpp:186: warning: @copybrief or @copydoc target 'IForceProvider::calculateForces()' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/electricfield.cpp:187: warning: @copydetails or @copydoc target 'IForceProvider::calculateForces()' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/energydata.cpp:402: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{energydata.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/expandedensembleelement.cpp:129: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{expandedensembleelement.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/firstorderpressurecoupling.cpp:183: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{firstorderpressurecoupling.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/freeenergydispatch.cpp:160: warning: Member dispatchFreeEnergyKernel(gmx::ArrayRef< const std::unique_ptr< t_nblist > > nbl_fep, const gmx::ArrayRefWithPadding< const gmx::RVec > &coords, bool useSimd, int ntype, const interaction_const_t &ic, gmx::ArrayRef< const gmx::RVec > shiftvec, gmx::ArrayRef< const real > nbfp, gmx::ArrayRef< const real > nbfp_grid, gmx::ArrayRef< const real > chargeA, gmx::ArrayRef< const real > chargeB, gmx::ArrayRef< const int > typeA, gmx::ArrayRef< const int > typeB, gmx::ArrayRef< const real > lambda, const bool clearForcesAndEnergies, gmx::ThreadedForceBuffer< gmx::RVec > *threadedForceBuffer, gmx::ThreadedForceBuffer< gmx::RVec > *threadedForeignEnergyBuffer, gmx_grppairener_t *foreignGroupPairEnergies, gmx_enerdata_t *enerd, const gmx::StepWorkload &stepWork, t_nrnb *nrnb) (function) of namespace gmx::anonymous_namespace{freeenergydispatch.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/freeenergyparameters.cpp:62: warning: Member lambdasAtState(const int stateIndex, gmx::ArrayRef< const std::vector< double > > lambdaArray, const int lambdaArrayExtent) (function) of namespace gmx::anonymous_namespace{freeenergyparameters.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/freeenergyperturbationdata.cpp:176: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{freeenergyperturbationdata.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/domdec/haloexchangesetup.cpp:157: warning: Member isMissingALink(const ArrayRef< const int > &links, const gmx_ga2la_t &ga2la) (function) of namespace gmx::anonymous_namespace{haloexchangesetup.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/hardwaretopology.cpp:1103: warning: Member detectCpuLimit(const std::string &root="") (function) of namespace gmx::anonymous_namespace{hardwaretopology.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/hardwaretopology.cpp:1184: warning: Member setMaxThreads(float cpuLimit, int topologyCpus, int systemCpus) (function) of namespace gmx::anonymous_namespace{hardwaretopology.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/mttk.cpp:281: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{mttk.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/hip/nbnxm_hip_data_mgmt.cpp:97: warning: Member hipRocprimWrapper(size_t temporaryBufferSize, char *temporaryBuffer, gmx::GpuPairlist *plist, const DeviceStream &deviceStream) (function) of namespace gmx::anonymous_namespace{nbnxm_hip_data_mgmt.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/neldermead.cpp:102: warning: Member defaultNelderMeadParameters (variable) of namespace gmx::anonymous_namespace{neldermead.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp:298: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{parrinellorahmanbarostat.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/plumed/tests/plumedOptions.cpp:191: warning: Member getTopologyFromSimulationDatabase(gmx_mtop_t *const mtop, const std::string &fileName) (function) of namespace gmx::anonymous_namespace{plumedOptions.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/propagator.cpp:63: warning: Member integrationStepNames (variable) of namespace gmx::anonymous_namespace{propagator.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator/pullelement.cpp:121: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{pullelement.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_kernel.h:110: warning: Member EnergyAccumulatorGetter(nbnxn_atomdata_output_t gmx_unused *out) (function) of class gmx::anonymous_namespace{simd_kernel.h}::EnergyAccumulatorGetter< false, false > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_kernel.h:112: warning: Member get() (function) of class gmx::anonymous_namespace{simd_kernel.h}::EnergyAccumulatorGetter< false, false > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_kernel.h:120: warning: Member EnergyAccumulatorGetter(nbnxn_atomdata_output_t *out) (function) of class gmx::anonymous_namespace{simd_kernel.h}::EnergyAccumulatorGetter< false, true > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_kernel.h:122: warning: Member get() (function) of class gmx::anonymous_namespace{simd_kernel.h}::EnergyAccumulatorGetter< false, true > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_kernel.h:136: warning: Member EnergyAccumulatorGetter(nbnxn_atomdata_output_t *out) (function) of class gmx::anonymous_namespace{simd_kernel.h}::EnergyAccumulatorGetter< true, true > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/simd_kernel.h:138: warning: Member get() (function) of class gmx::anonymous_namespace{simd_kernel.h}::EnergyAccumulatorGetter< true, true > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/pointers.h:194: warning: Member operator!=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() !=rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/pointers.h:200: warning: Member operator<(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get()< rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/pointers.h:206: warning: Member operator<=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get()<=rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/pointers.h:212: warning: Member operator>(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() > rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/pointers.h:218: warning: Member operator>=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() >=rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/pointers.h:134: warning: Member not_null(const not_null &other)=default (function) of class gmx::compat::not_null is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/pointers.h:135: warning: Member operator=(const not_null &other)=default (function) of class gmx::compat::not_null is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/pointers.h:146: warning: Member operator T() const (function) of class gmx::compat::not_null is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/compat/pointers.h:147: warning: Member operator->() const (function) of class gmx::compat::not_null is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:49: warning: Member c_nBoxZ (variable) of namespace gmx::detail is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:50: warning: Member c_nBoxY (variable) of namespace gmx::detail is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:51: warning: Member c_nBoxX (variable) of namespace gmx::detail is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:52: warning: Member c_numIvecs (variable) of namespace gmx::detail is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:180: warning: Member c_gpuNumClusterPerCellY (variable) of namespace gmx::detail is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/nbnxm_enums.h:181: warning: Member c_gpuNumClusterPerCellX (variable) of namespace gmx::detail is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:479: warning: Member SimdTraitsT (typedef) of namespace gmx::internal is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd.h:618: warning: Member Simd4TraitsT (typedef) of namespace gmx::internal is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:87: warning: Member IExceptionInfo(const IExceptionInfo &)=default (function) of class gmx::internal::IExceptionInfo is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:88: warning: Member IExceptionInfo(IExceptionInfo &&) noexcept=default (function) of class gmx::internal::IExceptionInfo is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:89: warning: Member operator=(const IExceptionInfo &)=default (function) of class gmx::internal::IExceptionInfo is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:90: warning: Member operator=(IExceptionInfo &&) noexcept=default (function) of class gmx::internal::IExceptionInfo is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/options/options_impl.h:200: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(OptionSectionImpl) (function) of class gmx::internal::OptionSectionImpl is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd_memory.h:154: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(pointer, pointer)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd_memory.h:163: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd_memory.h:154: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(pointer, pointer)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd_memory.h:155: warning: @copydetails or @copydoc target 'ArrayRef::ArrayRef(pointer, pointer)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd_memory.h:163: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/simd/include/gromacs/simd/simd_memory.h:164: warning: @copydetails or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/tests/fft_mpi.cpp:72: warning: Member GpuFftTestParams (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/tests/fft_mpi.cpp:77: warning: Member GpuFftTestGridParams (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/gyrate.cpp:71: warning: Member GyrateTestParamsMerge (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/hbond.cpp:71: warning: Member HbondTestParamsMerge (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/simulatorcomparison.h:62: warning: Member SimulationOptionTuple (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/tests/fft_mpi.cpp:79: warning: Member getGpuAwareMpiStatusForFftBackend(const FftBackend fftBackend) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/tests/device_availability.cpp:73: warning: Member getRequiredNumberOfDevices() (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gpu_utils/tests/typecasts_runner_hip.cpp:64: warning: Member saveFloat3InRVecFormat(ArrayRef< gmx::RVec > rVecOutput, const float3 *float3Output, int numElements) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:85: warning: Member EXPECT_EQ(0, reinterpret_cast< std::size_t >(p) &this->mask(a)) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:86: warning: Member deallocate(p, 1000) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:93: warning: Member v(10) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:94: warning: Member EXPECT_EQ(0, reinterpret_cast< std::size_t >(v.data()) &this->mask(v.get_allocator())) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:99: warning: Member for(std::size_t i=1000;i<=10000;i+=1000) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:125: warning: Member v1(1) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:127: warning: Member EXPECT_NE(data, nullptr) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:128: warning: Member v2(std::move(v1)) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:129: warning: Member EXPECT_EQ(data, v2.data()) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/simulatorcomparison.cpp:72: warning: Member runGrompp(SimulationRunner *runner, const std::vector< SimulationOptionTuple > &options) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/simulatorcomparison.cpp:85: warning: Member runMdrun(SimulationRunner *runner, const std::vector< SimulationOptionTuple > &options) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/simulatorcomparison.cpp:98: warning: Member compareEnergies(const std::string &edr1Name, const std::string &edr2Name, const EnergyTermsToCompare &energyTermsToCompare, const MaxNumFrames maxNumFrames) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/simulatorcomparison.cpp:119: warning: Member compareTrajectories(const std::string &trajectory1Name, const std::string &trajectory2Name, const TrajectoryComparison &trajectoryComparison) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/tests/pmegathertest.cpp:445: warning: Member registerDynamicalPmeGatherTests(const Range< int > hardwareContextIndexRange) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/tests/pmesolvetest.cpp:435: warning: Member registerDynamicalPmeSolveTests(const Range< int > hardwareContextIndexRange) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/trajectorycomparison.cpp:425: warning: Member checkTrajectoryAgainstReferenceData(const std::string &trajectoryFilename, const TrajectoryComparison &trajectoryComparison, TestReferenceChecker *checker, MaxNumFrames maxNumFrames) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/friction_metric.cpp:82: warning: Member g_sampleWeightCentral (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/friction_metric.cpp:83: warning: Member g_sampleWeightNeighbor (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/friction_metric.cpp:84: warning: Member g_sampleTimeStep (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/friction_metric.cpp:85: warning: Member g_numPointsPerDim (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/tests/fft_mpi.cpp:266: warning: Member inputGrids (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/tests/fft_mpi.cpp:270: warning: Member inputBackends (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:82: warning: Member a (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:83: warning: Member p (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/alignedallocator_impl.h:126: warning: Member data (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/awh_setup.h:74: warning: Member AwhTestParameters(ISerializer *serializer) (function) of struct gmx::test::AwhTestParameters is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/moduletest.h:211: warning: Member createModule() override (function) of class TrajectoryAnalysisModuleTestFixture< gmx::analysismodules::GyrateInfo > is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/moduletest.h:211: warning: Member createModule() override (function) of class TrajectoryAnalysisModuleTestFixture< gmx::analysismodules::HbondInfo > is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/naming.h:414: warning: Member Formatters (typedef) of class gmx::test::NameOfTestFromTuple is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/naming.h:530: warning: Member operator()(const T &t) (function) of struct gmx::test::PrefixFormatter is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/naming.h:529: warning: Member prefix (variable) of struct gmx::test::PrefixFormatter is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/replicaexchange_equivalence.cpp:276: warning: Member operator()(const testing::TestParamInfo< ParamType > ¶meter) const (function) of struct gmx::test::PrintReplicaExchangeParametersToString is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/naming.h:464: warning: Member Formatters (typedef) of class gmx::test::RefDataFilenameMaker is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/moduletest.h:162: warning: Member topFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/moduletest.h:163: warning: Member groFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/moduletest.h:164: warning: Member mdpFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/moduletest.h:165: warning: Member fullPrecisionTrajectoryFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/moduletest.h:166: warning: Member reducedPrecisionTrajectoryFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/moduletest.h:167: warning: Member groOutputFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/moduletest.h:168: warning: Member cptOutputFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/moduletest.h:169: warning: Member ndxFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/moduletest.h:170: warning: Member mdpOutputFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/moduletest.h:171: warning: Member tprFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/moduletest.h:172: warning: Member logFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/moduletest.h:173: warning: Member edrFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/moduletest.h:174: warning: Member mtxFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/moduletest.h:175: warning: Member swapFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/moduletest.h:176: warning: Member dhdlFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/moduletest.h:177: warning: Member nsteps_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/moduletest.h:178: warning: Member maxwarn_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/tests/toputils.h:73: warning: Member requestVelocities() (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/tests/toputils.h:74: warning: Member requestForces() (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/tests/toputils.h:75: warning: Member initFrameIndices(const ArrayRef< const int > &index) (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/tests/toputils.h:86: warning: Member initAtomTypes(const ArrayRef< const char *const > &types) (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/tests/toputils.h:87: warning: Member initUniformResidues(int residueSize) (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/tests/toputils.h:88: warning: Member initUniformMolecules(int moleculeSize) (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/tests/toputils.h:104: warning: Member setMoleculeType(int moleculeTypeIndex, ArrayRef< const int > residueSizes) (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/tests/toputils.h:105: warning: Member setMoleculeBlock(int moleculeBlockIndex, int moleculeTypeIndex, int numMoleculesToAdd) (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/tests/toputils.h:106: warning: Member finalizeTopology() (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/tests/toputils.h:112: warning: Member atoms() (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/tests/toputils.h:113: warning: Member frame() (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/trajectorycomparison.h:68: warning: Member coordinates (variable) of struct gmx::test::TrajectoryTolerances is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/trajectorycomparison.h:68: warning: Member velocities (variable) of struct gmx::test::TrajectoryTolerances is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/trajectorycomparison.h:68: warning: Member forces (variable) of struct gmx::test::TrajectoryTolerances is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/biasstate.cpp:147: warning: Member grid_ (variable) of class gmx::test::UserInputTest is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/biasstate.cpp:148: warning: Member gridIndexToDataIndex_ (variable) of class gmx::test::UserInputTest is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/biasstate.cpp:149: warning: Member data_ (variable) of class gmx::test::UserInputTest is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/biasstate.cpp:150: warning: Member numColumns_ (variable) of class gmx::test::UserInputTest is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/biasstate.cpp:151: warning: Member numRows_ (variable) of class gmx::test::UserInputTest is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/applied_forces/awh/tests/biasstate.cpp:152: warning: Member filename_ (variable) of class gmx::test::UserInputTest is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/options/abstractoptionstorage.h:144: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/options/abstractoptionstorage.h:144: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/options/abstractoptionstorage.h:145: warning: @copydetails or @copydoc target 'OptionInfo::normalizeValues()' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/checkpointdata.cpp:361: warning: Member WriteFunction (typedef) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::CheckpointDataTest is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/checkpointdata.cpp:362: warning: Member TestFunction (typedef) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::CheckpointDataTest is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/checkpointdata.cpp:371: warning: Member addTestValues() (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::CheckpointDataTest is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/checkpointdata.cpp:389: warning: Member test() (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::CheckpointDataTest is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/checkpointdata.cpp:365: warning: Member writeFunctions_ (variable) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::CheckpointDataTest is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/checkpointdata.cpp:367: warning: Member testFunctions_ (variable) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::CheckpointDataTest is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/checkpointdata.cpp:437: warning: Member addTestValueFunctions_ (variable) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::CheckpointDataTest is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/checkpointdata.cpp:453: warning: Member testingTypes_ (variable) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::CheckpointDataTest is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/checkpointdata.cpp:467: warning: Member fileManager_ (variable) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::CheckpointDataTest is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/checkpointdata.cpp:468: warning: Member filename_ (variable) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::CheckpointDataTest is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/checkpointdata.cpp:77: warning: Member value (variable) of struct gmx::test::anonymous_namespace{checkpointdata.cpp}::IsVectorOfSerializableType is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/checkpointdata.cpp:184: warning: Member getTestVector() (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::TestValues is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/checkpointdata.cpp:190: warning: Member getTestVector() (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::TestValues is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/checkpointdata.cpp:196: warning: Member getTestVector() (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::TestValues is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/checkpointdata.cpp:202: warning: Member getTestVector() (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::TestValues is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/checkpointdata.cpp:208: warning: Member getTestVector() (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::TestValues is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/checkpointdata.cpp:118: warning: Member begin() const (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::TestValues::TestValueGenerator is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/checkpointdata.cpp:119: warning: Member end() const (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::TestValues::TestValueGenerator is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/checkpointdata.cpp:109: warning: Member Iterator(const T *ptr) (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::TestValues::TestValueGenerator::Iterator is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/checkpointdata.cpp:110: warning: Member operator++() (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::TestValues::TestValueGenerator::Iterator is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/checkpointdata.cpp:111: warning: Member operator!=(const Iterator &other) const (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::TestValues::TestValueGenerator::Iterator is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/checkpointdata.cpp:112: warning: Member operator*() const (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::TestValues::TestValueGenerator::Iterator is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/cmdlinetest.cpp:266: warning: Member ViewMatchesCString(const std::string_view view) (function) of struct gmx::test::anonymous_namespace{cmdlinetest.cpp}::ViewMatchesCString is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/cmdlinetest.cpp:265: warning: Member view_ (variable) of struct gmx::test::anonymous_namespace{cmdlinetest.cpp}::ViewMatchesCString is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/pbcutil/tests/com.cpp:128: warning: Member COMInPlaceTestParams (typedef) of namespace gmx::test::anonymous_namespace{com.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/constr.cpp:98: warning: Member c_pbcs (variable) of namespace gmx::test::anonymous_namespace{constr.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/constr.cpp:172: warning: Member c_constraintsTestSystemList (variable) of namespace gmx::test::anonymous_namespace{constr.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/convparm.cpp:210: warning: Member ftypeToName(const int ftype) (function) of namespace gmx::test::anonymous_namespace{convparm.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/convparm.cpp:216: warning: Member sc_testNamer (variable) of namespace gmx::test::anonymous_namespace{convparm.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/cstringutil.cpp:103: warning: Member testInplace(F f, const char *input, const char *expectedOutput) (function) of namespace gmx::test::anonymous_namespace{cstringutil.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/tests/device_management.cpp:111: warning: Member uuidToString(const std::array< std::byte, 16 > &uuid) (function) of namespace gmx::test::anonymous_namespace{device_management.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/dssp.cpp:76: warning: Member DsspTestParams (typedef) of namespace gmx::test::anonymous_namespace{dssp.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/moduletest.h:211: warning: Member createModule() override (function) of class TrajectoryAnalysisModuleTestFixture< gmx::analysismodules::DsspInfo > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/enerdata.cpp:78: warning: Member makeFepvals(const std::vector< double > &lambdaVdw, const std::vector< double > &lambdaCoul) (function) of namespace gmx::test::anonymous_namespace{enerdata.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/enerdata.cpp:69: warning: Member c_numLambdas (variable) of namespace gmx::test::anonymous_namespace{enerdata.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/enerdata.cpp:71: warning: Member dhdlVdw (variable) of namespace gmx::test::anonymous_namespace{enerdata.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/enerdata.cpp:72: warning: Member dhdlCoul (variable) of namespace gmx::test::anonymous_namespace{enerdata.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/enerdata.cpp:74: warning: Member dhdlLinearZero (variable) of namespace gmx::test::anonymous_namespace{enerdata.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/enumerationhelpers.cpp:183: warning: Member Unsuitable (enumeration) of namespace gmx::test::anonymous_namespace{enumerationhelpers.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/tests/exclusions.cpp:228: warning: Member testKernelTypes (variable) of namespace gmx::test::anonymous_namespace{exclusions.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/expandedensemble.cpp:93: warning: Member currentState (variable) of struct gmx::test::anonymous_namespace{expandedensemble.cpp}::LambdaInformation is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/expandedensemble.cpp:94: warning: Member perLambdaInformation (variable) of struct gmx::test::anonymous_namespace{expandedensemble.cpp}::LambdaInformation is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/expandedensemble.cpp:95: warning: Member finalPos (variable) of struct gmx::test::anonymous_namespace{expandedensemble.cpp}::LambdaInformation is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/expandedensemble.cpp:82: warning: Member index (variable) of struct gmx::test::anonymous_namespace{expandedensemble.cpp}::PerLambdaInformation is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/expandedensemble.cpp:83: warning: Member count (variable) of struct gmx::test::anonymous_namespace{expandedensemble.cpp}::PerLambdaInformation is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/expandedensemble.cpp:83: warning: Member G (variable) of struct gmx::test::anonymous_namespace{expandedensemble.cpp}::PerLambdaInformation is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/expandedensemble.cpp:83: warning: Member dG (variable) of struct gmx::test::anonymous_namespace{expandedensemble.cpp}::PerLambdaInformation is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/fft/tests/fft.cpp:303: warning: Member FFTTest3DParameters (typedef) of namespace gmx::test::anonymous_namespace{fft.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/fileioxdrserializer.cpp:82: warning: Member c_int32Value (variable) of namespace gmx::test::anonymous_namespace{fileioxdrserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/fileioxdrserializer.cpp:83: warning: Member c_int64Value (variable) of namespace gmx::test::anonymous_namespace{fileioxdrserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/fileioxdrserializer.cpp:85: warning: Member c_intAndFloat32 (variable) of namespace gmx::test::anonymous_namespace{fileioxdrserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/fileioxdrserializer.cpp:86: warning: Member c_intAndFloat64 (variable) of namespace gmx::test::anonymous_namespace{fileioxdrserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/filetypes.cpp:63: warning: Member TypeAndName (typedef) of namespace gmx::test::anonymous_namespace{filetypes.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/filetypes.cpp:65: warning: Member FileTypeTestParams (typedef) of namespace gmx::test::anonymous_namespace{filetypes.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/filetypes.cpp:116: warning: Member testParams (variable) of namespace gmx::test::anonymous_namespace{filetypes.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/filetypes.cpp:125: warning: Member prefixes (variable) of namespace gmx::test::anonymous_namespace{filetypes.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/forcebuffers.cpp:66: warning: Member c_forces (variable) of namespace gmx::test::anonymous_namespace{forcebuffers.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/freeenergy.cpp:88: warning: Member ListOfInteractionsToTest (typedef) of namespace gmx::test::anonymous_namespace{freeenergy.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/freeenergy.cpp:89: warning: Member FreeEnergyReferenceTestParams (typedef) of namespace gmx::test::anonymous_namespace{freeenergy.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/functions.cpp:399: warning: Member IntegerTypes (typedef) of namespace gmx::test::anonymous_namespace{functions.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/grompp_directives.cpp:76: warning: Member ExpectedResult (enumeration) of namespace gmx::test::anonymous_namespace{grompp_directives.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/grompp_directives.cpp:222: warning: Member cmapValidInputOutput (variable) of namespace gmx::test::anonymous_namespace{grompp_directives.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/index.cpp:72: warning: Member checkIndexGroup(TestReferenceChecker *checker, const IndexGroup &group) (function) of namespace gmx::test::anonymous_namespace{index.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/index.cpp:79: warning: Member checkBlocks(TestReferenceChecker *checker, ArrayRef< const IndexGroup > blocks) (function) of namespace gmx::test::anonymous_namespace{index.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/index.cpp:86: warning: Member compareBlocks(ArrayRef< const IndexGroup > one, ArrayRef< const IndexGroup > two) (function) of namespace gmx::test::anonymous_namespace{index.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/topology/tests/index.cpp:100: warning: Member checkFileMatch(TestReferenceChecker *checker, const std::string &fileName, const std::string &fullPath) (function) of namespace gmx::test::anonymous_namespace{index.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/tests/indexutil.cpp:102: warning: Member setGroup(const int(&atoms)[count]) (function) of class gmx::test::anonymous_namespace{indexutil.cpp}::IndexBlockTest is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/inmemoryserializer.cpp:80: warning: Member c_int16ValueSwapped (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/inmemoryserializer.cpp:81: warning: Member c_int32Value (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/inmemoryserializer.cpp:82: warning: Member c_int32ValueSwapped (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/inmemoryserializer.cpp:83: warning: Member c_int64Value (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/inmemoryserializer.cpp:84: warning: Member c_int64ValueSwapped (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/inmemoryserializer.cpp:86: warning: Member c_intAndFloat32 (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/inmemoryserializer.cpp:87: warning: Member c_intAndFloat64 (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/inmemoryserializer.cpp:89: warning: Member c_intAndFloat32Swapped (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/inmemoryserializer.cpp:90: warning: Member c_intAndFloat64Swapped (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/tests/kernel_test.cpp:404: warning: Member isTabulated(const CoulombKernelType coulombKernelType) (function) of namespace gmx::test::anonymous_namespace{kernel_test.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/tests/kernel_test.cpp:357: warning: Member coulombKernelTypeName (variable) of namespace gmx::test::anonymous_namespace{kernel_test.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/tests/kernel_test.cpp:363: warning: Member vdwKernelTypeName (variable) of namespace gmx::test::anonymous_namespace{kernel_test.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/nbnxm/tests/kernel_test.cpp:280: warning: Member KernelInputParameters(TupleT t) (function) of struct gmx::test::anonymous_namespace{kernel_test.cpp}::KernelInputParameters is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxpreprocess/tests/massrepartitioning.cpp:62: warning: Member setupMTop(gmx_mtop_t *mtop, ArrayRef< const real > masses, ArrayRef< const int > bonds) (function) of namespace gmx::test::anonymous_namespace{massrepartitioning.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/matio.cpp:76: warning: Member generateStdReferenceFile(gmx::ArrayRef< const t_mapping > refMaps) (function) of namespace gmx::test::anonymous_namespace{matio.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/matio.cpp:94: warning: Member getReferenceMapping() (function) of namespace gmx::test::anonymous_namespace{matio.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/matio.cpp:211: warning: Member generateReferenceMatrix4x3() (function) of namespace gmx::test::anonymous_namespace{matio.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/matio.cpp:234: warning: Member compareRealValues(const t_matrix &input, real **values, basic_mdspan< const float, extents< 4, 3 > > ref) (function) of namespace gmx::test::anonymous_namespace{matio.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/minimize.cpp:176: warning: Member minimizersToTest_g (variable) of namespace gmx::test::anonymous_namespace{minimize.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/minimize.cpp:178: warning: Member constrainedSystemsToTest_g (variable) of namespace gmx::test::anonymous_namespace{minimize.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/minimize.cpp:181: warning: Member minimizersToTestWithConstraints_g (variable) of namespace gmx::test::anonymous_namespace{minimize.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/tests/mockhardwaretopology.cpp:166: warning: Member checkHardwareTopology(TestReferenceChecker *checker, const HardwareTopology &hwTop) (function) of namespace gmx::test::anonymous_namespace{mockhardwaretopology.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/hardware/tests/mockhardwaretopology.cpp:260: warning: Member runTest(const HardwareTopology &hwTop) (function) of class gmx::test::anonymous_namespace{mockhardwaretopology.cpp}::MockHardwareTopologyTest is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/msd.cpp:99: warning: Member checkDiffusionCoefficientDataPoint(TestReferenceChecker *checker, const std::string &value) (function) of namespace gmx::test::anonymous_namespace{msd.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdtypes/tests/multipletimestepping.cpp:147: warning: Member simpleMtsOpts() (function) of namespace gmx::test::anonymous_namespace{multipletimestepping.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:110: warning: Member c_numAtomTypes (variable) of namespace gmx::test::anonymous_namespace{nb_free_energy.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:520: warning: Member c_softcoreBeutlerAlphaOrGapsysLinpointScaling (variable) of namespace gmx::test::anonymous_namespace{nb_free_energy.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:521: warning: Member c_softcoreCoulomb (variable) of namespace gmx::test::anonymous_namespace{nb_free_energy.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:522: warning: Member c_softcoreType (variable) of namespace gmx::test::anonymous_namespace{nb_free_energy.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:361: warning: Member getNbList() (function) of struct gmx::test::anonymous_namespace{nb_free_energy.cpp}::AtomData is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:344: warning: Member idef (variable) of struct gmx::test::anonymous_namespace{nb_free_energy.cpp}::AtomData is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:347: warning: Member chargeA (variable) of struct gmx::test::anonymous_namespace{nb_free_energy.cpp}::AtomData is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:348: warning: Member chargeB (variable) of struct gmx::test::anonymous_namespace{nb_free_energy.cpp}::AtomData is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:349: warning: Member typeA (variable) of struct gmx::test::anonymous_namespace{nb_free_energy.cpp}::AtomData is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:350: warning: Member typeB (variable) of struct gmx::test::anonymous_namespace{nb_free_energy.cpp}::AtomData is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:354: warning: Member iAtoms (variable) of struct gmx::test::anonymous_namespace{nb_free_energy.cpp}::AtomData is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:355: warning: Member jAtoms (variable) of struct gmx::test::anonymous_namespace{nb_free_energy.cpp}::AtomData is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:356: warning: Member shift (variable) of struct gmx::test::anonymous_namespace{nb_free_energy.cpp}::AtomData is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:357: warning: Member gid (variable) of struct gmx::test::anonymous_namespace{nb_free_energy.cpp}::AtomData is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:358: warning: Member exclFep (variable) of struct gmx::test::anonymous_namespace{nb_free_energy.cpp}::AtomData is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/normalmodes.cpp:171: warning: Member GTEST_ALLOW_UNINSTANTIATED_PARAMETERIZED_TEST(NormalModesTest) (function) of namespace gmx::test::anonymous_namespace{normalmodes.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/math/tests/optimization.cpp:66: warning: Member mcCormick(ArrayRef< const real > x) (function) of namespace gmx::test::anonymous_namespace{optimization.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/tests/pairs.cpp:209: warning: Member frHelper (variable) of namespace gmx::test::anonymous_namespace{pairs.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/tests/pairs.cpp:111: warning: Member OutputQuantities(int energyGroup) (function) of struct gmx::test::anonymous_namespace{pairs.cpp}::OutputQuantities is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/parrinellorahman.cpp:149: warning: Member sc_boxShapeNames (variable) of namespace gmx::test::anonymous_namespace{parrinellorahman.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/parrinellorahman.cpp:180: warning: Member operator()(const Matrix3x3 &matrix) const (function) of struct gmx::test::anonymous_namespace{parrinellorahman.cpp}::Matrix3x3ToString is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/mdlib/tests/parrinellorahman.cpp:179: warning: Member prefix (variable) of struct gmx::test::anonymous_namespace{parrinellorahman.cpp}::Matrix3x3ToString is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/tests/pmesolvetest.cpp:129: warning: Member enumValueToString(PmeSolveAlgorithm enumValue) (function) of namespace gmx::test::anonymous_namespace{pmesolvetest.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/tests/pmesolvetest.cpp:136: warning: Member enumValueToString(GridOrdering enumValue) (function) of namespace gmx::test::anonymous_namespace{pmesolvetest.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:192: warning: Member enumValueToString(SplineAndSpreadOptions enumValue) (function) of namespace gmx::test::anonymous_namespace{pmesplinespreadtest.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:104: warning: Member c_testSystems (variable) of namespace gmx::test::anonymous_namespace{pmesplinespreadtest.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/pmetest.cpp:116: warning: Member PmeTestParameters (typedef) of namespace gmx::test::anonymous_namespace{pmetest.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/pmetest.cpp:382: warning: Member c_reproducesEnergies (variable) of namespace gmx::test::anonymous_namespace{pmetest.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/listed_forces/tests/position_restraints.cpp:159: warning: Member c_emptyLambdas (variable) of namespace gmx::test::anonymous_namespace{position_restraints.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/pull.cpp:178: warning: Member isTransformationPullSetup(const std::string &pullSetupName) (function) of namespace gmx::test::anonymous_namespace{pull.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/pull.cpp:84: warning: Member c_mdpPullParams (variable) of namespace gmx::test::anonymous_namespace{pull.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/refdata_xml.cpp:102: warning: Member getCDataChildNode(XMLNodePtr node) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/refdata_xml.cpp:112: warning: Member hasCDataContent(XMLNodePtr node) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/refdata_xml.cpp:340: warning: Member createElementAndContents(XMLElementPtr parentElement, const ReferenceDataEntry &entry) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/refdata_xml.cpp:253: warning: Member setIdAttribute(XMLElementPtr element, const std::string &id) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/refdata_xml.cpp:261: warning: Member createElement(XMLElementPtr parentElement, const ReferenceDataEntry &entry) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/refdata_xml.cpp:269: warning: Member createChildElements(XMLElementPtr parentElement, const ReferenceDataEntry &entry) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/refdata_xml.cpp:311: warning: Member createElementContents(XMLElementPtr element, const ReferenceDataEntry &entry) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/refdata_xml.cpp:346: warning: Member createRootElement(XMLDocumentPtr document) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/rerun.cpp:126: warning: Member executeRerunTest(TestFileManager *fileManager, SimulationRunner *runner, const std::string &simulationName, int numWarningsToTolerate, const MdpFieldValues &mdpFieldValues, const EnergyTermsToCompare &energyTermsToCompare, const TrajectoryComparison &trajectoryComparison) (function) of namespace gmx::test::anonymous_namespace{rerun.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/scattering.cpp:71: warning: Member ScatteringTestDirectModeParams (typedef) of namespace gmx::test::anonymous_namespace{scattering.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2025.0/src/gromacs/trajectoryanalysis/tests/moduletest.h:211: warning: Member createModule() override (function) of class TrajectoryAnalysisModuleTestFixture< gmx::analysismodules::ScatteringInfo > is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/scope_guard.cpp:61: warning: Member DeleterType (typedef) of namespace gmx::test::anonymous_namespace{scope_guard.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/scope_guard.cpp:79: warning: Member deleterSetter(int object) (function) of namespace gmx::test::anonymous_namespace{scope_guard.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/scope_guard.cpp:105: warning: Member makeGuard(int object, DeleterType deleter) (function) of namespace gmx::test::anonymous_namespace{scope_guard.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/simple_mdrun.cpp:196: warning: Member GTEST_ALLOW_UNINSTANTIATED_PARAMETERIZED_TEST(SimpleMdrunTest) (function) of namespace gmx::test::anonymous_namespace{simple_mdrun.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/template_mp.cpp:49: warning: Member Options (enumeration) of namespace gmx::test::anonymous_namespace{template_mp.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/template_mp.cpp:58: warning: Member testEnumTwoIPlusJPlusK(int k) (function) of namespace gmx::test::anonymous_namespace{template_mp.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/template_mp.cpp:64: warning: Member testBoolEnumTwoIPlusJPlusK(int k) (function) of namespace gmx::test::anonymous_namespace{template_mp.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/utility/tests/template_mp.cpp:70: warning: Member testBoolDoubleOrNot(int k) (function) of namespace gmx::test::anonymous_namespace{template_mp.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/timing/tests/timing.cpp:79: warning: Member delayInMilliseconds (variable) of class gmx::test::anonymous_namespace{timing.cpp}::TimingTest is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/timing/tests/timing.cpp:80: warning: Member wcycle (variable) of class gmx::test::anonymous_namespace{timing.cpp}::TimingTest is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/tools/tests/trjconv.cpp:160: warning: Member DumpTestParameters (typedef) of namespace gmx::test::anonymous_namespace{trjconv.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/programs/mdrun/tests/virtualsites.cpp:107: warning: Member VirtualSiteTestParams (typedef) of namespace gmx::test::anonymous_namespace{virtualsites.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/gromacs/fileio/tests/xvgio.cpp:76: warning: Member compareValues(basic_mdspan< const double, dynamicExtents2D > ref, basic_mdspan< const double, dynamicExtents2D > test) (function) of namespace gmx::test::anonymous_namespace{xvgio.cpp} is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/naming.h:195: warning: Member Variant (typedef) of struct gmx::test::detail::FormatterVariant is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/naming.h:211: warning: Member Variant (typedef) of struct gmx::test::detail::FormatterVariant< Enum, typename std::enable_if_t< std::is_enum_v< Enum > > > is not documented. /build/reproducible-path/gromacs-2025.0/src/testutils/include/testutils/naming.h:228: warning: Member type (typedef) of struct gmx::test::detail::ParamsToFormatterVariants< std::tuple< Ts... > > is not documented. /build/reproducible-path/gromacs-2025.0/docs/doxygen/directories.cpp:96: warning: unable to resolve reference to 'sm_insolidangle' for \ref command /build/reproducible-path/gromacs-2025.0/src/gromacs/selection/sm_insolidangle.cpp:99: warning: unable to resolve reference to 'sm_insolidangle' for \ref command cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen && /usr/bin/cmake -E touch /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen/doxygen-full-timestamp.txt make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [100%] Built target doxygen-full /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-all.dir/build.make docs/doxygen/CMakeFiles/doxygen-all.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/docs/doxygen /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen /build/reproducible-path/gromacs-2025.0/build/documentation/docs/doxygen/CMakeFiles/doxygen-all.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-all.dir/build.make docs/doxygen/CMakeFiles/doxygen-all.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[4]: Nothing to be done for 'docs/doxygen/CMakeFiles/doxygen-all.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [100%] Built target doxygen-all /usr/bin/make -f docs/CMakeFiles/webpage.dir/build.make docs/CMakeFiles/webpage.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/docs /build/reproducible-path/gromacs-2025.0/build/documentation /build/reproducible-path/gromacs-2025.0/build/documentation/docs /build/reproducible-path/gromacs-2025.0/build/documentation/docs/CMakeFiles/webpage.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/make -f docs/CMakeFiles/webpage.dir/build.make docs/CMakeFiles/webpage.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/documentation' cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E remove -f /build/reproducible-path/gromacs-2025.0/build/documentation/docs/html/manual-2025.0-Debian_2025.0_2.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2025.0/build/documentation/docs/manual/gromacs.pdf /build/reproducible-path/gromacs-2025.0/build/documentation/docs/html/manual-2025.0-Debian_2025.0_2.pdf cd /build/reproducible-path/gromacs-2025.0/build/documentation/docs && /usr/bin/cmake -E echo "Webpage output: file:///build/reproducible-path/gromacs-2025.0/build/documentation/docs/html/index.html" Webpage output: file:///build/reproducible-path/gromacs-2025.0/build/documentation/docs/html/index.html make[4]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' [100%] Built target webpage make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.0/build/documentation/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' make[1]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/documentation' touch build-manual dh_testdir dh_testroot dh_prep dh_installdirs /usr/bin/make -j20 -C build/mpi install DESTDIR=/build/reproducible-path/gromacs-2025.0/debian/tmp make[1]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/cmake -P /build/reproducible-path/gromacs-2025.0/build/mpi/CMakeFiles/VerifyGlobs.cmake /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.0 -B/build/reproducible-path/gromacs-2025.0/build/mpi --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.0/build/mpi/CMakeFiles /build/reproducible-path/gromacs-2025.0/build/mpi//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/selection /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/selection /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/CMakeFiles/release-version-info.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.0/build/mpi/src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/CMakeFiles/colvars_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2025.0-Debian_2025.0_2 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2025.0 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.0/build/mpi/VersionInfo-partial.cmake.cmakein -D 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'/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Nothing to be done for 'src/gromacs/selection/CMakeFiles/scanner.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Nothing to be done for 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'/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Nothing to be done for 'src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Nothing to be done for 'src/gromacs/options/CMakeFiles/options.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 0%] Built target thread_mpi [ 0%] Built target release-version-info [ 0%] Built target scanner make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend [ 0%] Built target internal_rpc_xdr /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend [ 2%] Built target lmfit_objlib [ 2%] Built target tng_io_obj make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" [ 4%] Built target linearalgebra make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/colvars_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 6%] Built target options make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/CMakeFiles/gmx_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/pulling /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" [ 10%] Built target colvars_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Nothing to be done for 'src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Nothing to be done for 'src/programs/CMakeFiles/gmx_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 10%] Built target energyanalysis make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Nothing to be done for 'src/gromacs/pulling/CMakeFiles/pulling.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 10%] Built target mdrun_objlib [ 12%] Built target pulling /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend [ 14%] Built target gmx_objlib /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Nothing to be done for 'src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 14%] Built target taskassignment make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 18%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 94%] Built target libgromacs /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/depend /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/depend /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/gmxapi /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi /build/reproducible-path/gromacs-2025.0/build/mpi/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs /build/reproducible-path/gromacs-2025.0/build/mpi/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/CMakeFiles/nblib.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/build /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Nothing to be done for 'src/programs/CMakeFiles/gmx.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Nothing to be done for 'api/nblib/CMakeFiles/nblib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Nothing to be done for 'api/gmxapi/CMakeFiles/gmxapi.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 94%] Built target gmx [ 96%] Built target nblib /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/samples/CMakeFiles/argon-forces-integration.dir/DependInfo.cmake "--color=" [ 98%] Built target gmxapi make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/mpi/api/nblib/samples/CMakeFiles/methane-water-integration.dir/DependInfo.cmake "--color=" /usr/bin/make -f python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build.make python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/depend /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/python_packaging/gmxapi /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/gmxapi /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Nothing to be done for 'api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Nothing to be done for 'api/nblib/samples/CMakeFiles/methane-water-integration.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Nothing to be done for 'python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 98%] Built target argon-forces-integration [ 98%] Built target methane-water-integration [ 98%] Built target gmxapi_extension_resources /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/depend /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build.make python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Nothing to be done for 'python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Nothing to be done for 'python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Nothing to be done for 'python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [ 98%] Built target _gmxapi [ 98%] Built target gmxapi_extension_test [ 98%] Built target gmxapi_extension_ensemblepotential /usr/bin/make -f python_packaging/sample_restraint/src/pythonmodule/CMakeFiles/gmxapi_extension.dir/build.make python_packaging/sample_restraint/src/pythonmodule/CMakeFiles/gmxapi_extension.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' cd /build/reproducible-path/gromacs-2025.0/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/python_packaging/sample_restraint/src/pythonmodule /build/reproducible-path/gromacs-2025.0/build/mpi /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/src/pythonmodule /build/reproducible-path/gromacs-2025.0/build/mpi/python_packaging/sample_restraint/src/pythonmodule/CMakeFiles/gmxapi_extension.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -f python_packaging/sample_restraint/src/pythonmodule/CMakeFiles/gmxapi_extension.dir/build.make python_packaging/sample_restraint/src/pythonmodule/CMakeFiles/gmxapi_extension.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[3]: Nothing to be done for 'python_packaging/sample_restraint/src/pythonmodule/CMakeFiles/gmxapi_extension.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' [100%] Built target gmxapi_extension make[2]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.0/build/mpi/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/README.tutor -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/README_FreeEnergyModifications.txt -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/residues.dtd -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/specbond.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/flexwat-ferguson.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/atommass.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ffG53a6.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/surface.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/elements.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ss.map -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/atomname2type.n2t -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ff_dum.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/bonds.dlg -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/cb-shift.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ffG45a3.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/vdw-msms.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/dppc.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ff_dum.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/popc.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tmcl.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/tip4p.gro -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/dgsolv.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/flexspce.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/scatteringfactors.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/phbres.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/table6-11.xvg -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ha-shift.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/residuetypes.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ca-shift.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip4pew.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.hdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.arn -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.c.tdb -- Installing: 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/build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ff_dum.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/methanol.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/table6-10.xvg -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ffoplsaa-n.tst -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/nsfactor.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/spc.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/tip5p.gro -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ps.m2p -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/tip4pew.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.hdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.arn -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.r2b -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.rtp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.arn -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.hdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.arn -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/urea.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.rtp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.r2b -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/tip5p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ffG43a1.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ff_dum.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/tip4pew.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.hdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.arn -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.r2b -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.rtp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.arn -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.hdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.arn -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/urea.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.rtp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.r2b -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/tip5p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ffG43a2.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/edissoc.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/xlateat.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/atomname2type.n2t -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/1propanol.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip4pew.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip5pe.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ethanol.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/methanol.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip5p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/electroneg.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/residues.xml -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/tip4pew.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.hdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.arn -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.r2b -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.rtp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.arn -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.hdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.arn -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/urea.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.rtp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.r2b -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/tip5p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ff_dum.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/spce.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/spc216.gro -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip4pew.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.hdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.arn -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.r2b -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.rtp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.arn -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.hdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.arn -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/urea.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.rtp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.r2b -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip5p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/table6-8.xvg -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip4pew.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.hdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.arn -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.r2b -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.rtp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.arn -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.hdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.arn -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/urea.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.rtp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.r2b -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip5p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.hdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.arn -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.c.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffnanonbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.c.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.r2b -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/tips3p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.rtp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.arn -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/lipids.rtp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.hdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffnabonded.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.n.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.arn -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/lipids.hdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.rtp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/tip5p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/cmap.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.n.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ffoplsaa.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ff_dum.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/random.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/table6-9.xvg -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/refi_aa.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/export.dlg -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ions.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/atom_nom.tbl -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/table6-12.xvg -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/README -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/tip4pew.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.hdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.arn -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.r2b -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.rtp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.arn -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.hdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.arn -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/urea.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.rtp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.r2b -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/tip5p.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/flexspc.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ffG53a5.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/sfactor.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/defselection.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/co-shift.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/vdwradii.dat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/sw.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/GMXRC -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/GMXRC.bash -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/GMXRC.zsh -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/GMXRC.csh -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/demux.pl -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/xplor2gmx.pl -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/x86_64-linux-gnu/libgmxapi_mpi.so.0.4.0 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/x86_64-linux-gnu/libgmxapi_mpi.so.0 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/x86_64-linux-gnu/libgmxapi_mpi.so -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gmxapi/gmxapi.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gmxapi/gmxapi-release.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gmxapi/gmxapi-config-version.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gmxapi/gmxapi-config.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/session.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/mpi -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/mpi/gmxapi_mpi.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/exceptions.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/context.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/gmxapicompat.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/md.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/gmxapi.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/system.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/compat -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/compat/tpr.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/compat/mdparams.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/session -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/session/resources.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/md -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/md/mdsignals.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/md/mdmodule.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/status.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/gromacsfwd.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/version.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/mpi/resourceassignment.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/x86_64-linux-gnu/libnblib_gmx.so.0.1.0 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/x86_64-linux-gnu/libnblib_gmx.so.0 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/x86_64-linux-gnu/libnblib_gmx.so -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/particlesequencer.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/vector.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/box.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/nbnxmsetuphelpers.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/tpr.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/exception.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/gmxcalculatorcpu.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/topology.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/util -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/util/util.hpp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/util/traits.hpp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/util/setup.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/listed_forces -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/listed_forces/bondtypes.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/listed_forces/definitions.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/listed_forces/calculator.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/basicdefinitions.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/integrator.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/kerneloptions.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/particletype.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/nblib.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/simulationstate.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/molecules.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/interactions.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/mdrun/simulationinputhandle.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/x86_64-linux-gnu/libgromacs_mpi.so.10.0.0 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/x86_64-linux-gnu/libgromacs_mpi.so.10 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/x86_64-linux-gnu/libgromacs_mpi.so -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig/libgromacs_mpi.pc -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gromacs_mpi/libgromacs.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gromacs_mpi/libgromacs-release.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gromacs_mpi/gromacs_mpi-config.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gromacs_mpi/gromacs_mpi-config-version.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/gmx_mpi -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/gmx-completion.bash -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/gmx-completion-gmx_mpi.bash -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-dump.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-bundle.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-gangle.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-make_ndx.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-tcaf.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-help.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-grompp.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-h2order.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-traj.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-x2top.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-mdmat.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-energy.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-gyrate-legacy.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-mk_angndx.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-editconf.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-angle.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-sasa.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-pairdist.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-dipoles.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-check.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-wheel.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-rms.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-distance.1 -- Installing: 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/build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-nonbonded-benchmark.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-solvate.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-mdrun.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-spatial.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-rdf.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-xpm2ps.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-confrms.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-trjconv.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-pdb2gmx.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-dielectric.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-trajectory.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-nmr.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-velacc.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-current.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-sigeps.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-gyrate.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-hydorder.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-sans-legacy.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-make_edi.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-order.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-eneconv.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-nmens.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-dssp.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-clustsize.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-sham.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-potential.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-convert-tpr.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-rotmat.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-trjorder.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-lie.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-analyze.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-densorder.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-awh.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-freevolume.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-hbond-legacy.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-saltbr.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-chi.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-spol.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-nmeig.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-densmap.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-rama.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-genrestr.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-pme_error.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-nmtraj.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-enemat.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-wham.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-hbond.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-genion.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-scattering.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-disre.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-sorient.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-saxs-legacy.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-anaeig.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-rmsf.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-report-methods.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-convert-trj.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-dyecoupl.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-density.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-principal.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-tune_pme.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-trjcat.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-mindist.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-helix.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-select.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-dos.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-covar.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-vanhove.1 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-insert-molecules.1 make[1]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi' /usr/bin/make -j20 -C build/mpi-dp install DESTDIR=/build/reproducible-path/gromacs-2025.0/debian/tmp make[1]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.0 -B/build/reproducible-path/gromacs-2025.0/build/mpi-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.0/build/mpi-dp/CMakeFiles /build/reproducible-path/gromacs-2025.0/build/mpi-dp//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/selection /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/selection /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/CMakeFiles/release-version-info.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2025.0-Debian_2025.0_2 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2025.0 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.0/build/mpi-dp/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2025.0/build/mpi-dp/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2025.0-2 -P /build/reproducible-path/gromacs-2025.0/cmake/gmxGenerateVersionInfoWithoutGit.cmake make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/CMakeFiles/colvars_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/options /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/options /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/programs /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/programs /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/programs/CMakeFiles/gmx_objlib.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Nothing to be done for 'src/gromacs/selection/CMakeFiles/scanner.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Nothing to be done for 'src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' [ 0%] Built target release-version-info make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build [ 0%] Built target scanner /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Nothing to be done for 'src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' [ 0%] Built target internal_rpc_xdr make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' [ 0%] Built target thread_mpi /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' [ 0%] Built target lmfit_objlib /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Nothing to be done for 'src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Nothing to be done for 'src/programs/CMakeFiles/gmx_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Nothing to be done for 'src/gromacs/options/CMakeFiles/options.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' [ 0%] Built target tng_io_obj [ 0%] Built target energyanalysis [ 0%] Built target mdrun_objlib [ 0%] Built target linearalgebra [ 0%] Built target gmx_objlib /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/pulling /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" [ 0%] Built target options make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Nothing to be done for 'src/gromacs/pulling/CMakeFiles/pulling.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' [ 0%] Built target pulling /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/colvars_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Leaving directory 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'/build/reproducible-path/gromacs-2025.0/build/mpi-dp' [ 6%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' 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src/programs/CMakeFiles/gmx.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib /build/reproducible-path/gromacs-2025.0/build/mpi-dp/api/nblib/CMakeFiles/nblib.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs /build/reproducible-path/gromacs-2025.0/build/mpi-dp /build/reproducible-path/gromacs-2025.0/build/mpi-dp/src/programs 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directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Nothing to be done for 'api/nblib/CMakeFiles/nblib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' [ 97%] Built target gmxapi [100%] Built target nblib /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' cd /build/reproducible-path/gromacs-2025.0/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 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api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Nothing to be done for 'api/nblib/samples/CMakeFiles/methane-water-integration.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[3]: Nothing to be done for 'api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' [100%] Built target methane-water-integration [100%] Built target argon-forces-integration make[2]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.0/build/mpi-dp/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/README.tutor -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/README_FreeEnergyModifications.txt -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/residues.dtd -- Up-to-date: 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/build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.arn -- Up-to-date: 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/build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ps.m2p -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/watermodels.dat -- Up-to-date: 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Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ffG43a1.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ff_dum.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ffG43a2.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/edissoc.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/xlateat.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/atomname2type.n2t -- Up-to-date: 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Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ethanol.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/methanol.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/electroneg.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/residues.xml -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.r2b -- Up-to-date: 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Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/ffbonded.itp -- Up-to-date: 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/build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/spc216.gro -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/table6-8.xvg -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffnanonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/tips3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/lipids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffnabonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/lipids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/cmap.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ffoplsaa.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ff_dum.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/random.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/table6-9.xvg -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/refi_aa.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/export.dlg -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/atom_nom.tbl -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/table6-12.xvg -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/README -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/flexspc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ffG53a5.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/sfactor.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/defselection.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/co-shift.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/vdwradii.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/sw.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/GMXRC -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/GMXRC.bash -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/GMXRC.zsh -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/GMXRC.csh -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/demux.pl -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/xplor2gmx.pl -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/x86_64-linux-gnu/libgmxapi_mpi_d.so.0.4.0 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/x86_64-linux-gnu/libgmxapi_mpi_d.so.0 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/x86_64-linux-gnu/libgmxapi_mpi_d.so -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gmxapi/gmxapi.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gmxapi/gmxapi-release.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gmxapi/gmxapi-config-version.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gmxapi/gmxapi-config.cmake -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/session.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/mpi -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/mpi/gmxapi_mpi.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/exceptions.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/context.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/gmxapicompat.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/md.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/gmxapi.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/system.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/compat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/compat/tpr.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/compat/mdparams.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/session -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/session/resources.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/md -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/md/mdsignals.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/md/mdmodule.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/status.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/gromacsfwd.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/version.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/mpi/resourceassignment.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/x86_64-linux-gnu/libnblib_gmx.so.0.1.0 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/x86_64-linux-gnu/libnblib_gmx.so.0 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/x86_64-linux-gnu/libnblib_gmx.so -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/particlesequencer.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/vector.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/box.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/nbnxmsetuphelpers.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/tpr.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/exception.h -- Up-to-date: 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Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/basicdefinitions.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/integrator.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/kerneloptions.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/particletype.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/nblib.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/simulationstate.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/molecules.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/interactions.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/mdrun/simulationinputhandle.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/x86_64-linux-gnu/libgromacs_mpi_d.so.10.0.0 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/x86_64-linux-gnu/libgromacs_mpi_d.so.10 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/x86_64-linux-gnu/libgromacs_mpi_d.so -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig/libgromacs_mpi_d.pc -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gromacs_mpi_d/libgromacs.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gromacs_mpi_d/libgromacs-release.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gromacs_mpi_d/gromacs_mpi_d-config.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gromacs_mpi_d/gromacs_mpi_d-config-version.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gromacs_mpi_d/gromacs-hints_mpi_d.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/gmx_mpi_d -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/gmx-completion.bash -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/gmx-completion-gmx_mpi_d.bash -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-dump.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-bundle.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-gangle.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-make_ndx.1 -- Up-to-date: 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/build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-genrestr.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-pme_error.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-nmtraj.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-enemat.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-wham.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-hbond.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-genion.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-scattering.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-disre.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-sorient.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-saxs-legacy.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-anaeig.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-rmsf.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-report-methods.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-convert-trj.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-dyecoupl.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-density.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-principal.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-tune_pme.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-trjcat.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-mindist.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-helix.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-select.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-dos.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-covar.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-vanhove.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-insert-molecules.1 make[1]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/mpi-dp' /usr/bin/make -j20 -C build/basic install DESTDIR=/build/reproducible-path/gromacs-2025.0/debian/tmp make[1]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.0 -B/build/reproducible-path/gromacs-2025.0/build/basic --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.0/build/basic/CMakeFiles /build/reproducible-path/gromacs-2025.0/build/basic//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/selection /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/selection /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic 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/build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/external/rpc_xdr /build/reproducible-path/gromacs-2025.0/build/basic/src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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&& /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/programs /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/CMakeFiles/gmx_objlib.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/programs /build/reproducible-path/gromacs-2025.0/build/basic/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd 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make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/CMakeFiles/colvars_objlib.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2025.0-Debian_2025.0_2 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2025.0 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2025.0/build/basic/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2025.0/build/basic/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2025.0-2 -P /build/reproducible-path/gromacs-2025.0/cmake/gmxGenerateVersionInfoWithoutGit.cmake make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[3]: Leaving directory 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'/build/reproducible-path/gromacs-2025.0/build/basic' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[3]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[3]: Nothing to be done for 'src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[3]: Entering 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target scanner [ 2%] Built target linearalgebra make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build [ 2%] Built target mdrun_objlib [ 4%] Built target energyanalysis [ 6%] Built target tng_io_obj [ 8%] Built target thread_mpi [ 8%] Built target internal_rpc_xdr make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling /build/reproducible-path/gromacs-2025.0/build/basic 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'/build/reproducible-path/gromacs-2025.0/build/basic' [ 16%] Built target pulling /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.0/build/basic /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/taskassignment /build/reproducible-path/gromacs-2025.0/build/basic/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" make[3]: Entering directory 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'/build/reproducible-path/gromacs-2025.0/build/basic' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build [ 16%] Built target taskassignment make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' make[3]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic' [ 18%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic' cd /build/reproducible-path/gromacs-2025.0/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 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'/build/reproducible-path/gromacs-2025.0/build/basic' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/template/CMakeLists.txt -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/template/README -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/template/template.cpp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/template/Makefile.pkg -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/template/cmake/FindGROMACS.cmake -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/README.tutor -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/README_FreeEnergyModifications.txt -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top -- 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/build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/methanol.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/table6-10.xvg -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ffoplsaa-n.tst -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/nsfactor.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/tip5p.gro -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ps.m2p -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ffG43a1.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ff_dum.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ffG43a2.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/edissoc.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/xlateat.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/atomname2type.n2t -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/1propanol.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip5pe.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ethanol.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/methanol.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/electroneg.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/residues.xml -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ff_dum.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/spc216.gro -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/table6-8.xvg -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffnanonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/tips3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/lipids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffnabonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/lipids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/cmap.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ffoplsaa.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ff_dum.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/random.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/table6-9.xvg -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/refi_aa.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/export.dlg -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/atom_nom.tbl -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/table6-12.xvg -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/README -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/flexspc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ffG53a5.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/sfactor.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/defselection.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/co-shift.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/vdwradii.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/sw.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/GMXRC -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/GMXRC.bash -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/GMXRC.zsh -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/GMXRC.csh -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/demux.pl -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/xplor2gmx.pl -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/utility -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/utility/flags.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/utility/real.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/utility/pleasecite.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/utility/programcontext.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/utility/basedefinitions.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/utility/gmxassert.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/utility/fileptr.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/utility/enumerationhelpers.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/utility/exceptions.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/utility/classhelpers.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/utility/current_function.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/utility/baseversion.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/utility/smalloc.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/utility/futil.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/utility/range.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/utility/stringutil.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/utility/arrayref.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/utility/listoflists.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/utility/unique_cptr.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/topology -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/topology/ifunc.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/topology/idef.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/topology/atoms.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/topology/index.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/topology/topology.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/topology/forcefieldparameters.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/topology/topology_enums.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/topology/atomprop.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/topology/block.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/topology/symtab.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/selection -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/selection/selectionoptionbehavior.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/selection/selectionoptionmanager.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/selection/selection.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/selection/indexutil.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/selection/selectionoption.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/selection/selectionenums.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/selection/position.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/selection/nbsearch.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/selection/selectioncollection.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/math -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/math/units.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/math/functions.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/math/do_fit.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/math/vectypes.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/math/utilities.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/math/vec.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/restraint -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/restraint/restraintpotential.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/mdtypes -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/mdtypes/md_enums.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/mdtypes/inputrec.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/fileio -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/fileio/filetypes.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/fileio/oenv.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/fileio/tpxio.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/fileio/pdbio.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/fileio/confio.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/fileio/trxio.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/pbcutil -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/pbcutil/pbc.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/trajectoryanalysis -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/trajectoryanalysis/analysissettings.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/trajectoryanalysis/analysismodule.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/trajectoryanalysis/topologyinformation.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/trajectoryanalysis/cmdlinerunner.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/analysisdata -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/analysisdata/datamodule.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/analysisdata/arraydata.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/analysisdata/modules -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/analysisdata/modules/lifetime.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/analysisdata/modules/average.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/analysisdata/modules/displacement.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/analysisdata/modules/plot.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/analysisdata/modules/histogram.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/analysisdata/analysisdata.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/analysisdata/abstractdata.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/analysisdata/dataframe.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/options -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/options/options.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/options/optionflags.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/options/ioptionsbehavior.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/options/timeunitmanager.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/options/basicoptions.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/options/ioptionscontainer.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/options/filenameoption.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/options/ivaluestore.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/options/optionfiletype.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/options/ioptionscontainerwithsections.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/options/abstractoption.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/options/filenameoptionmanager.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/trajectory -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/trajectory/trajectoryframe.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/version.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/libgromacs_export.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/x86_64-linux-gnu/libgmxapi.so.0.4.0 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/x86_64-linux-gnu/libgmxapi.so.0 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/x86_64-linux-gnu/libgmxapi.so -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gmxapi/gmxapi.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gmxapi/gmxapi-release.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gmxapi/gmxapi-config-version.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gmxapi/gmxapi-config.cmake -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/session.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/mpi -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/mpi/gmxapi_mpi.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/exceptions.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/context.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/gmxapicompat.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/md.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/gmxapi.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/system.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/compat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/compat/tpr.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/compat/mdparams.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/session -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/session/resources.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/md -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/md/mdsignals.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/md/mdmodule.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/status.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/gromacsfwd.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/version.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/mpi/resourceassignment.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/x86_64-linux-gnu/libnblib_gmx.so.0.1.0 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/x86_64-linux-gnu/libnblib_gmx.so.0 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/x86_64-linux-gnu/libnblib_gmx.so -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/particlesequencer.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/vector.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/box.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/nbnxmsetuphelpers.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/tpr.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/exception.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/gmxcalculatorcpu.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/topology.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/util -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/util/util.hpp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/util/traits.hpp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/util/setup.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/listed_forces -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/listed_forces/bondtypes.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/listed_forces/definitions.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/listed_forces/calculator.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/basicdefinitions.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/integrator.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/kerneloptions.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/particletype.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/nblib.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/simulationstate.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/molecules.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/interactions.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/external/boost/stl_interfaces/fwd.hpp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/external/boost/stl_interfaces/iterator_interface.hpp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/mdrun/simulationinputhandle.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/x86_64-linux-gnu/libgromacs.so.10.0.0 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/x86_64-linux-gnu/libgromacs.so.10 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/x86_64-linux-gnu/libgromacs.so -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig/libgromacs.pc -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gromacs/libgromacs.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gromacs/libgromacs-release.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gromacs/gromacs-config.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gromacs/gromacs-config-version.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gromacs/gromacs-hints.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/gmx -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/gmx-completion.bash -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/gmx-completion-gmx.bash -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-dump.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-bundle.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-gangle.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-make_ndx.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-tcaf.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-help.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-grompp.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-h2order.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-traj.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-x2top.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-mdmat.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-energy.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-gyrate-legacy.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-mk_angndx.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-editconf.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-angle.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-sasa.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-pairdist.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-dipoles.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-check.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-wheel.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-rms.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-distance.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-bar.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-filter.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-genconf.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-rmsdist.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-cluster.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-msd.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-helixorient.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-rotacf.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-polystat.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-extract-cluster.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-nonbonded-benchmark.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-solvate.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-mdrun.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-spatial.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-rdf.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-xpm2ps.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-confrms.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-trjconv.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-pdb2gmx.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-dielectric.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-trajectory.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-nmr.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-velacc.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-current.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-sigeps.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-gyrate.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-hydorder.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-sans-legacy.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-make_edi.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-order.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-eneconv.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-nmens.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-dssp.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-clustsize.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-sham.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-potential.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-convert-tpr.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-rotmat.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-trjorder.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-lie.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-analyze.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-densorder.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-awh.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-freevolume.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-hbond-legacy.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-saltbr.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-chi.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-spol.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-nmeig.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-densmap.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-rama.1 -- Up-to-date: 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'/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/cmake -S/build/reproducible-path/gromacs-2025.0 -B/build/reproducible-path/gromacs-2025.0/build/basic-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.0/build/basic-dp/CMakeFiles /build/reproducible-path/gromacs-2025.0/build/basic-dp//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/selection 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src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/CMakeFiles/release-version-info.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend /usr/bin/make 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'/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/options /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/linearalgebra 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src/gromacs/CMakeFiles/tng_io_obj.dir/build /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Nothing to be done for 'src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make 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src/gromacs/CMakeFiles/colvars_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/colvars_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 0%] Built target internal_rpc_xdr make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 0%] Built target energyanalysis [ 2%] Built target tng_io_obj [ 10%] Built target options [ 10%] Built target thread_mpi [ 2%] Built target linearalgebra [ 2%] Built target mdrun_objlib [ 2%] Built target lmfit_objlib [ 2%] Built target scanner [ 12%] Built target colvars_objlib /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs/pulling /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/pulling /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" [ 12%] Built target release-version-info make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Nothing to be done for 'src/programs/CMakeFiles/gmx_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Nothing to be done for 'src/gromacs/pulling/CMakeFiles/pulling.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 12%] Built target gmx_objlib [ 14%] Built target pulling /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 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'/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Nothing to be done for 'src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 14%] Built target taskassignment [ 16%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [ 95%] Built target libgromacs /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/depend /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/depend /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/src/programs /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs /build/reproducible-path/gromacs-2025.0/build/basic-dp/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/gmxapi /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib 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Built target nblib /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/samples/CMakeFiles/argon-forces-integration.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' cd /build/reproducible-path/gromacs-2025.0/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2025.0 /build/reproducible-path/gromacs-2025.0/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/basic-dp /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/samples /build/reproducible-path/gromacs-2025.0/build/basic-dp/api/nblib/samples/CMakeFiles/methane-water-integration.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Nothing to be done for 'api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Nothing to be done for 'api/nblib/samples/CMakeFiles/methane-water-integration.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [100%] Built target argon-forces-integration [100%] Built target methane-water-integration make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[3]: Nothing to be done for 'src/programs/CMakeFiles/gmx.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' [100%] Built target gmx make[2]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2025.0/build/basic-dp/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/README.tutor -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/README_FreeEnergyModifications.txt -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/residues.dtd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/specbond.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/flexwat-ferguson.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/atommass.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ffG53a6.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/surface.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/elements.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ss.map -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a5.ff -- Up-to-date: 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Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/methanol216.gro -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ff_dum.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/tip4p.itp -- Up-to-date: 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/build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/tip5p.gro -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ps.m2p -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.arn -- Up-to-date: 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Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber94.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ffG43a1.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ff_dum.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.vsd -- Up-to-date: 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/build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99.ff/ions.itp -- Up-to-date: 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Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ethanol.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/methanol.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/electroneg.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/residues.xml -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/atomtypes.atp -- Up-to-date: 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Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.n.tdb -- Up-to-date: 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/build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/spc216.gro -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amberGS.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/table6-8.xvg -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffnanonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/tips3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/lipids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffnabonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/lipids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/cmap.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ffoplsaa.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ff_dum.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/random.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/table6-9.xvg -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/refi_aa.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/export.dlg -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/atom_nom.tbl -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/table6-12.xvg -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/README -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/amber03.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/flexspc.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/ffG53a5.itp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/sfactor.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/defselection.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/co-shift.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/vdwradii.dat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/gromacs/top/sw.itp -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/GMXRC -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/GMXRC.bash -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/GMXRC.zsh -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/GMXRC.csh -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/demux.pl -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/xplor2gmx.pl -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/x86_64-linux-gnu/libgmxapi_d.so.0.4.0 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/x86_64-linux-gnu/libgmxapi_d.so.0 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/x86_64-linux-gnu/libgmxapi_d.so -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gmxapi/gmxapi.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gmxapi/gmxapi-release.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gmxapi/gmxapi-config-version.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gmxapi/gmxapi-config.cmake -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/session.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/mpi -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/mpi/gmxapi_mpi.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/exceptions.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/context.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/gmxapicompat.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/md.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/gmxapi.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/system.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/compat -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/compat/tpr.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/compat/mdparams.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/session -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/session/resources.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/md -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/md/mdsignals.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/md/mdmodule.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/status.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/gromacsfwd.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/version.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gmxapi/mpi/resourceassignment.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/x86_64-linux-gnu/libnblib_gmx.so.0.1.0 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/x86_64-linux-gnu/libnblib_gmx.so.0 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/x86_64-linux-gnu/libnblib_gmx.so -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/particlesequencer.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/vector.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/box.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/nbnxmsetuphelpers.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/tpr.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/exception.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/gmxcalculatorcpu.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/topology.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/util -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/util/util.hpp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/util/traits.hpp -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/util/setup.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/listed_forces -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/listed_forces/bondtypes.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/listed_forces/definitions.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/listed_forces/calculator.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/basicdefinitions.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/integrator.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/kerneloptions.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/particletype.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/nblib.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/simulationstate.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/molecules.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/nblib/interactions.h -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/include/gromacs/mdrun/simulationinputhandle.h -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/x86_64-linux-gnu/libgromacs_d.so.10.0.0 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/x86_64-linux-gnu/libgromacs_d.so.10 -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/x86_64-linux-gnu/libgromacs_d.so -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig/libgromacs_d.pc -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gromacs_d/libgromacs.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gromacs_d/libgromacs-release.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gromacs_d/gromacs_d-config.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gromacs_d/gromacs_d-config-version.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/cmake/gromacs_d/gromacs-hints_d.cmake -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/gmx_d -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/gmx-completion.bash -- Installing: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/gmx-completion-gmx_d.bash -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-dump.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-bundle.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-gangle.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-make_ndx.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-tcaf.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-help.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-grompp.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-h2order.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-traj.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-x2top.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-mdmat.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-energy.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-gyrate-legacy.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-mk_angndx.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-editconf.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-angle.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-sasa.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-pairdist.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-dipoles.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-check.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-wheel.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-rms.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-distance.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-bar.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-filter.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-genconf.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-rmsdist.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-cluster.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-msd.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-helixorient.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-rotacf.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-polystat.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-extract-cluster.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-nonbonded-benchmark.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-solvate.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-mdrun.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-spatial.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-rdf.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-xpm2ps.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-confrms.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-trjconv.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-pdb2gmx.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-dielectric.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-trajectory.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-nmr.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-velacc.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-current.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-sigeps.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-gyrate.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-hydorder.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-sans-legacy.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-make_edi.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-order.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-eneconv.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-nmens.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-dssp.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-clustsize.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-sham.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-potential.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-convert-tpr.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-rotmat.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-trjorder.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-lie.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-analyze.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-densorder.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-awh.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-freevolume.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-hbond-legacy.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-saltbr.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-chi.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-spol.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-nmeig.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-densmap.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-rama.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-genrestr.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-pme_error.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-nmtraj.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-enemat.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-wham.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-hbond.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-genion.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-scattering.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-disre.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-sorient.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-saxs-legacy.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-anaeig.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-rmsf.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-report-methods.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-convert-trj.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-dyecoupl.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-density.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-principal.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-tune_pme.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-trjcat.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-mindist.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-helix.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-select.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-dos.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-covar.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-vanhove.1 -- Up-to-date: /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/share/man/man1/gmx-insert-molecules.1 make[1]: Leaving directory '/build/reproducible-path/gromacs-2025.0/build/basic-dp' chrpath -d /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/gmx_mpi /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/gmx_mpi_d chrpath -d /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/lib/*/libgromacs_mpi*.so.* perl -lne 'print' /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/gmx-completion.bash \ /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/gmx-completion-*.bash > \ /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/gmx-completion-concat mv /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/demux.pl /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/demux mv /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/xplor2gmx.pl /build/reproducible-path/gromacs-2025.0/debian/tmp/usr/bin/xplor2gmx dh_install -a dh_installdocs -a dh_installchangelogs -a dh_installman -a dh_bash-completion -a dh_lintian -a dh_link -a dh_testdir -i dh_testroot -i dh_installdirs -i dh_install -i dh_installdocs -i dh_installchangelogs -i dh_installman -i find /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/ -type f -a \( -name '*.md5' -o -name '*.map' \) -delete rdfind -outputname /dev/null -makesymlinks true /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/ Now scanning "/build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc", found 24745 files. Now have 24745 files in total. Removed 0 files due to nonunique device and inode. Total size is 413584398 bytes or 394 MiB Removed 8201 files due to unique sizes from list. 16544 files left. Now eliminating candidates based on first bytes: removed 3532 files from list. 13012 files left. Now eliminating candidates based on last bytes: removed 1798 files from list. 11214 files left. Now eliminating candidates based on sha1 checksum: removed 3651 files from list. 7563 files left. It seems like you have 7563 files that are not unique Totally, 25 MiB can be reduced. Now making results file /dev/null Now making symbolic links. creating Making 4403 links. symlinks -r -s -c /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/ absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000017_000063.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000017_000063.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000017_000063.xhtml -> ../html-full/dir_000017_000063.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000097_000169.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000097_000169.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000097_000169.xhtml -> ../html-full/dir_000097_000169.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1RepeatingOptionSectionHandle__coll__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RepeatingOptionSectionHandle__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1RepeatingOptionSectionHandle__coll__graph.svg -> ../html-full/classgmx_1_1RepeatingOptionSectionHandle__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/keyvaluetreetransform_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/keyvaluetreetransform_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/keyvaluetreetransform_8h__incl.svg -> ../html-full/keyvaluetreetransform_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionsTypeVisitor.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1OptionsTypeVisitor.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1OptionsTypeVisitor.xhtml -> ../html-full/classgmx_1_1OptionsTypeVisitor.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000087_000002.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000087_000002.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000087_000002.xhtml -> ../html-full/dir_000087_000002.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_1.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_20.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_1.svg -> ../html-full/inherit_graph_20.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structPreprocessResidue-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structPreprocessResidue-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structPreprocessResidue-members.xhtml -> ../html-full/structPreprocessResidue-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_302.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_527.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_302.svg -> ../html-full/inherit_graph_527.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1FlagTest__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1FlagTest__inherit__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1test_1_1FlagTest__inherit__graph.svg -> ../html-full/classgmx_1_1test_1_1FlagTest__inherit__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_6.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_32.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_6.svg -> ../html-full/inherit_graph_32.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__module__correlationfunctions.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/group__module__correlationfunctions.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/group__module__correlationfunctions.svg -> ../html-full/group__module__correlationfunctions.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ExponentialDistribution-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ExponentialDistribution-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ExponentialDistribution-members.xhtml -> ../html-full/classgmx_1_1ExponentialDistribution-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/device__management__sycl__intel__device__ids_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/device__management__sycl__intel__device__ids_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/device__management__sycl__intel__device__ids_8h__incl.svg -> ../html-full/device__management__sycl__intel__device__ids_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1accessor__basic.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1accessor__basic.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1accessor__basic.xhtml -> ../html-full/classgmx_1_1accessor__basic.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gpuregiontimer__hip_8h.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/gpuregiontimer__hip_8h.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/gpuregiontimer__hip_8h.xhtml -> ../html-full/gpuregiontimer__hip_8h.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1StringOutputStream__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StringOutputStream__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1StringOutputStream__inherit__graph.svg -> ../html-full/classgmx_1_1StringOutputStream__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_54.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_141.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_54.svg -> ../html-full/inherit_graph_141.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_29f1a674ba1859f41704372482980b85_dep.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_29f1a674ba1859f41704372482980b85_dep.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_29f1a674ba1859f41704372482980b85_dep.svg -> ../html-full/dir_29f1a674ba1859f41704372482980b85_dep.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structSettleWaterTopology.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structSettleWaterTopology.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/structSettleWaterTopology.xhtml -> ../html-full/structSettleWaterTopology.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_7.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_33.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_7.svg -> ../html-full/inherit_graph_33.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/polynomials_8h__incl.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/polynomials_8h__incl.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/polynomials_8h__incl.svg -> ../html-full/polynomials_8h__incl.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataFrameRef-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataFrameRef-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataFrameRef-members.xhtml -> ../html-full/classgmx_1_1AnalysisDataFrameRef-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_401.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/inherit_graph_675.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/inherit_graph_401.svg -> ../html-full/inherit_graph_675.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimulationAlgorithmSetupError-members.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimulationAlgorithmSetupError-members.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SimulationAlgorithmSetupError-members.xhtml -> ../html-full/classgmx_1_1SimulationAlgorithmSetupError-members.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000082_000169.xhtml -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/dir_000082_000169.xhtml changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000082_000169.xhtml -> ../html-full/dir_000082_000169.xhtml absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/related_3.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/related_4.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/related_3.js -> ../../html-full/search/related_4.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/mag_sel.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/mag_sel.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/mag_sel.svg -> ../../html-full/search/mag_sel.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_6.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_6.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_6.js -> 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/build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_8.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_8.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_8.js -> ../../html-full/search/groups_8.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_3.js -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/groups_3.js changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/groups_3.js -> ../../html-full/search/groups_3.js absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/enums_a.js -> 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/build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/inherit_graph_131.svg -> ../html-full/inherit_graph_527.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1MissingElementConnectionError__inherit__graph.svg -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1MissingElementConnectionError__coll__graph.svg changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1MissingElementConnectionError__inherit__graph.svg -> ../html-full/classgmx_1_1MissingElementConnectionError__coll__graph.svg absolute: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/_sources/release-notes/2025/major/api.rst.txt -> /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/_sources/release-notes/2024/major/api.rst.txt changed: /build/reproducible-path/gromacs-2025.0/debian/gromacs-data/usr/share/doc/gromacs/html/_sources/release-notes/2025/major/api.rst.txt -> ../../2024/major/api.rst.txt dh_bash-completion -i dh_lintian -i dh_link -i dh_strip_nondeterminism -i dh_compress -i -X.pdf dh_fixperms -i dh_missing -i dh_installdeb -i dh_gencontrol -i dh_md5sums -i dh_builddeb -i dpkg-deb: building package 'gromacs-data' in '../gromacs-data_2025.0-2_all.deb'. dh_testdir -a dh_testroot -a dh_installchangelogs -a dh_installdocs -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_strip -A dh_makeshlibs -a dh_shlibdeps -plibgromacs10 -L libgromacs10 -l debian/libgromacs10/usr/lib dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib64/ld-linux-x86-64.so.2 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib64/ld-linux-x86-64.so.2.usr-is-merged dh_shlibdeps -plibnblib-gmx0 -L libnblib-gmx0 -l debian/libnblib-gmx0/usr/lib:debian/libgromacs10/usr/lib dh_shlibdeps -pgromacs -L libgromacs10 -l debian/libgromacs10/usr/lib:debian/gromacs/usr/lib dh_installdeb -a dh_gencontrol -a dpkg-gencontrol: warning: Depends field of package libnblib-gmx-dev: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package libgromacs-dev: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'gromacs-dbgsym' in '../gromacs-dbgsym_2025.0-2_amd64.deb'. dpkg-deb: building package 'gromacs' in '../gromacs_2025.0-2_amd64.deb'. dpkg-deb: building package 'libgromacs-dev' in '../libgromacs-dev_2025.0-2_amd64.deb'. dpkg-deb: building package 'libnblib-gmx0' in '../libnblib-gmx0_2025.0-2_amd64.deb'. dpkg-deb: building package 'libnblib-gmx0-dbgsym' in '../libnblib-gmx0-dbgsym_2025.0-2_amd64.deb'. dpkg-deb: building package 'libgromacs10' in '../libgromacs10_2025.0-2_amd64.deb'. dpkg-deb: building package 'libnblib-gmx-dev' in '../libnblib-gmx-dev_2025.0-2_amd64.deb'. dpkg-deb: building package 'libgromacs10-dbgsym' in '../libgromacs10-dbgsym_2025.0-2_amd64.deb'. dpkg-genbuildinfo --build=binary -O../gromacs_2025.0-2_amd64.buildinfo dpkg-genchanges --build=binary -O../gromacs_2025.0-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/3465466 and its subdirectories I: Current time: Mon Feb 17 23:56:22 -12 2025 I: pbuilder-time-stamp: 1739879782 Tue Feb 18 11:56:29 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos5-amd64.debian.net. Tue Feb 18 11:56:29 UTC 2025 I: Preparing to do remote build '2' on ionos5-amd64.debian.net. Tue Feb 18 12:42:51 UTC 2025 I: Deleting $TMPDIR on ionos5-amd64.debian.net. Tue Feb 18 12:42:52 UTC 2025 I: gromacs_2025.0-2_amd64.changes: Format: 1.8 Date: Sat, 15 Feb 2025 10:22:37 -0800 Source: gromacs Binary: gromacs gromacs-data gromacs-dbgsym libgromacs-dev libgromacs10 libgromacs10-dbgsym libnblib-gmx-dev libnblib-gmx0 libnblib-gmx0-dbgsym Architecture: all amd64 Version: 2025.0-2 Distribution: unstable Urgency: medium Maintainer: Debichem Team Changed-By: Nicholas Breen Description: gromacs - Molecular dynamics simulator, with building and analysis tools gromacs-data - GROMACS molecular dynamics sim, data and documentation libgromacs-dev - GROMACS molecular dynamics sim, development kit libgromacs10 - GROMACS molecular dynamics sim, shared libraries libnblib-gmx-dev - GROMACS molecular dynamics sim, NB-LIB development kit libnblib-gmx0 - GROMACS molecular dynamics sim, NB-LIB shared libraries Changes: gromacs (2025.0-2) unstable; urgency=medium . * autopkgtest: Designate complex/swap_[xyz] test as flaky on amd64 only. (https://gitlab.com/gromacs/gromacs/-/issues/5226) Checksums-Sha1: 26139028161f98f5edddc3013c240a8778525e83 46010136 gromacs-data_2025.0-2_all.deb d0f5244c6671b14f18febeded8b9ab45baf6e94b 1039308 gromacs-dbgsym_2025.0-2_amd64.deb a77cbffe728627cb2b31d76e092bfbc4fe665951 17107 gromacs_2025.0-2_amd64.buildinfo dd20d68a16c2778f36225443f7c1563cf336243f 60784 gromacs_2025.0-2_amd64.deb 5853e0bd98b2406a9cad0f9ffcaae5558d52c69f 174860 libgromacs-dev_2025.0-2_amd64.deb 69caec636cca5e46eff8d5e46d8d0430aaee0a0f 568168532 libgromacs10-dbgsym_2025.0-2_amd64.deb 1c01cf1e77886adfc29ef1c2003761e19af120bd 33088500 libgromacs10_2025.0-2_amd64.deb 71f6259d2136be148be191d4a58e2add8de58b48 33560 libnblib-gmx-dev_2025.0-2_amd64.deb e8a552c075a4f90ccbf28e2df0fe5c29ccd2d4dc 7497092 libnblib-gmx0-dbgsym_2025.0-2_amd64.deb 3f163f2c5e71d4c074cbc35d73af2b2265adaaf5 355868 libnblib-gmx0_2025.0-2_amd64.deb Checksums-Sha256: 39a06a74b80879bcf929f6baba77b2af133d419600c46a477e05ba54c20055e3 46010136 gromacs-data_2025.0-2_all.deb 7f3c0c9b59551ce4a85823a2e6c3e809de4c1a83a46ff52bcaee8779788271da 1039308 gromacs-dbgsym_2025.0-2_amd64.deb 9066e3e760380eca12d46e27427d88cf9187805d195aac43357e0bf357c2cdfa 17107 gromacs_2025.0-2_amd64.buildinfo 4d1001651af0d0e8d66503640f41b3ad5f2b21de2829179fba66ba4af1f36150 60784 gromacs_2025.0-2_amd64.deb 96173b6e472eff82e8c69a9b2b8d9f75046a55b6c31cf208c32a29919d3ce225 174860 libgromacs-dev_2025.0-2_amd64.deb 1d82e7f1ec9db15456e434540d09b7fe5500eed5019b79ac441ed7dcca5f75fb 568168532 libgromacs10-dbgsym_2025.0-2_amd64.deb 12da31e89a2506ebe05c31042bd1839f407a4a8f28e6dfc41efb6857445a414b 33088500 libgromacs10_2025.0-2_amd64.deb a21c05e64da4f2d34d9c38cdd2ffafe3bfc602259d205908e188026d75b7a4ae 33560 libnblib-gmx-dev_2025.0-2_amd64.deb c83cf1f4cfd04b1d4f31aecc3d0edfd391cb80cf868bdc3ad84b7d567356d34e 7497092 libnblib-gmx0-dbgsym_2025.0-2_amd64.deb 8bd118e7aaf60c3755f5dbd57cc70d7bad2004584e676c17aa634b2c2f009364 355868 libnblib-gmx0_2025.0-2_amd64.deb Files: 08f5907a4030ecb62bc6e41c2efa226f 46010136 science optional gromacs-data_2025.0-2_all.deb 746240d4d8722f7d40fef1ed4b5a4c11 1039308 debug optional gromacs-dbgsym_2025.0-2_amd64.deb be2928a44f9f4405b41a866a5af4c2b0 17107 science optional gromacs_2025.0-2_amd64.buildinfo 7862631fcff6c03c45c562a89d0ba6bd 60784 science optional gromacs_2025.0-2_amd64.deb cb801b0bb2f4074188b9fbb75b8f2a23 174860 libdevel optional libgromacs-dev_2025.0-2_amd64.deb 5ce8af164dfbd2c022df7f9775e117be 568168532 debug optional libgromacs10-dbgsym_2025.0-2_amd64.deb 9a8c5e11e943373b81cf2318c2ca956a 33088500 libs optional libgromacs10_2025.0-2_amd64.deb 972abb309a334c195d890e0886ae74dd 33560 libdevel optional libnblib-gmx-dev_2025.0-2_amd64.deb bfe1722b582c318bc8caf5e073f6dd7a 7497092 debug optional libnblib-gmx0-dbgsym_2025.0-2_amd64.deb 0786fe769cf35af14451bd807cb3e27b 355868 libs optional libnblib-gmx0_2025.0-2_amd64.deb Tue Feb 18 12:42:59 UTC 2025 I: diffoscope 288 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_1-30716.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.9nJ0JTN3/gromacs_2025.0-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.9nJ0JTN3/gromacs_2025.0-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.9nJ0JTN3/gromacs_2025.0-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.9nJ0JTN3/b1/gromacs_2025.0-2_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.9nJ0JTN3/b2/gromacs_2025.0-2_amd64.changes ## close_archive (total time: 0.000s) 0.000s 6 calls diffoscope.comparators.xz.XzContainer 0.000s 4 calls diffoscope.comparators.gzip.GzipContainer 0.000s 2 calls diffoscope.comparators.deb.DebContainer 0.000s 2 calls diffoscope.comparators.deb.DebTarContainer 0.000s 4 calls diffoscope.comparators.tar.TarContainer ## command (total time: 13.848s) 6.923s 56 calls diff 1.715s 6 calls xz 1.337s 429 calls js-beautify 1.186s 11 calls pdftotext 0.915s 12 calls cmp 0.915s 12 calls cmp (external) 0.368s 20 calls xxd 0.348s 4456 calls cmp (internal) 0.081s 4 calls gzip 0.059s 33 calls html2text ## compare_files (cumulative) (total time: 685.952s) 152.733s 1 call abc.DotChangesFile 151.828s 1 call abc.DebFile 151.605s 2 calls abc.XzFile 149.379s 1 call abc.DebDataTarFile 44.942s 39 calls abc.JavaScriptFile 28.031s 1 call abc.PdfFile 5.896s 2 calls abc.GzipFile 0.450s 1 call abc.TarFile 0.382s 1 call abc.Md5sumsFile 0.275s 3 calls abc.HtmlFile 0.225s 1 call diffoscope.comparators.utils.libarchive.LibarchiveMember 0.191s 2 calls abc.XMLFile 0.015s 1 call abc.TextFile ## container_extract (total time: 11.619s) 9.629s 41760 calls diffoscope.comparators.deb.DebTarContainer 1.715s 6 calls diffoscope.comparators.xz.XzContainer 0.172s 8 calls diffoscope.comparators.deb.DebContainer 0.081s 4 calls diffoscope.comparators.gzip.GzipContainer 0.021s 6 calls diffoscope.comparators.tar.TarContainer ## diff (total time: 6.733s) 6.733s 476 calls linediff ## has_same_content_as (total time: 1.500s) 0.785s 9 calls abc.DebFile 0.576s 4414 calls diffoscope.comparators.utils.libarchive.LibarchiveSymlink 0.117s 1 call abc.DebDataTarFile 0.007s 2 calls abc.XMLFile 0.006s 39 calls abc.JavaScriptFile 0.006s 2 calls abc.Md5sumsFile 0.002s 3 calls abc.HtmlFile 0.000s 1 call abc.TarFile 0.000s 2 calls abc.TextFile 0.000s 1 call diffoscope.comparators.binary.FilesystemFile 0.000s 1 call abc.DotChangesFile 0.000s 2 calls abc.GzipFile 0.000s 2 calls abc.XzFile 0.000s 1 call abc.PdfFile 0.000s 1 call diffoscope.comparators.utils.libarchive.LibarchiveMember ## main (total time: 168.577s) 168.480s 2 calls outputs 0.097s 1 call cleanup ## open_archive (total time: 0.000s) 0.000s 6 calls diffoscope.comparators.xz.XzContainer 0.000s 4 calls diffoscope.comparators.tar.TarContainer 0.000s 4 calls diffoscope.comparators.gzip.GzipContainer 0.000s 2 calls diffoscope.comparators.deb.DebContainer 0.000s 2 calls diffoscope.comparators.deb.DebTarContainer ## output (total time: 9.460s) 9.408s 1 call html 0.027s 1 call text 0.025s 1 call json ## recognizes (total time: 12.411s) 5.957s 12 calls diffoscope.comparators.binary.FilesystemFile 5.712s 336 calls diffoscope.comparators.utils.archive.ArchiveMember 0.639s 2614 calls diffoscope.comparators.utils.libarchive.LibarchiveMember 0.104s 486 calls diffoscope.comparators.debian.DebControlMember ## specialize (total time: 12.727s) 12.727s 4480 calls specialize Finished with result: success Main processes terminated with: code=exited/status=1 Service runtime: 2min 48.936s CPU time consumed: 2min 53.903s Tue Feb 18 12:45:48 UTC 2025 W: Diffoscope claims the build is reproducible, but there is a diffoscope file. Please investigate. Tue Feb 18 12:45:48 UTC 2025 E: gromacs failed to build reproducibly in trixie on amd64. Tue Feb 18 12:45:52 UTC 2025 I: Submitting .buildinfo files to external archives: Tue Feb 18 12:45:52 UTC 2025 I: Submitting 20K b1/gromacs_2025.0-2_amd64.buildinfo.asc Tue Feb 18 12:45:53 UTC 2025 I: Submitting 20K b2/gromacs_2025.0-2_amd64.buildinfo.asc Tue Feb 18 12:45:54 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Feb 18 12:45:54 UTC 2025 I: Done submitting .buildinfo files. Tue Feb 18 12:45:54 UTC 2025 I: Removing signed gromacs_2025.0-2_amd64.buildinfo.asc files: removed './b1/gromacs_2025.0-2_amd64.buildinfo.asc' removed './b2/gromacs_2025.0-2_amd64.buildinfo.asc'